Running: ./ninja_build.py debug -v -remake -j64
['z', 'zlib', 'cppdb', 'sqlite3', 'cifparse', 'libxml2', 'libzmq', 'rdkit', 'bcl', 'cmaes']
Running versioning script ... Done. (0.1 seconds)
Number of option files updated: 0
Total 4707 options.
Updating submodules needed for compilation.
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Examining external z
Examining external zlib
making external project files for project zlib ...done.
Examining external cppdb
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Found /home/benchmark/rosetta/source/src/pilot_apps.src.settings.all and going to use it!
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CMake Warning:
No source or binary directory provided. Both will be assumed to be the
same as the current working directory, but note that this warning will
become a fatal error in future CMake releases.
CMake Warning (dev) in CMakeLists.txt:
No project() command is present. The top-level CMakeLists.txt file must
contain a literal, direct call to the project() command. Add a line of
code such as
project(ProjectName)
near the top of the file, but after cmake_minimum_required().
CMake is pretending there is a "project(Project)" command on the first
line.
This warning is for project developers. Use -Wno-dev to suppress it.
>> CMAKE identifies C++ compiler as 'GNU', interpreting this as 'gcc'
>> To change, set CXX and CC environment variables (or pass -DCMAKE_CXX_COMPILER) and do a clean rebuild.
>> current settings: CXX='' CC=''
-- Compiler: gcc
Updating submodules needed for compilation.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/benchmark/rosetta/source/cmake/build_debug
ninja: Entering directory `/home/benchmark/rosetta/source/cmake/build_debug'
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[174/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/4dka.aho.pdb protocols/antibody/4dka.aho.pdb
[175/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer1.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer1.u
[176/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/design/AntibodySeqDesign_graft_tf.u protocols/antibody/design/AntibodySeqDesign_graft_tf.u
[177/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/2j88.pdb protocols/antibody/2j88.pdb
[178/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/analysis/simple_metrics/trp_cage_constraints.cst protocols/analysis/simple_metrics/trp_cage_constraints.cst
[179/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/abscript/ubq_frag.pdb protocols/abinitio/abscript/ubq_frag.pdb
[180/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/analysis/simple_metrics/trp_cage.pssm protocols/analysis/simple_metrics/trp_cage.pssm
[181/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/abscript/one_frag3_per_pos protocols/abinitio/abscript/one_frag3_per_pos
[182/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/aho_with_antigen.pdb protocols/antibody/aho_with_antigen.pdb
[183/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer6.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer6.u
[184/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer7.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer7.u
[185/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer1.u protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer1.u
[186/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/score3_pcs_only.wts_patch protocols/abinitio/score3_pcs_only.wts_patch
[187/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/score5_pcs_only.wts_patch protocols/abinitio/score5_pcs_only.wts_patch
[188/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/chainbreak_eval.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/chainbreak_eval.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/chainbreak_eval.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/methods/chainbreak_eval.cc
[189/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/design/graft_des_instructions.txt protocols/antibody/design/graft_des_instructions.txt
[190/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/database/cdr_set_instructions.txt protocols/antibody/database/cdr_set_instructions.txt
[191/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer4.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer4.u
[192/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer5.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer5.u
[193/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/score1_pcs_only.wts_patch protocols/abinitio/score1_pcs_only.wts_patch
[194/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/RestrictCDRsOperation_UTracer2.u protocols/antibody/task_operations/RestrictCDRsOperation_UTracer2.u
[195/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/BuildInstruction.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/BuildInstruction.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/BuildInstruction.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/BuildInstruction.cc
[196/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/RestrictCDRsOperation_UTracer3.u protocols/antibody/task_operations/RestrictCDRsOperation_UTracer3.u
[197/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowRight.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowRight.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowRight.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/GrowRight.cc
[198/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/RestrictCDRsOperation_UTracer4.u protocols/antibody/task_operations/RestrictCDRsOperation_UTracer4.u
[199/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/score2_pcs_only.wts_patch protocols/abinitio/score2_pcs_only.wts_patch
[200/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/backbone_moves/local_backbone_mover/1arb.pdb protocols/backbone_moves/local_backbone_mover/1arb.pdb
[201/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/RestrictCDRsOperation_UTracer1.u protocols/antibody/task_operations/RestrictCDRsOperation_UTracer1.u
[202/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/design/AntibodySeqDesign_general_tf.u protocols/antibody/design/AntibodySeqDesign_general_tf.u
[203/4561] /usr/bin/cc -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dcmaes_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -g -fPIC -Wno-error -w -MD -MT CMakeFiles/cmaes.dir/home/benchmark/rosetta/source/external/c-cmaes/c-cmaes/src/cmaes.c.o -MF CMakeFiles/cmaes.dir/home/benchmark/rosetta/source/external/c-cmaes/c-cmaes/src/cmaes.c.o.d -o CMakeFiles/cmaes.dir/home/benchmark/rosetta/source/external/c-cmaes/c-cmaes/src/cmaes.c.o -c /home/benchmark/rosetta/source/external/c-cmaes/c-cmaes/src/cmaes.c
[204/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/1bln_AB_aho.pdb protocols/antibody/1bln_AB_aho.pdb
[205/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/2r0l_1_1.pdb protocols/antibody/2r0l_1_1.pdb
[206/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer2.u protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer2.u
[207/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/1bln_AB_chothia.pdb protocols/antibody/1bln_AB_chothia.pdb
[208/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer4.u protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer4.u
[209/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer3.u protocols/antibody/task_operations/AddCDRProfileSetsOperation_UTracer3.u
[210/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/design/seq_des_instructions.txt protocols/antibody/design/seq_des_instructions.txt
[211/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/camelid_with_antigen.pdb protocols/antibody/camelid_with_antigen.pdb
[212/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowLeft.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowLeft.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/GrowLeft.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/GrowLeft.cc
[213/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/grafting/cdr-test-data.json protocols/antibody/grafting/cdr-test-data.json
[214/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/grafting/cdr_def_1emt.json protocols/antibody/grafting/cdr_def_1emt.json
[215/4561] : && /usr/bin/cc -fPIC -g -shared -Wl,-soname,libcmaes.so -o libcmaes.so CMakeFiles/cmaes.dir/home/benchmark/rosetta/source/external/c-cmaes/c-cmaes/src/cmaes.c.o -L/home/benchmark/rosetta/source/cmake/build_debug/../../external/boost_submod -L/home/benchmark/rosetta/source/cmake/build_debug/../../external/lib -Wl,-rpath,::::::::::::::::::::::::::::::::::::::::::::::::::::: && :
[216/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/database/cdr_set_instructions_load_test.txt protocols/antibody/database/cdr_set_instructions_load_test.txt
[217/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/4LGS_AHO.pdb protocols/antibody/4LGS_AHO.pdb
[218/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/pcs_broker_setup.txt protocols/abinitio/pcs_broker_setup.txt
[219/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/score0_pcs_only.wts_patch protocols/abinitio/score0_pcs_only.wts_patch
[220/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer2.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer2.u
[221/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer3.u protocols/antibody/task_operations/AddCDRProfilesOperation_UTracer3.u
[222/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/frag9_for_pcs_test.tab.gz protocols/abinitio/frag9_for_pcs_test.tab.gz
[223/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/pcs_data1.npc protocols/abinitio/pcs_data1.npc
[224/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/pcs_data2.npc protocols/abinitio/pcs_data2.npc
[225/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/valid_ss.dat protocols/abinitio/valid_ss.dat
[226/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/frag3_for_pcs_test.tab.gz protocols/abinitio/frag3_for_pcs_test.tab.gz
[227/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/pdb_idealized_for_pcs_test.pdb protocols/abinitio/pdb_idealized_for_pcs_test.pdb
[228/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/aa_composition/2ND2_state1.pdb protocols/aa_composition/2ND2_state1.pdb
[229/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/2GB3.pdb protocols/abinitio/2GB3.pdb
[230/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/branch_angle/BranchAngleOptimizer.u protocols/branch_angle/BranchAngleOptimizer.u
[231/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/mfr_aa2GB3_03_05.200_v1_3 protocols/abinitio/mfr_aa2GB3_03_05.200_v1_3
[232/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/branch_angle/branch_angle_1.txt protocols/branch_angle/branch_angle_1.txt
[233/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/branch_angle/branch_angle_2.txt protocols/branch_angle/branch_angle_2.txt
[234/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/abinitio/mfr_aa2GB3_09_05.200_v1_3 protocols/abinitio/mfr_aa2GB3_09_05.200_v1_3
[235/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/carbohydrates/N-linked_14-mer_glycan.pdb protocols/carbohydrates/N-linked_14-mer_glycan.pdb
[236/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/chromophore/test.pdb protocols/chromophore/test.pdb
[237/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/chromophore/sample_CRO_data_file.txt protocols/chromophore/sample_CRO_data_file.txt
[238/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/comparative_modeling/4gat_protein.pdb protocols/comparative_modeling/4gat_protein.pdb
[239/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/comparative_modeling/1f4pA.pdb protocols/comparative_modeling/1f4pA.pdb
[240/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/comparative_modeling/4gat_all.pdb protocols/comparative_modeling/4gat_all.pdb
[241/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/CoordinateConstraintGenerator_native_harmonic_default.cst protocols/constraint_generator/CoordinateConstraintGenerator_native_harmonic_default.cst
[242/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/AtomPairConstraintGenerator_input_default.cst protocols/constraint_generator/AtomPairConstraintGenerator_input_default.cst
[243/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/AtomPairConstraintGenerator_input_distance.cst protocols/constraint_generator/AtomPairConstraintGenerator_input_distance.cst
[244/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/AtomPairConstraintGenerator_input_selector.cst protocols/constraint_generator/AtomPairConstraintGenerator_input_selector.cst
[245/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/AtomPairConstraintGenerator_native_default.cst protocols/constraint_generator/AtomPairConstraintGenerator_native_default.cst
[246/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/AtomPairConstraintGenerator_input_ca_cb.cst protocols/constraint_generator/AtomPairConstraintGenerator_input_ca_cb.cst
[247/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/HydrogenBondConstraintGenerator_complicated.cst protocols/constraint_generator/HydrogenBondConstraintGenerator_complicated.cst
[248/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/HydrogenBondConstraintGenerator_default.cst protocols/constraint_generator/HydrogenBondConstraintGenerator_default.cst
[249/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/HydrogenBondConstraintGenerator_complicated.pdb.gz protocols/constraint_generator/HydrogenBondConstraintGenerator_complicated.pdb.gz
[250/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/coupled_moves/input_files/1A80.resfile protocols/coupled_moves/input_files/1A80.resfile
[251/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/constraint_generator/HydrogenBondConstraintGenerator_9_OD1_16_NH2.cst protocols/constraint_generator/HydrogenBondConstraintGenerator_9_OD1_16_NH2.cst
[252/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/coupled_moves/input_files/1A80_with_NAD_truncated.pdb protocols/coupled_moves/input_files/1A80_with_NAD_truncated.pdb
[253/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/coupled_moves/input_files/NAD_from_1A80.params protocols/coupled_moves/input_files/NAD_from_1A80.params
[254/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/AIB_pose.pdb protocols/cyclic_peptide/AIB_pose.pdb
[255/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/asymm.pdb protocols/cyclic_peptide/asymm.pdb
[256/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c2_symm.pdb protocols/cyclic_peptide/c2_symm.pdb
[257/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c2m_symm.pdb protocols/cyclic_peptide/c2m_symm.pdb
[258/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c3_symm_tbmb.pdb protocols/cyclic_peptide/c3_symm_tbmb.pdb
[259/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c4m_bad.pdb protocols/cyclic_peptide/c4m_bad.pdb
[260/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c4m_symm.pdb protocols/cyclic_peptide/c4m_symm.pdb
[261/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c4m.symm protocols/cyclic_peptide/c4m.symm
[262/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/c4m_test_pose.pdb protocols/cyclic_peptide/c4m_test_pose.pdb
[263/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/dVdPN_A.pdb protocols/cyclic_peptide/dVdPN_A.pdb
[264/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/mixed_disulf_test.pdb protocols/cyclic_peptide/mixed_disulf_test.pdb
[265/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/NDM1_bound_example.pdb protocols/cyclic_peptide/NDM1_bound_example.pdb
[266/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/oversaturated_bb_bb_bb.pdb protocols/cyclic_peptide/oversaturated_bb_bb_bb.pdb
[267/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/peptidestubmover_test_pose.pdb protocols/cyclic_peptide/peptidestubmover_test_pose.pdb
[268/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide/sample_cycpep_8mer.pdb protocols/cyclic_peptide/sample_cycpep_8mer.pdb
[269/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide_predict/allowed_residues.txt protocols/cyclic_peptide_predict/allowed_residues.txt
[270/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide_predict/design_setup_test.txt protocols/cyclic_peptide_predict/design_setup_test.txt
[271/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide_predict/seq_gly.txt protocols/cyclic_peptide_predict/seq_gly.txt
[272/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide_predict/native.pdb protocols/cyclic_peptide_predict/native.pdb
[273/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/cyclic_peptide_predict/seq.txt protocols/cyclic_peptide_predict/seq.txt
[274/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/4b2v_disulf_test.pdb protocols/denovo_design/4b2v_disulf_test.pdb
[275/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/test_structuredata_nonpeptidic.pdb protocols/denovo_design/test_structuredata_nonpeptidic.pdb
[276/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/disulf_test.pdb protocols/denovo_design/disulf_test.pdb
[277/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/QTS.params protocols/denovo_design/QTS.params
[278/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/QTS_connectC6.txt protocols/denovo_design/QTS_connectC6.txt
[279/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/QTS_conformers.pdb protocols/denovo_design/QTS_conformers.pdb
[280/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/test_pdbcomp.pdb protocols/denovo_design/test_pdbcomp.pdb
[281/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/CYS_connectSG.txt protocols/denovo_design/CYS_connectSG.txt
[282/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/test_sd.xml protocols/denovo_design/test_sd.xml
[283/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/helix14.pdb protocols/denovo_design/components/helix14.pdb
[284/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/helix15.pdb protocols/denovo_design/components/helix15.pdb
[285/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/C3_Z.sym protocols/denovo_design/components/C3_Z.sym
[286/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/test_enz_remark_input.pdb protocols/denovo_design/components/test_enz_remark_input.pdb
[287/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/test_propeller.pdb.gz protocols/denovo_design/components/test_propeller.pdb.gz
[288/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/test_fixed_trimer.pdb protocols/denovo_design/components/test_fixed_trimer.pdb
[289/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/connection/twohelix_structuredata.pdb protocols/denovo_design/connection/twohelix_structuredata.pdb
[290/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/connection/test_bundle_disconnected.pdb protocols/denovo_design/connection/test_bundle_disconnected.pdb
[291/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/ResidueVicinityRCG.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/ResidueVicinityRCG.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/ResidueVicinityRCG.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/remodel/ResidueVicinityRCG.cc
[292/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/components/DivideAndConquerorTests_NTF2.xml protocols/denovo_design/components/DivideAndConquerorTests_NTF2.xml
[293/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/connection/test_input_loopremoved.pdb protocols/denovo_design/connection/test_input_loopremoved.pdb
[294/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingProtocolFunctions.u protocols/docking/DockingProtocolFunctions.u
[295/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/denovo_design/connection/test_pdbcomp_BridgeChains.pdb protocols/denovo_design/connection/test_pdbcomp_BridgeChains.pdb
[296/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingTest.pdb protocols/docking/DockingTest.pdb
[297/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingDecoy.pdb protocols/docking/DockingDecoy.pdb
[298/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingMultiChain.pdb protocols/docking/DockingMultiChain.pdb
[299/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingSlideIntoContact.pdb protocols/docking/DockingSlideIntoContact.pdb
[300/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingPacking.pdb protocols/docking/DockingPacking.pdb
[301/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/docking/DockingRigidBodyMinimize.pdb protocols/docking/DockingRigidBodyMinimize.pdb
[302/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_6_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc.o -c /home/benchmark/rosetta/source/src/protocols/fold_from_loops/utils/utils.cc
[303/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/energy_based_clustering/alpha_aa.silent protocols/energy_based_clustering/alpha_aa.silent
[304/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/drug_design/carboxypyrimidine.sdf protocols/drug_design/carboxypyrimidine.sdf
[305/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/energy_based_clustering/oligourea.silent protocols/energy_based_clustering/oligourea.silent
[306/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/VS_rbzm_P2P3P6_align_ALIGN_4r4v.pdb protocols/rna/VS_rbzm_P2P3P6_align_ALIGN_4r4v.pdb
[307/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/D2N.params protocols/enzdes/D2N.params
[308/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/ligtest_it.pdb protocols/enzdes/ligtest_it.pdb
[309/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/ligtest_it.cst protocols/enzdes/ligtest_it.cst
[310/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/D2MX.params protocols/enzdes/D2MX.params
[311/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/mcfi_test.cst protocols/enzdes/mcfi_test.cst
[312/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/parse_cst_test.xml protocols/enzdes/parse_cst_test.xml
[313/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/enzdes/resfile_remap.resfile protocols/enzdes/resfile_remap.resfile
[314/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/farna_rebuild.fasta protocols/rna/farna_rebuild.fasta
[315/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/farna_rebuild.params protocols/rna/farna_rebuild.params
[316/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/srl_fixed_START1_1q9a_RNA.pdb protocols/rna/srl_fixed_START1_1q9a_RNA.pdb
[317/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/bps_test.params protocols/rna/bps_test.params
[318/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_default.cst protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_default.cst
[319/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/features/2J88.pdb protocols/features/2J88.pdb
[320/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rna/swm_rebuild.out.1.pdb protocols/rna/swm_rebuild.out.1.pdb
[321/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/features/3B83_nochain.pdb protocols/features/3B83_nochain.pdb
[322/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fldsgn/filters/ss_filter_test.pdb protocols/fldsgn/filters/ss_filter_test.pdb
[323/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fldsgn/filters/test_sheet.pdb protocols/fldsgn/filters/test_sheet.pdb
[324/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_inner.cst protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_inner.cst
[325/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_outer.cst protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator_input_outer.cst
[326/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/forge/remodel/bad_pair.blueprint protocols/forge/remodel/bad_pair.blueprint
[327/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fold_from_loops/movers/frags.200.3mers protocols/fold_from_loops/movers/frags.200.3mers
[328/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/fold_from_loops/movers/frags.200.9mers protocols/fold_from_loops/movers/frags.200.9mers
[329/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/forge/remodel/test.blueprint protocols/forge/remodel/test.blueprint
[330/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/forge/remodel/test.pdb protocols/forge/remodel/test.pdb
[331/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/frag_picker/t286_.6.csts protocols/frag_picker/t286_.6.csts
[332/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/Bridge.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/Bridge.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/Bridge.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/Bridge.cc
[333/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/frag_picker/1a32A-H1.9mers protocols/frag_picker/1a32A-H1.9mers
[334/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/grafting/2j88_NoL1.pdb protocols/grafting/2j88_NoL1.pdb
[335/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/grafting/2j88_L1_overhang3_rotated.pdb protocols/grafting/2j88_L1_overhang3_rotated.pdb
[336/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/hbnet/SB13.pdb protocols/hbnet/SB13.pdb
[337/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/grafting/2aabL_L1.pdb protocols/grafting/2aabL_L1.pdb
[338/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/helical_bundle/helical_bundle_input.pdb protocols/helical_bundle/helical_bundle_input.pdb
[339/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/helical_bundle_predict/three_helix.helix_assignments protocols/helical_bundle_predict/three_helix.helix_assignments
[340/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store.h5 protocols/indexed_structure_store/test_store.h5
[341/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/hotspot_hashing/3ve0_IJ.pdb protocols/hotspot_hashing/3ve0_IJ.pdb
[342/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_structure.pdb protocols/indexed_structure_store/test_structure.pdb
[343/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/metadata.json protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/metadata.json
[344/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_structure_store.h5 protocols/indexed_structure_store/test_structure_store.h5
[345/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_structure_store.json protocols/indexed_structure_store/test_structure_store.json
[346/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/threshold_distance.dat protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/threshold_distance.dat
[347/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/frag_picker/1a32A-H1.vall protocols/frag_picker/1a32A-H1.vall
[348/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/coordinates.dat protocols/indexed_structure_store/test_store/fragments/partial_test_fragments/coordinates.dat
[349/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/full_test_fragments/metadata.json protocols/indexed_structure_store/test_store/fragments/full_test_fragments/metadata.json
[350/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/full_test_fragments/coordinates.dat protocols/indexed_structure_store/test_store/fragments/full_test_fragments/coordinates.dat
[351/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/fragments/full_test_fragments/threshold_distance.dat protocols/indexed_structure_store/test_store/fragments/full_test_fragments/threshold_distance.dat
[352/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_n.pdb protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_n.pdb
[353/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_a.pdb protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_a.pdb
[354/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jd3/pose_inputters/relaxed_decoys.out protocols/jd3/pose_inputters/relaxed_decoys.out
[355/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_s.pdb protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_s.pdb
[356/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/structure/silent_store.silent protocols/indexed_structure_store/test_store/structure/silent_store.silent
[357/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_v.pdb protocols/indexed_structure_store/test_store/structure/pdb_dir/test_structure_v.pdb
[358/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/parser/test.bbskel protocols/parser/test.bbskel
[359/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jd3/example_bad.xml protocols/jd3/example_bad.xml
[360/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jd3/pose_inputters/four_pdbs.list protocols/jd3/pose_inputters/four_pdbs.list
[361/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jobdist/PlainSilentFileJobDistributor_test.out protocols/jobdist/PlainSilentFileJobDistributor_test.out
[362/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/jump_test.pdb protocols/jumping/jump_test.pdb
[363/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/gb3_secondary_structure.dat protocols/jumping/gb3_secondary_structure.dat
[364/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/jumps.def protocols/jumping/jumps.def
[365/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/gold_distance_jump1.dat protocols/jumping/gold_distance_jump1.dat
[366/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/pairings.dat protocols/jumping/pairings.dat
[367/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/gold_distance_jump2.dat protocols/jumping/gold_distance_jump2.dat
[368/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/jumping/test_in.pdb protocols/jumping/test_in.pdb
[369/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/7cpa_7cpa_native.pdb protocols/ligand_docking/7cpa_7cpa_native.pdb
[370/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/kinematic_closure/inputs/1srp.pdb protocols/kinematic_closure/inputs/1srp.pdb
[371/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/kinematic_closure/inputs/1ubq.pdb protocols/kinematic_closure/inputs/1ubq.pdb
[372/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/kinematic_closure/inputs/1exm.pdb protocols/kinematic_closure/inputs/1exm.pdb
[373/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/kinematic_closure/inputs/3cla.pdb protocols/kinematic_closure/inputs/3cla.pdb
[374/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/legacy_sewing/inputs/1ten_m8.db3 protocols/legacy_sewing/inputs/1ten_m8.db3
[375/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/AO.params protocols/ligand_docking/AO.params
[376/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/AO_conformers.pdb protocols/ligand_docking/AO_conformers.pdb
[377/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/AP_conformers.pdb protocols/ligand_docking/AP_conformers.pdb
[378/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/BG_conformers.pdb protocols/ligand_docking/BG_conformers.pdb
[379/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/AP.params protocols/ligand_docking/AP.params
[380/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/BG.params protocols/ligand_docking/BG.params
[381/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/BH.params protocols/ligand_docking/BH.params
[382/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/BH_conformers.pdb protocols/ligand_docking/BH_conformers.pdb
[383/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/7cpa.params protocols/ligand_docking/7cpa.params
[384/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loops/2GB3.pdb protocols/loops/2GB3.pdb
[385/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/7cpa_confs.pdb protocols/ligand_docking/7cpa_confs.pdb
[386/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/ZNx.params protocols/ligand_docking/ZNx.params
[387/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/ligand_pos.json protocols/ligand_docking/ligand_pos.json
[388/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/ligand_docking/ligand_pos.pdb protocols/ligand_docking/ligand_pos.pdb
[389/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loops/4DZM.pdb protocols/loops/4DZM.pdb
[390/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loop_modeling/inputs/loophash_db/backbone.db protocols/loop_modeling/inputs/loophash_db/backbone.db
[391/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loop_modeling/inputs/2pia.pdb protocols/loop_modeling/inputs/2pia.pdb
[392/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loop_modeling/inputs/2pia.loop protocols/loop_modeling/inputs/2pia.loop
[393/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/loop_modeling/inputs/loophash_db/loopdb.6.db protocols/loop_modeling/inputs/loophash_db/loopdb.6.db
[394/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/all_dist_rotamers.txt protocols/make_rot_lib/all_dist_rotamers.txt
[395/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/NVL_rot_lib_options_-60_-40.in protocols/make_rot_lib/NVL_rot_lib_options_-60_-40.in
[396/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/calc_centroids.txt protocols/make_rot_lib/calc_centroids.txt
[397/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/init_centroids.txt protocols/make_rot_lib/init_centroids.txt
[398/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/cluster_rotamers.txt protocols/make_rot_lib/cluster_rotamers.txt
[399/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/init_rotamers.txt protocols/make_rot_lib/init_rotamers.txt
[400/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/make_rot_lib/min_rotamers.txt protocols/make_rot_lib/min_rotamers.txt
[401/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/E1cb_carbaryl_1his_oxy_1bb_10_2.pdb protocols/match/E1cb_carbaryl_1his_oxy_1bb_10_2.pdb
[402/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/carbaryl_LG1.params protocols/match/carbaryl_LG1.params
[403/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/PBF.params protocols/match/PBF.params
[404/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/MBH_LG.params protocols/match/MBH_LG.params
[405/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/mbh_lg_0001.pdb protocols/match/mbh_lg_0001.pdb
[406/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/test_in.pdb protocols/moves/test_in.pdb
[407/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match/pbf_on_trpcage_res2_gold.kin protocols/match/pbf_on_trpcage_res2_gold.kin
[408/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/centroid_typeset.test_in_short.pdb protocols/moves/centroid_typeset.test_in_short.pdb
[409/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/fullatom_typeset.test_in_short.pdb protocols/moves/fullatom_typeset.test_in_short.pdb
[410/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/score12.pdb protocols/moves/score12.pdb
[411/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match_enzdes_util/1ney_invtree_unittest.pdb protocols/match_enzdes_util/1ney_invtree_unittest.pdb
[412/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/shearmoves_out.pdb protocols/moves/shearmoves_out.pdb
[413/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/smallmoves_out.pdb protocols/moves/smallmoves_out.pdb
[414/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match_enzdes_util/mocktim.cst protocols/match_enzdes_util/mocktim.cst
[415/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/test_in_short.pdb protocols/moves/test_in_short.pdb
[416/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/2nm1_motif_1fragment.pdb protocols/motif_grafting/2nm1_motif_1fragment.pdb
[417/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/match_enzdes_util/1n1.params protocols/match_enzdes_util/1n1.params
[418/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/2nm1_motif_2fragment.pdb protocols/motif_grafting/2nm1_motif_2fragment.pdb
[419/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/2nm1_context.pdb protocols/motif_grafting/2nm1_context.pdb
[420/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/1zx3a_translated_and_rotated.pdb protocols/motif_grafting/1zx3a_translated_and_rotated.pdb
[421/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/2nm1_1zx3a_hybrid.pdb protocols/motif_grafting/2nm1_1zx3a_hybrid.pdb
[422/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/1zx3a_as_motif_2fragment.pdb protocols/motif_grafting/1zx3a_as_motif_2fragment.pdb
[423/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/1zx3a.pdb protocols/motif_grafting/1zx3a.pdb
[424/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/1zx3a_as_motif_3fragment.pdb protocols/motif_grafting/1zx3a_as_motif_3fragment.pdb
[425/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/motif_grafting/1zx3a_as_motif_1fragment.pdb protocols/motif_grafting/1zx3a_as_motif_1fragment.pdb
[426/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/FastGapMover.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/FastGapMover.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/FastGapMover.cc.o -c /home/benchmark/rosetta/source/src/protocols/loophash/FastGapMover.cc
[427/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1mp6.pdb protocols/membrane/1mp6.pdb
[428/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/moves/kinematic_closure/VicinitySamplingKinematicPerturber.u protocols/moves/kinematic_closure/VicinitySamplingKinematicPerturber.u
[429/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1A11_native.pdb protocols/membrane/1A11_native.pdb
[430/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1C3W_TR_A.pdb protocols/membrane/1C3W_TR_A.pdb
[431/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1C3W_A.span protocols/membrane/1C3W_A.span
[432/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1C3W_w_mem.span protocols/membrane/1C3W_w_mem.span
[433/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1C17_tr.span protocols/membrane/1C17_tr.span
[434/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1C17_tr.pdb protocols/membrane/1C17_tr.pdb
[435/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1AFO_AB.pdb protocols/membrane/1AFO_AB.pdb
[436/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1AFO_AB_multi.pdb protocols/membrane/1AFO_AB_multi.pdb
[437/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1AFO_AB.span protocols/membrane/1AFO_AB.span
[438/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1AFO_AB_before_out.pdb protocols/membrane/1AFO_AB_before_out.pdb
[439/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1H2S__tr.pdb protocols/membrane/1H2S__tr.pdb
[440/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1H2S__tr.span protocols/membrane/1H2S__tr.span
[441/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1mp6_transformed.pdb protocols/membrane/1mp6_transformed.pdb
[442/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3PXO_A_tr.pdb protocols/membrane/3PXO_A_tr.pdb
[443/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1mp6.span protocols/membrane/1mp6.span
[444/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3EFF_TR.span protocols/membrane/3EFF_TR.span
[445/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3EFF_TR.pdb protocols/membrane/3EFF_TR.pdb
[446/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3PXO_A_tr.span protocols/membrane/3PXO_A_tr.span
[447/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1U19__tr.span protocols/membrane/1U19__tr.span
[448/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1U19__tr.pdb protocols/membrane/1U19__tr.pdb
[449/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3CSL__tr.span protocols/membrane/3CSL__tr.span
[450/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3CSL__tr.pdb protocols/membrane/3CSL__tr.pdb
[451/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3TUI__tr.span protocols/membrane/3TUI__tr.span
[452/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/4DXW__tr.span protocols/membrane/4DXW__tr.span
[453/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/4ENE__tr.pdb protocols/membrane/4ENE__tr.pdb
[454/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/3TUI__tr.pdb protocols/membrane/3TUI__tr.pdb
[455/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/4DXW__tr.pdb protocols/membrane/4DXW__tr.pdb
[456/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/4ENE__tr.span protocols/membrane/4ENE__tr.span
[457/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/RET.params protocols/membrane/RET.params
[458/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1afo_in.pdb protocols/membrane/1afo_in.pdb
[459/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1afo_decoy.pdb protocols/membrane/1afo_decoy.pdb
[460/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/1afo_tr.span protocols/membrane/1afo_tr.span
[461/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/2zup_model.span protocols/membrane/2zup_model.span
[462/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/2zup_model.pdb protocols/membrane/2zup_model.pdb
[463/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1AFO_AB.pdb protocols/membrane/geometry/1AFO_AB.pdb
[464/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1AFO_AB.span protocols/membrane/geometry/1AFO_AB.span
[465/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1AFO__tr.span protocols/membrane/geometry/1AFO__tr.span
[466/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1AFO_.pdb protocols/membrane/geometry/1AFO_.pdb
[467/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1BL8__tr.span protocols/membrane/geometry/1BL8__tr.span
[468/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1QJP__tr.span protocols/membrane/geometry/1QJP__tr.span
[469/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1BL8_.pdb protocols/membrane/geometry/1BL8_.pdb
[470/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2MPN__tr.span protocols/membrane/geometry/2MPN__tr.span
[471/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/1QJP_.pdb protocols/membrane/geometry/1QJP_.pdb
[472/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2BS2_CF.pdb protocols/membrane/geometry/2BS2_CF.pdb
[473/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2BS2_CF_tr.span protocols/membrane/geometry/2BS2_CF_tr.span
[474/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2MPN_.pdb protocols/membrane/geometry/2MPN_.pdb
[475/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2OAR_.pdb protocols/membrane/geometry/2OAR_.pdb
[476/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2UUH__tr.pdb protocols/membrane/geometry/2UUH__tr.pdb
[477/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2OAR__tr.span protocols/membrane/geometry/2OAR__tr.span
[478/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/2UUH__tr.span protocols/membrane/geometry/2UUH__tr.span
[479/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/symmetry/1afo_tr.span protocols/membrane/symmetry/1afo_tr.span
[480/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/symmetry/1afo_tr_input.pdb protocols/membrane/symmetry/1afo_tr_input.pdb
[481/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/symmetry/1afo_tr.c2.symm protocols/membrane/symmetry/1afo_tr.c2.symm
[482/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/3PXO_.pdb protocols/membrane/geometry/3PXO_.pdb
[483/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/membrane/geometry/3PXO__tr.span protocols/membrane/geometry/3PXO__tr.span
[484/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/metal_interface/1spd_cleaned.pdb protocols/metal_interface/1spd_cleaned.pdb
[485/4561] : && /usr/bin/c++ -fPIC -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -shared -Wl,-soname,libObjexxFCL.so -o libObjexxFCL.so CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Cstring.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Dimension.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/DimensionExpression.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/DimensionExpressionRef.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/DynamicIndexRange.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Fstring.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/IndexRange.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Observer.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/ObserverGraph.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/ObserverMediator.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/ObserverMulti.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Star.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/Time_Date.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/char.functions.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/format.cc.o CMakeFiles/ObjexxFCL.dir/home/benchmark/rosetta/source/src/ObjexxFCL/string.functions.cc.o -L/home/benchmark/rosetta/source/cmake/build_debug/../../external/boost_submod -L/home/benchmark/rosetta/source/cmake/build_debug/../../external/lib -Wl,-rpath,/home/benchmark/rosetta/source/cmake/build_debug/../../external/boost_submod:/home/benchmark/rosetta/source/cmake/build_debug/../../external/lib:/home/benchmark/rosetta/source/cmake/build_debug: -lz -ldl -lstdc++ libcifparse.so liblibxml2.so librdkit.so libcmaes.so libcppdb.so libsqlite3.so && :
[486/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.xml protocols/multistage_rosetta_scripts/job_def_file.xml
[487/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.pdblist.xml protocols/multistage_rosetta_scripts/job_def_file.pdblist.xml
[488/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.bad3.xml protocols/multistage_rosetta_scripts/job_def_file.bad3.xml
[489/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.bad1.xml protocols/multistage_rosetta_scripts/job_def_file.bad1.xml
[490/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.bad2.xml protocols/multistage_rosetta_scripts/job_def_file.bad2.xml
[491/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/job_def_file.nofiltername.xml protocols/multistage_rosetta_scripts/job_def_file.nofiltername.xml
[492/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/3U3B_A.pdb protocols/multistage_rosetta_scripts/3U3B_A.pdb
[493/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/3U3B_B.pdb protocols/multistage_rosetta_scripts/3U3B_B.pdb
[494/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/multistage_rosetta_scripts/pdblist protocols/multistage_rosetta_scripts/pdblist
[495/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_tb.txt protocols/nmr/pcs/sim_pcs_val_tb.txt
[496/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_6_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc.o -c /home/benchmark/rosetta/source/src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc
[497/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/pcs_data_2ksy_input_file.txt protocols/nmr/pcs/pcs_data_2ksy_input_file.txt
[498/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_dy.txt protocols/nmr/pcs/sim_pcs_val_dy.txt
[499/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_tm.txt protocols/nmr/pcs/sim_pcs_val_tm.txt
[500/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/1x0n_model1_renum.pdb protocols/nmr/pcs/1x0n_model1_renum.pdb
[501/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_l56c_tb.txt protocols/nmr/pcs/sim_pcs_val_l56c_tb.txt
[502/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_er.txt protocols/nmr/pcs/sim_pcs_val_er.txt
[503/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/2ksy_chainA_renum.pdb protocols/nmr/pcs/2ksy_chainA_renum.pdb
[504/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/gb1_.pdb protocols/nmr/pre/gb1_.pdb
[505/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelRotamerLinks.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelRotamerLinks.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelRotamerLinks.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelRotamerLinks.cc
[506/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_l56c_dy.txt protocols/nmr/pcs/sim_pcs_val_l56c_dy.txt
[507/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_l56c_yb.txt protocols/nmr/pcs/sim_pcs_val_l56c_yb.txt
[508/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_l56c_tm.txt protocols/nmr/pcs/sim_pcs_val_l56c_tm.txt
[509/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_i121c_tm.txt protocols/nmr/pcs/sim_pcs_val_i121c_tm.txt
[510/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_i121c_dy.txt protocols/nmr/pcs/sim_pcs_val_i121c_dy.txt
[511/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_i121c_tb.txt protocols/nmr/pcs/sim_pcs_val_i121c_tb.txt
[512/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pcs/sim_pcs_val_i121c_yb.txt protocols/nmr/pcs/sim_pcs_val_i121c_yb.txt
[513/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_t1z_r2_1h.txt protocols/nmr/pre/sim_pre_t1z_r2_1h.txt
[514/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/r1a_pre_n_distance_potential.histogram protocols/nmr/pre/r1a_pre_n_distance_potential.histogram
[515/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/pre_data_input.txt protocols/nmr/pre/pre_data_input.txt
[516/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_c13z_r2_1h.txt protocols/nmr/pre/sim_pre_c13z_r2_1h.txt
[517/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_d46z_r2_1h.txt protocols/nmr/pre/sim_pre_d46z_r2_1h.txt
[518/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_e119z_r2_1h.txt protocols/nmr/pre/sim_pre_e119z_r2_1h.txt
[519/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/3v1e_AB_Mn.pdb protocols/nmr/pre/3v1e_AB_Mn.pdb
[520/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_e83z_r2_1h.txt protocols/nmr/pre/sim_pre_e83z_r2_1h.txt
[521/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pre_t142z_r2_1h.txt protocols/nmr/pre/sim_pre_t142z_r2_1h.txt
[522/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/bicelles_hnc_norm_toNH.txt protocols/nmr/rdc/bicelles_hnc_norm_toNH.txt
[523/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/3v1e_AB_Cu.pdb protocols/nmr/pre/3v1e_AB_Cu.pdb
[524/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pres_cu2_1h_r1.txt protocols/nmr/pre/sim_pres_cu2_1h_r1.txt
[525/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pres_cu2_1h_r2.txt protocols/nmr/pre/sim_pres_cu2_1h_r2.txt
[526/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pres_mn2_1h_r1.txt protocols/nmr/pre/sim_pres_mn2_1h_r1.txt
[527/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/tmv107_nh_norm_toNH.txt protocols/nmr/rdc/tmv107_nh_norm_toNH.txt
[528/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/rdc_data_g_input_file.txt protocols/nmr/rdc/rdc_data_g_input_file.txt
[529/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/g_nmr_A.pdb protocols/nmr/rdc/g_nmr_A.pdb
[530/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/bicelles_nh_norm_toNH.txt protocols/nmr/rdc/bicelles_nh_norm_toNH.txt
[531/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/pre/sim_pres_mn2_1h_r2.txt protocols/nmr/pre/sim_pres_mn2_1h_r2.txt
[532/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/bicelles_nc_norm_toNH.txt protocols/nmr/rdc/bicelles_nc_norm_toNH.txt
[533/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nonlocal/2GB3.pdb protocols/nonlocal/2GB3.pdb
[534/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/tmv107_hnc_norm_toNH.txt protocols/nmr/rdc/tmv107_hnc_norm_toNH.txt
[535/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/optimize_weights/1UAD.wt_complex.pdb protocols/optimize_weights/1UAD.wt_complex.pdb
[536/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nonlocal/alignment.filt protocols/nonlocal/alignment.filt
[537/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/nmr/rdc/tmv107_nc_norm_toNH.txt protocols/nmr/rdc/tmv107_nc_norm_toNH.txt
[538/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pack_interface/4SER_buriedASP.pdb.gz protocols/pack_interface/4SER_buriedASP.pdb.gz
[539/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/optimize_weights/1UAD.E38A.mut_unbounded.pdb protocols/optimize_weights/1UAD.E38A.mut_unbounded.pdb
[540/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/optimize_weights/1UAD.wt_unbounded.pdb protocols/optimize_weights/1UAD.wt_unbounded.pdb
[541/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/peptide_deriver/PeptideDeriverFilter.u protocols/peptide_deriver/PeptideDeriverFilter.u
[542/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/peptide_deriver/2hle_remixed.pdb protocols/peptide_deriver/2hle_remixed.pdb
[543/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/peptide_deriver/test_peptiderive.xml protocols/peptide_deriver/test_peptiderive.xml
[544/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/optimize_weights/1UAD.E38A.mut_complex.pdb protocols/optimize_weights/1UAD.E38A.mut_complex.pdb
[545/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pdbinfo_manipulations/5GRU_full.pdb protocols/pdbinfo_manipulations/5GRU_full.pdb
[546/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/peptide_deriver/1sfi_short.pdb protocols/peptide_deriver/1sfi_short.pdb
[547/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pdbinfo_manipulations/aln6q6h.pdb.gz protocols/pdbinfo_manipulations/aln6q6h.pdb.gz
[548/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pdbinfo_manipulations/6q6h.pdb.gz protocols/pdbinfo_manipulations/6q6h.pdb.gz
[549/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pdbinfo_manipulations/6q6h_seqs.json.gz protocols/pdbinfo_manipulations/6q6h_seqs.json.gz
[550/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pose_creation/PFSM_01.fasta protocols/pose_creation/PFSM_01.fasta
[551/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pmut_scan/shortloop.01.pdb.gz protocols/pmut_scan/shortloop.01.pdb.gz
[552/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pdbinfo_manipulations/4gatA.pdb protocols/pdbinfo_manipulations/4gatA.pdb
[553/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pmut_scan/mutants.txt protocols/pmut_scan/mutants.txt
[554/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pmut_scan/shortloop.02.pdb.gz protocols/pmut_scan/shortloop.02.pdb.gz
[555/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/pose_creation/PFSM_02.fasta protocols/pose_creation/PFSM_02.fasta
[556/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/protein_mpnn/6MRR.pdb protocols/protein_mpnn/6MRR.pdb
[557/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/recon_design/design.resfile protocols/recon_design/design.resfile
[558/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/recon_design/design2.resfile protocols/recon_design/design2.resfile
[559/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/protein_mpnn/5L33.pdb protocols/protein_mpnn/5L33.pdb
[560/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/2JJC.pdb protocols/qsar/scoring_grid/2JJC.pdb
[561/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/LIG.params protocols/qsar/scoring_grid/LIG.params
[562/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/sim_pcs_val_tb.txt protocols/qsar/scoring_grid/sim_pcs_val_tb.txt
[563/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/1x0n_model1_renum.pdb protocols/qsar/scoring_grid/1x0n_model1_renum.pdb
[564/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/sim_pcs_val_tm.txt protocols/qsar/scoring_grid/sim_pcs_val_tm.txt
[565/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/qsar/scoring_grid/sh2_pcs_data_input.txt protocols/qsar/scoring_grid/sh2_pcs_data_input.txt
[566/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/1a19.pdb protocols/relax/1a19.pdb
[567/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_native.pdb protocols/relax/AtomCoordinateCstMover_native.pdb
[568/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/1a19_trunc.pdb protocols/relax/1a19_trunc.pdb
[569/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_input_harmonic_default.cst protocols/relax/AtomCoordinateCstMover_input_harmonic_default.cst
[570/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/residue_selectors/two_alanines.pdb protocols/residue_selectors/two_alanines.pdb
[571/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_input_bounded_default.cst protocols/relax/AtomCoordinateCstMover_input_bounded_default.cst
[572/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_native_harmonic_default.cst protocols/relax/AtomCoordinateCstMover_native_harmonic_default.cst
[573/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_native_harmonic_sidechain.cst protocols/relax/AtomCoordinateCstMover_native_harmonic_sidechain.cst
[574/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_input_harmonic_sidechain.cst protocols/relax/AtomCoordinateCstMover_input_harmonic_sidechain.cst
[575/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/membrane/2mpn_tr_native.pdb protocols/relax/membrane/2mpn_tr_native.pdb
[576/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/fast_relax_test_script.dat protocols/relax/fast_relax_test_script.dat
[577/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/AtomCoordinateCstMover_integration_native.cst protocols/relax/AtomCoordinateCstMover_integration_native.cst
[578/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/relax/membrane/2mpn_tr.span protocols/relax/membrane/2mpn_tr.span
[579/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/residue_selectors/one_serine.pdb protocols/residue_selectors/one_serine.pdb
[580/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/residue_selectors/two_serines.pdb protocols/residue_selectors/two_serines.pdb
[581/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyMover.pdb protocols/rigid/RigidBodyMover.pdb
[582/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyPerturbMover_no_int.pdb protocols/rigid/RigidBodyPerturbMover_no_int.pdb
[583/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyPerturbNoCenterMover.pdb protocols/rigid/RigidBodyPerturbNoCenterMover.pdb
[584/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyPerturbMover_int.pdb protocols/rigid/RigidBodyPerturbMover_int.pdb
[585/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyRandomizeMover.pdb protocols/rigid/RigidBodyRandomizeMover.pdb
[586/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodySpinMover.pdb protocols/rigid/RigidBodySpinMover.pdb
[587/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RotateJumpAxisMover_range.pdb protocols/rigid/RotateJumpAxisMover_range.pdb
[588/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RotateJumpAxisMover.pdb protocols/rigid/RotateJumpAxisMover.pdb
[589/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RigidBodyTransMover.pdb protocols/rigid/RigidBodyTransMover.pdb
[590/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RotateJumpAxisMover_random.pdb protocols/rigid/RotateJumpAxisMover_random.pdb
[591/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RotateJumpAxisMover_single.pdb protocols/rigid/RotateJumpAxisMover_single.pdb
[592/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rigid/RotateJumpAxisMover_underspecified_jump.pdb protocols/rigid/RotateJumpAxisMover_underspecified_jump.pdb
[593/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/1abc.pdb protocols/rosetta_scripts/1abc.pdb
[594/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/include1.xml protocols/rosetta_scripts/include1.xml
[595/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/example_resource_using_script.xml protocols/rosetta_scripts/example_resource_using_script.xml
[596/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/2def.pdb protocols/rosetta_scripts/2def.pdb
[597/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/include2.xml protocols/rosetta_scripts/include2.xml
[598/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/include3.xml protocols/rosetta_scripts/include3.xml
[599/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_filters/interface_hbonds_input.pdb protocols/simple_filters/interface_hbonds_input.pdb
[600/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/modern_include2.xml protocols/rosetta_scripts/modern_include2.xml
[601/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/modern_test1.xml protocols/rosetta_scripts/modern_test1.xml
[602/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/permitted1.xml protocols/rosetta_scripts/permitted1.xml
[603/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/permitted2.xml protocols/rosetta_scripts/permitted2.xml
[604/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/prohibited1.xml protocols/rosetta_scripts/prohibited1.xml
[605/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/prohibited2.xml protocols/rosetta_scripts/prohibited2.xml
[606/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/test1.xml protocols/rosetta_scripts/test1.xml
[607/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/rosetta_scripts/test2.xml protocols/rosetta_scripts/test2.xml
[608/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/scoring/dock_in.pdb protocols/scoring/dock_in.pdb
[609/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/scoring/Interface.u protocols/scoring/Interface.u
[610/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sewing/inputs/test.segments protocols/sewing/inputs/test.segments
[611/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sewing/inputs/single_helix.pdb protocols/sewing/inputs/single_helix.pdb
[612/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sewing/inputs/zinc_site_10_12.pdb protocols/sewing/inputs/zinc_site_10_12.pdb
[613/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/concatenate_inputs/component_file protocols/simple_moves/concatenate_inputs/component_file
[614/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/1A2A_A.pdb protocols/simple_moves/1A2A_A.pdb
[615/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/DisulfideInsertionMover.xml protocols/simple_moves/DisulfideInsertionMover.xml
[616/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/1bl0_auto.fasta.pssm protocols/simple_moves/1bl0_auto.fasta.pssm
[617/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/test_input.pdb protocols/simple_moves/test_input.pdb
[618/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/data_16988.tab protocols/sparta/data_16988.tab
[619/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/D2I.params protocols/simple_moves/D2I.params
[620/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/2kywA.pdb protocols/sparta/2kywA.pdb
[621/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/simple_moves/oop/oop_test.pdb protocols/simple_moves/oop/oop_test.pdb
[622/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/17280_trim.tab protocols/sparta/17280_trim.tab
[623/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/solution_0022372568.ir_solution.pdb protocols/sparta/solution_0022372568.ir_solution.pdb
[624/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/data_17280.tab protocols/sparta/data_17280.tab
[625/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/modeler/align/scaff_subset_stepwise_input_seq_1_mutated_to_DNA.pdb protocols/stepwise/modeler/align/scaff_subset_stepwise_input_seq_1_mutated_to_DNA.pdb
[626/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/modeler/align/1_scaff_subset_stepwise_input_seq_1.pdb protocols/stepwise/modeler/align/1_scaff_subset_stepwise_input_seq_1.pdb
[627/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/sparta/SAM-T08-server_TS3.pdb protocols/sparta/SAM-T08-server_TS3.pdb
[628/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/modeler/align/2_scaff_subset_stepwise_input_seq_1.pdb protocols/stepwise/modeler/align/2_scaff_subset_stepwise_input_seq_1.pdb
[629/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/monte_carlo/mover/t_loop.fasta protocols/stepwise/monte_carlo/mover/t_loop.fasta
[630/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/modeler/align/seq_with_AAmismatch.fasta protocols/stepwise/modeler/align/seq_with_AAmismatch.fasta
[631/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/modeler/align/scaff_subset_stepwise_input_seq_1.pdb protocols/stepwise/modeler/align/scaff_subset_stepwise_input_seq_1.pdb
[632/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/stepwise/monte_carlo/mover/up_to_ua_handle_t_loop_3l0u_RNA.pdb protocols/stepwise/monte_carlo/mover/up_to_ua_handle_t_loop_3l0u_RNA.pdb
[633/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/arg_and_two_ser.pdb protocols/task_operations/arg_and_two_ser.pdb
[634/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/asn_to_satisfied_bb.pdb protocols/task_operations/asn_to_satisfied_bb.pdb
[635/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/switches/GraftSwitchMoverTest.pdb protocols/switches/GraftSwitchMoverTest.pdb
[636/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/SequenceMotifOperation.u protocols/task_operations/SequenceMotifOperation.u
[637/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/asn_to_bb.pdb protocols/task_operations/asn_to_bb.pdb
[638/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loop_modeler/perturbers/LoopHashPerturber.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loop_modeler/perturbers/LoopHashPerturber.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loop_modeler/perturbers/LoopHashPerturber.cc.o -c /home/benchmark/rosetta/source/src/protocols/loop_modeler/perturbers/LoopHashPerturber.cc
[639/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/asn_to_satisfied_ser.pdb protocols/task_operations/asn_to_satisfied_ser.pdb
[640/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/asn_to_ser.pdb protocols/task_operations/asn_to_ser.pdb
[641/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ConservativeDesignOperation_defaults.u protocols/task_operations/ConservativeDesignOperation_defaults.u
[642/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/DsspDesignOperation.u protocols/task_operations/DsspDesignOperation.u
[643/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ConservativeDesignOperation_no_native.u protocols/task_operations/ConservativeDesignOperation_no_native.u
[644/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/dssp_in.pdb protocols/task_operations/dssp_in.pdb
[645/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ConservativeDesignOperation_blosum62.u protocols/task_operations/ConservativeDesignOperation_blosum62.u
[646/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/pose_with_ionizable_side_chains.pdb protocols/task_operations/pose_with_ionizable_side_chains.pdb
[647/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictToInterfaceOperation.u protocols/task_operations/RestrictToInterfaceOperation.u
[648/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/loops.txt protocols/task_operations/loops.txt
[649/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/dssp_in.blueprint protocols/task_operations/dssp_in.blueprint
[650/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictToInterfaceVectorOperation.u protocols/task_operations/RestrictToInterfaceVectorOperation.u
[651/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictToNeighborhoodOperation.u protocols/task_operations/RestrictToNeighborhoodOperation.u
[652/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictByCalculatorsOperation.u protocols/task_operations/RestrictByCalculatorsOperation.u
[653/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ProteinInterfaceDesignOperation.u protocols/task_operations/ProteinInterfaceDesignOperation.u
[654/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ProteinInterfaceDesignOperation_all.u protocols/task_operations/ProteinInterfaceDesignOperation_all.u
[655/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictInterGroupVector.u protocols/task_operations/RestrictInterGroupVector.u
[656/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_defaults.u protocols/task_operations/ResidueProbDesignOperation_defaults.u
[657/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_no_native.u protocols/task_operations/ResidueProbDesignOperation_no_native.u
[658/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_set_all_aa_probs.u protocols/task_operations/ResidueProbDesignOperation_set_all_aa_probs.u
[659/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_picks_5.u protocols/task_operations/ResidueProbDesignOperation_picks_5.u
[660/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_set_position.u protocols/task_operations/ResidueProbDesignOperation_set_position.u
[661/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/ResidueProbDesignOperation_zero_at_.05.u protocols/task_operations/ResidueProbDesignOperation_zero_at_.05.u
[662/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/util/test_in.pdb protocols/util/test_in.pdb
[663/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/tcr/4x6b_aho.pdb protocols/tcr/4x6b_aho.pdb
[664/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/task_operations/RestrictToMoveMapChiWNeighbors.u protocols/task_operations/RestrictToMoveMapChiWNeighbors.u
[665/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/util/demo_loopfile.loops protocols/util/demo_loopfile.loops
[666/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/protocols/util/aHo_antibody.pdb protocols/util/aHo_antibody.pdb
[667/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/TYR.dot.u core/chemical/TYR.dot.u
[668/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/codes_to_roots.map core/chemical/carbohydrates/codes_to_roots.map
[669/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/alpha-L-Fucp-_1-6_-D-GlcpNAc-_1-4_-D-GlcpNAc.pdb core/chemical/carbohydrates/alpha-L-Fucp-_1-6_-D-GlcpNAc-_1-4_-D-GlcpNAc.pdb
[670/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/SXX.params core/chemical/gasteiger/SXX.params
[671/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/SOx.params core/chemical/gasteiger/SOx.params
[672/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/NXX.params core/chemical/gasteiger/NXX.params
[673/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/PXX.params core/chemical/gasteiger/PXX.params
[674/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/POx.params core/chemical/gasteiger/POx.params
[675/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/THI.params core/chemical/gasteiger/THI.params
[676/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/uk.pp.1_001.mol2.params core/chemical/params/uk.pp.1_001.mol2.params
[677/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p1m1.params core/chemical/modifications/1p1m1.params
[678/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p1m0.params core/chemical/modifications/1p1m0.params
[679/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p2m0.params core/chemical/modifications/1p2m0.params
[680/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p2m2.params core/chemical/modifications/1p2m2.params
[681/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p2m1.params core/chemical/modifications/1p2m1.params
[682/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p3m0.params core/chemical/modifications/1p3m0.params
[683/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/conflict_patch.txt core/chemical/conflict_patch.txt
[684/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p3m1.params core/chemical/modifications/1p3m1.params
[685/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p3m2.params core/chemical/modifications/1p3m2.params
[686/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/1p3m3.params core/chemical/modifications/1p3m3.params
[687/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p1m0.params core/chemical/modifications/2p1m0.params
[688/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p2m1.params core/chemical/modifications/2p2m1.params
[689/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p2m0.params core/chemical/modifications/2p2m0.params
[690/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p3m1.params core/chemical/modifications/2p3m1.params
[691/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p3m0.params core/chemical/modifications/2p3m0.params
[692/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/Lex.pdb core/chemical/carbohydrates/Lex.pdb
[693/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/stereochem_test.key core/chemical/carbohydrates/stereochem_test.key
[694/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/1pqc.params core/chemical/1pqc.params
[695/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/ring_size_to_morphemes.map core/chemical/carbohydrates/ring_size_to_morphemes.map
[696/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/AZO.params core/chemical/gasteiger/AZO.params
[697/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/gasteiger/GST.params core/chemical/gasteiger/GST.params
[698/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/sucrose.pdb core/chemical/carbohydrates/sucrose.pdb
[699/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/foldit_ligand.params core/chemical/modifications/foldit_ligand.params
[700/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/amylopectin_fragment.pdb core/chemical/carbohydrates/amylopectin_fragment.pdb
[701/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/GlcN.pdb core/chemical/carbohydrates/GlcN.pdb
[702/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/gp120_2glycans_man5.pdb core/chemical/carbohydrates/gp120_2glycans_man5.pdb
[703/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/Neu.pdb core/chemical/carbohydrates/Neu.pdb
[704/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/maltotriose.pdb core/chemical/carbohydrates/maltotriose.pdb
[705/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/nomenclature.table core/chemical/carbohydrates/nomenclature.table
[706/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/conn.pdb core/chemical/conn.pdb
[707/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/ring_size_to_morphemes.bad_map core/chemical/carbohydrates/ring_size_to_morphemes.bad_map
[708/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/1pqc_test.patch core/chemical/1pqc_test.patch
[709/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/atom_properties.txt core/chemical/atom_properties.txt
[710/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/gp120_2glycans_man5_chainC.pdb core/chemical/carbohydrates/gp120_2glycans_man5_chainC.pdb
[711/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/ASX.params core/chemical/ASX.params
[712/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/LYX.params core/chemical/LYX.params
[713/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/test_linkage_data_table.tsv core/chemical/carbohydrates/test_linkage_data_table.tsv
[714/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/isomaltose.pdb core/chemical/carbohydrates/isomaltose.pdb
[715/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/beta-psicose.pdb core/chemical/carbohydrates/beta-psicose.pdb
[716/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/extra_atom_properties.txt core/chemical/extra_atom_properties.txt
[717/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/lactose.pdb core/chemical/carbohydrates/lactose.pdb
[718/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/uk002.params core/chemical/uk002.params
[719/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/2p3m2.params core/chemical/modifications/2p3m2.params
[720/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/mm_atom_properties.txt core/chemical/mm_atom_properties.txt
[721/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/3p3m0.params core/chemical/modifications/3p3m0.params
[722/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/extra_mm_atom_properties.txt core/chemical/extra_mm_atom_properties.txt
[723/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/3p3m1.params core/chemical/modifications/3p3m1.params
[724/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/DEP.params core/chemical/modifications/DEP.params
[725/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/modifications/PRO.params core/chemical/modifications/PRO.params
[726/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1aq1.mol2.params core/chemical/params/1aq1.mol2.params
[727/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1dwd.mol2.params core/chemical/params/1dwd.mol2.params
[728/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1fm9.mol2.params core/chemical/params/1fm9.mol2.params
[729/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1dwc.mol2.params core/chemical/params/1dwc.mol2.params
[730/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1ney_lig.mol.params core/chemical/params/1ney_lig.mol.params
[731/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1ppc.mol2.params core/chemical/params/1ppc.mol2.params
[732/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1pph.mol2.params core/chemical/params/1pph.mol2.params
[733/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/2dbl.mol2.params core/chemical/params/2dbl.mol2.params
[734/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1pq6.mol2.params core/chemical/params/1pq6.mol2.params
[735/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1p8d.mol2.params core/chemical/params/1p8d.mol2.params
[736/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/1pqc.mol2.params core/chemical/params/1pqc.mol2.params
[737/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/2ctc.mol2.params core/chemical/params/2ctc.mol2.params
[738/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/2prg.mol2.params core/chemical/params/2prg.mol2.params
[739/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/4tim.mol2.params core/chemical/params/4tim.mol2.params
[740/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/7cpa.mol2.params core/chemical/params/7cpa.mol2.params
[741/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/cen_types_list.txt core/chemical/params/cen_types_list.txt
[742/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/retype_list.txt core/chemical/params/retype_list.txt
[743/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/6tim.mol2.params core/chemical/params/6tim.mol2.params
[744/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/type_test1.params core/chemical/params/type_test1.params
[745/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/uk.pp.1_002.mol2.params core/chemical/params/uk.pp.1_002.mol2.params
[746/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/uk.pp.1_003.mol2.params core/chemical/params/uk.pp.1_003.mol2.params
[747/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/uk.pp.1_004.mol2.params core/chemical/params/uk.pp.1_004.mol2.params
[748/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/uk.pp.1_005.mol2.params core/chemical/params/uk.pp.1_005.mol2.params
[749/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/carbohydrates/glycosylated_peptide.pdb core/chemical/carbohydrates/glycosylated_peptide.pdb
[750/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U21.mol core/chemical/params/U21.mol
[751/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U22.mol core/chemical/params/U22.mol
[752/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U23.mol core/chemical/params/U23.mol
[753/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U26.mol core/chemical/params/U26.mol
[754/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U24.mol core/chemical/params/U24.mol
[755/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U25.mol core/chemical/params/U25.mol
[756/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U28.mol core/chemical/params/U28.mol
[757/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U27.mol core/chemical/params/U27.mol
[758/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dbasic_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc.o -MF CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc.o.d -o CMakeFiles/basic.dir/home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc.o -c /home/benchmark/rosetta/source/src/basic/resource_manager/ResourceManager.cc
[759/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U29.mol core/chemical/params/U29.mol
[760/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U30.mol core/chemical/params/U30.mol
[761/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U32.mol core/chemical/params/U32.mol
[762/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U31.mol core/chemical/params/U31.mol
[763/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U34.mol core/chemical/params/U34.mol
[764/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U33.mol core/chemical/params/U33.mol
[765/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/odd_edta.mol core/chemical/params/odd_edta.mol
[766/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U01_v3.mol core/chemical/params/U01_v3.mol
[767/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U02_v3.mol core/chemical/params/U02_v3.mol
[768/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/VA1_model.sdf core/chemical/params/VA1_model.sdf
[769/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U03_v3.mol core/chemical/params/U03_v3.mol
[770/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U05_v3.mol core/chemical/params/U05_v3.mol
[771/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U04_v3.mol core/chemical/params/U04_v3.mol
[772/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U09_v3.mol core/chemical/params/U09_v3.mol
[773/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U06_v3.mol core/chemical/params/U06_v3.mol
[774/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U07_v3.mol core/chemical/params/U07_v3.mol
[775/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U08_v3.mol core/chemical/params/U08_v3.mol
[776/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/TT1.params core/chemical/params/TT1.params
[777/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U01.params core/chemical/params/U01.params
[778/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U02.params core/chemical/params/U02.params
[779/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U03.params core/chemical/params/U03.params
[780/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U05.params core/chemical/params/U05.params
[781/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U04.params core/chemical/params/U04.params
[782/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U06.params core/chemical/params/U06.params
[783/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U07.params core/chemical/params/U07.params
[784/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U08.params core/chemical/params/U08.params
[785/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U11.params core/chemical/params/U11.params
[786/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U09.params core/chemical/params/U09.params
[787/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U10.params core/chemical/params/U10.params
[788/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U12.params core/chemical/params/U12.params
[789/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U14.params core/chemical/params/U14.params
[790/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U19.params core/chemical/params/U19.params
[791/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U15.params core/chemical/params/U15.params
[792/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U17.params core/chemical/params/U17.params
[793/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U13.params core/chemical/params/U13.params
[794/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U16.params core/chemical/params/U16.params
[795/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U18.params core/chemical/params/U18.params
[796/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U20.params core/chemical/params/U20.params
[797/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U23.params core/chemical/params/U23.params
[798/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U22.params core/chemical/params/U22.params
[799/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U21.params core/chemical/params/U21.params
[800/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U25.params core/chemical/params/U25.params
[801/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U24.params core/chemical/params/U24.params
[802/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U28.params core/chemical/params/U28.params
[803/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U31.params core/chemical/params/U31.params
[804/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U32.params core/chemical/params/U32.params
[805/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U26.params core/chemical/params/U26.params
[806/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U27.params core/chemical/params/U27.params
[807/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U29.params core/chemical/params/U29.params
[808/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U30.params core/chemical/params/U30.params
[809/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U33.params core/chemical/params/U33.params
[810/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U34.params core/chemical/params/U34.params
[811/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/VA1_model.params core/chemical/params/VA1_model.params
[812/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/odd_edta.params core/chemical/params/odd_edta.params
[813/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U01.cen.params core/chemical/params/U01.cen.params
[814/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U02.cen.params core/chemical/params/U02.cen.params
[815/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U03.cen.params core/chemical/params/U03.cen.params
[816/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U06.cen.params core/chemical/params/U06.cen.params
[817/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U05.cen.params core/chemical/params/U05.cen.params
[818/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U04.cen.params core/chemical/params/U04.cen.params
[819/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U07.cen.params core/chemical/params/U07.cen.params
[820/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U08.cen.params core/chemical/params/U08.cen.params
[821/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U09.cen.params core/chemical/params/U09.cen.params
[822/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U10.cen.params core/chemical/params/U10.cen.params
[823/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U11.cen.params core/chemical/params/U11.cen.params
[824/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U12.cen.params core/chemical/params/U12.cen.params
[825/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U13.cen.params core/chemical/params/U13.cen.params
[826/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U14.cen.params core/chemical/params/U14.cen.params
[827/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U15.cen.params core/chemical/params/U15.cen.params
[828/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U17.cen.params core/chemical/params/U17.cen.params
[829/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U16.cen.params core/chemical/params/U16.cen.params
[830/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U18.cen.params core/chemical/params/U18.cen.params
[831/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U20.cen.params core/chemical/params/U20.cen.params
[832/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U19.cen.params core/chemical/params/U19.cen.params
[833/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U21.cen.params core/chemical/params/U21.cen.params
[834/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U22.cen.params core/chemical/params/U22.cen.params
[835/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U25.cen.params core/chemical/params/U25.cen.params
[836/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U24.cen.params core/chemical/params/U24.cen.params
[837/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U23.cen.params core/chemical/params/U23.cen.params
[838/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U26.cen.params core/chemical/params/U26.cen.params
[839/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U28.cen.params core/chemical/params/U28.cen.params
[840/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U27.cen.params core/chemical/params/U27.cen.params
[841/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U31.cen.params core/chemical/params/U31.cen.params
[842/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U29.cen.params core/chemical/params/U29.cen.params
[843/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U30.cen.params core/chemical/params/U30.cen.params
[844/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U32.cen.params core/chemical/params/U32.cen.params
[845/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U34.cen.params core/chemical/params/U34.cen.params
[846/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/params/U33.cen.params core/chemical/params/U33.cen.params
[847/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/ATP.sdf core/chemical/rdkit/ATP.sdf
[848/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/nitro.sdf core/chemical/rdkit/nitro.sdf
[849/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/pyridineNoxide.sdf core/chemical/rdkit/pyridineNoxide.sdf
[850/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/4gatA.pdb core/conformation/4gatA.pdb
[851/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/sdf/Components_trimmed.sdf core/chemical/sdf/Components_trimmed.sdf
[852/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/benzoate.sdf core/chemical/rdkit/benzoate.sdf
[853/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rings/dummy_conformers.data core/chemical/rings/dummy_conformers.data
[854/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/nmethylpyridine.sdf core/chemical/rdkit/nmethylpyridine.sdf
[855/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/rdkit/purine.sdf core/chemical/rdkit/purine.sdf
[856/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/sdf/paired_list_v3.txt core/chemical/sdf/paired_list_v3.txt
[857/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/sdf/paired_list.txt core/chemical/sdf/paired_list.txt
[858/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/sdf/multi_rotamers.sdf core/chemical/sdf/multi_rotamers.sdf
[859/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/chemical/sdf/example.sdf core/chemical/sdf/example.sdf
[860/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/test_in.pdb core/conformation/test_in.pdb
[861/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/test_simple_conformation.u core/conformation/test_simple_conformation.u
[862/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB.pdb core/conformation/membrane/1AFO_AB.pdb
[863/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB_invalid_too-long.span core/conformation/membrane/1AFO_AB_invalid_too-long.span
[864/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1U19_tr_ignorechain.pdb core/conformation/membrane/1U19_tr_ignorechain.pdb
[865/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/dock_in.pdb core/conformation/dock_in.pdb
[866/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB.span core/conformation/membrane/1AFO_AB.span
[867/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB_invalid_order.span core/conformation/membrane/1AFO_AB_invalid_order.span
[868/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB_invalid_spanorder.span core/conformation/membrane/1AFO_AB_invalid_spanorder.span
[869/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1AFO_AB_invalid_too-short.span core/conformation/membrane/1AFO_AB_invalid_too-short.span
[870/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/4DXW__tr.pdb core/conformation/membrane/4DXW__tr.pdb
[871/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/3gp6_opm_A.span core/conformation/membrane/3gp6_opm_A.span
[872/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/2LEG_B_tr.pdb core/conformation/membrane/2LEG_B_tr.pdb
[873/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/3gp6_opm_A.pdb core/conformation/membrane/3gp6_opm_A.pdb
[874/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/4DXW__tr.span core/conformation/membrane/4DXW__tr.span
[875/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/caln_tm_finalB.span core/conformation/membrane/caln_tm_finalB.span
[876/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/3MP7__tr.pdb core/conformation/membrane/3MP7__tr.pdb
[877/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/3UKM__tr.pdb core/conformation/membrane/3UKM__tr.pdb
[878/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/4WFE__tr.pdb core/conformation/membrane/4WFE__tr.pdb
[879/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/symm_test_in2.pdb core/conformation/symmetry/symm_test_in2.pdb
[880/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/pmp22_withSS_PPM_opt.span core/conformation/membrane/pmp22_withSS_PPM_opt.span
[881/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1PY6_mp_coords.pdb core/conformation/membrane/1PY6_mp_coords.pdb
[882/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/membrane/1PY6.span core/conformation/membrane/1PY6.span
[883/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/symm_def1.dat core/conformation/symmetry/symm_def1.dat
[884/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/symm_test2.pdb core/conformation/symmetry/symm_test2.pdb
[885/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/symm_def2.dat core/conformation/symmetry/symm_def2.dat
[886/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/database_location.txt core/database_location.txt
[887/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/mirror_symm.comp core/conformation/symmetry/mirror_symm.comp
[888/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/Cs_INPUT.pdb core/conformation/symmetry/Cs_INPUT.pdb
[889/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/Cs.symm core/conformation/symmetry/Cs.symm
[890/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/mtest1.pdb core/conformation/symmetry/mtest1.pdb
[891/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/conformation/symmetry/mtest6.pdb core/conformation/symmetry/mtest6.pdb
[892/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/enzymes/testase core/enzymes/testase
[893/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/grid/1dwc_3.gridbb.gz core/grid/1dwc_3.gridbb.gz
[894/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/enzymes/rosettase core/enzymes/rosettase
[895/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/fragment/picking/vall/vall_test.dat core/fragment/picking/vall/vall_test.dat
[896/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/import_pose/3KBA.pdb core/import_pose/3KBA.pdb
[897/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/1ten.pdb core/io/1ten.pdb
[898/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/1QYS.cif core/io/1QYS.cif
[899/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/1QYS.pdb core/io/1QYS.pdb
[900/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/1l2y_w_glucose.pdb core/io/1l2y_w_glucose.pdb
[901/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/daa.pdb core/io/daa.pdb
[902/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/test_CYD.out core/io/test_CYD.out
[903/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/GTP.params core/io/GTP.params
[904/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/bin_silentfile_test.out core/io/bin_silentfile_test.out
[905/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/bin_silentfile_test.pdb core/io/bin_silentfile_test.pdb
[906/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/1L8C.cif core/io/1L8C.cif
[907/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/merge_residue_behaviors.fake core/io/merge_residue_behaviors.fake
[908/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/split_residue_behaviors.fake core/io/split_residue_behaviors.fake
[909/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/test_in_idealized.pdb core/io/test_in_idealized.pdb
[910/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/test_in.pdb core/io/test_in.pdb
[911/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/5FYL_frag_1.pdb core/io/5FYL_frag_1.pdb
[912/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1ioo.pdb core/io/carbohydrates/1ioo.pdb
[913/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/fragment/aat049603_05.200_v1_3.gz core/fragment/aat049603_05.200_v1_3.gz
[914/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/two_lipids.pdb core/io/two_lipids.pdb
[915/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/5FYL.pdb core/io/5FYL.pdb
[916/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/1BH4.pdb core/io/pdb/1BH4.pdb
[917/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1x38.pdb core/io/carbohydrates/1x38.pdb
[918/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/3uue.pdb core/io/carbohydrates/3uue.pdb
[919/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/5FYL_correct_output.pdb core/io/5FYL_correct_output.pdb
[920/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/2cl2.pdb core/io/carbohydrates/2cl2.pdb
[921/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1jnd.pdb core/io/carbohydrates/1jnd.pdb
[922/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4f8x.pdb core/io/carbohydrates/4f8x.pdb
[923/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4q56.pdb core/io/carbohydrates/4q56.pdb
[924/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1ioo.ann_seq core/io/carbohydrates/1ioo.ann_seq
[925/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4nyq.pdb core/io/carbohydrates/4nyq.pdb
[926/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1x38.ann_seq core/io/carbohydrates/1x38.ann_seq
[927/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/3uue.ann_seq core/io/carbohydrates/3uue.ann_seq
[928/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/1jnd.ann_seq core/io/carbohydrates/1jnd.ann_seq
[929/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/2cl2.ann_seq core/io/carbohydrates/2cl2.ann_seq
[930/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4nyq.ann_seq core/io/carbohydrates/4nyq.ann_seq
[931/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4q56.ann_seq core/io/carbohydrates/4q56.ann_seq
[932/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/carbohydrates/4f8x.ann_seq core/io/carbohydrates/4f8x.ann_seq
[933/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/4TTL.pdb core/io/pdb/4TTL.pdb
[934/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/1e68_link.pdb core/io/pdb/1e68_link.pdb
[935/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/test.params core/io/pdb/test.params
[936/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/cycpep_with_ddpp.pdb core/io/pdb/cycpep_with_ddpp.pdb
[937/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/cycpep_with_ddpp_and_ldpp.pdb core/io/pdb/cycpep_with_ddpp_and_ldpp.pdb
[938/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_from_sfr/acetylated_and_methylated_alanine.pdb core/io/pose_from_sfr/acetylated_and_methylated_alanine.pdb
[939/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/fake_pdb_record_defs core/io/pdb/fake_pdb_record_defs
[940/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pdb/extra_res_pose.pdb core/io/pdb/extra_res_pose.pdb
[941/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_from_sfr/1rgr_apo.pdb core/io/pose_from_sfr/1rgr_apo.pdb
[942/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_from_sfr/cyclic_pep_with_link.pdb core/io/pose_from_sfr/cyclic_pep_with_link.pdb
[943/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_from_sfr/ace_from_1VDN.pdb core/io/pose_from_sfr/ace_from_1VDN.pdb
[944/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_to_sfr/2_peptides_2_glycan_ligands.pdb core/io/pose_to_sfr/2_peptides_2_glycan_ligands.pdb
[945/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/pose_from_sfr/1IJ3_cleaned.pdb core/io/pose_from_sfr/1IJ3_cleaned.pdb
[946/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/silent/cyclic_peptide_binary_silent_rnaremark.silent core/io/silent/cyclic_peptide_binary_silent_rnaremark.silent
[947/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/silent/cyclic_peptide_binary_silent.silent core/io/silent/cyclic_peptide_binary_silent.silent
[948/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/silent/cyclic_peptide_binary_silent_duplicated_header.silent core/io/silent/cyclic_peptide_binary_silent_duplicated_header.silent
[949/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/173D.mmtf core/io/mmtf/173D.mmtf
[950/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1CAG.mmtf core/io/mmtf/1CAG.mmtf
[951/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1AUY.mmtf core/io/mmtf/1AUY.mmtf
[952/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1IGT.mmtf core/io/mmtf/1IGT.mmtf
[953/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1LPV.mmtf core/io/mmtf/1LPV.mmtf
[954/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4CUP.mmtf core/io/mmtf/4CUP.mmtf
[955/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1O2F.mmtf core/io/mmtf/1O2F.mmtf
[956/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1SKM.mmtf core/io/mmtf/1SKM.mmtf
[957/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/3ZYB.mmtf core/io/mmtf/3ZYB.mmtf
[958/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/empty-numModels1.mmtf core/io/mmtf/empty-numModels1.mmtf
[959/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4Y60.cif core/io/mmtf/4Y60.cif
[960/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/173D.cif core/io/mmtf/173D.cif
[961/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/5ESW.cif core/io/mmtf/5ESW.cif
[962/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1LPV.cif core/io/mmtf/1LPV.cif
[963/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1AUY.cif core/io/mmtf/1AUY.cif
[964/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1CAG.cif core/io/mmtf/1CAG.cif
[965/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1O2F.cif core/io/mmtf/1O2F.cif
[966/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4P3R.mmtf core/io/mmtf/4P3R.mmtf
[967/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1IGT.cif core/io/mmtf/1IGT.cif
[968/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1AA6.mmtf core/io/mmtf/1AA6.mmtf
[969/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1SKM.cif core/io/mmtf/1SKM.cif
[970/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/5EMG.mmtf core/io/mmtf/5EMG.mmtf
[971/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4P3R.cif core/io/mmtf/4P3R.cif
[972/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/empty-all0.mmtf core/io/mmtf/empty-all0.mmtf
[973/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/3ZYB.cif core/io/mmtf/3ZYB.cif
[974/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4CUP.cif core/io/mmtf/4CUP.cif
[975/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1BNA.mmtf core/io/mmtf/1BNA.mmtf
[976/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1L2Q.mmtf core/io/mmtf/1L2Q.mmtf
[977/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1MSH.mmtf core/io/mmtf/1MSH.mmtf
[978/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1R9V.mmtf core/io/mmtf/1R9V.mmtf
[979/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/3NJW.mmtf core/io/mmtf/3NJW.mmtf
[980/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4OPJ.mmtf core/io/mmtf/4OPJ.mmtf
[981/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4CK4.mmtf core/io/mmtf/4CK4.mmtf
[982/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/5EMG.cif core/io/mmtf/5EMG.cif
[983/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/empty-mmtfVersion99999999.mmtf core/io/mmtf/empty-mmtfVersion99999999.mmtf
[984/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1BNA.cif core/io/mmtf/1BNA.cif
[985/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1AA6.cif core/io/mmtf/1AA6.cif
[986/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4V5A.mmtf core/io/mmtf/4V5A.mmtf
[987/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1L2Q.cif core/io/mmtf/1L2Q.cif
[988/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1MSH.cif core/io/mmtf/1MSH.cif
[989/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1R9V.cif core/io/mmtf/1R9V.cif
[990/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4OPJ.cif core/io/mmtf/4OPJ.cif
[991/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1HTQ.mmtf core/io/mmtf/1HTQ.mmtf
[992/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4Y60.mmtf core/io/mmtf/4Y60.mmtf
[993/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/5ESW.mmtf core/io/mmtf/5ESW.mmtf
[994/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1PEF.mmtf core/io/mmtf/1PEF.mmtf
[995/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/empty-numChains1.mmtf core/io/mmtf/empty-numChains1.mmtf
[996/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1PEF.pdb core/io/mmtf/1PEF.pdb
[997/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/3NJW.cif core/io/mmtf/3NJW.cif
[998/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/4CK4.cif core/io/mmtf/4CK4.cif
[999/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1V4F.pdb core/io/mmtf/1V4F.pdb
[1000/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1HTQ.cif core/io/mmtf/1HTQ.cif
[1001/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/1V4F.mmtf core/io/mmtf/1V4F.mmtf
[1002/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/binselector_input_S_0002.pdb core/io/mmtf/binselector_input_S_0002.pdb
[1003/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/crosslinkermover_octahedral_s2_symm_S_0008.pdb core/io/mmtf/crosslinkermover_octahedral_s2_symm_S_0008.pdb
[1004/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/kinematics/test.pdb core/kinematics/test.pdb
[1005/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/ncbb_packer_palette_cycpep_pre_stage_3.pdb core/io/mmtf/ncbb_packer_palette_cycpep_pre_stage_3.pdb
[1006/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/kinematics/inverse/3u3b.pdb.gz core/kinematics/inverse/3u3b.pdb.gz
[1007/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/1l2y_renameH.pdb core/pack/1l2y_renameH.pdb
[1008/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/io/mmtf/oligourea_predict_native.pdb core/io/mmtf/oligourea_predict_native.pdb
[1009/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/test_in.pdb core/optimization/test_in.pdb
[1010/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/3dg1_INPUT.pdb core/optimization/symmetry/3dg1_INPUT.pdb
[1011/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/fibril.symm core/optimization/symmetry/fibril.symm
[1012/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c2_after_min.pdb core/optimization/symmetry/c2_after_min.pdb
[1013/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/helix.symm core/optimization/symmetry/helix.symm
[1014/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c2_INPUT.pdb core/optimization/symmetry/c2_INPUT.pdb
[1015/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/2bw9_INPUT.pdb core/optimization/symmetry/2bw9_INPUT.pdb
[1016/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c3_INPUT.pdb core/optimization/symmetry/c3_INPUT.pdb
[1017/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c3_after_min.pdb core/optimization/symmetry/c3_after_min.pdb
[1018/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c3.sdef core/optimization/symmetry/c3.sdef
[1019/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/c2.sdef core/optimization/symmetry/c2.sdef
[1020/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/Cs_INPUT.pdb core/optimization/symmetry/Cs_INPUT.pdb
[1021/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/optimization/symmetry/Cs.sdef core/optimization/symmetry/Cs.sdef
[1022/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/1FKB.pdb.gz core/pack/1FKB.pdb.gz
[1023/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/4MRS__opm.pdb core/pack/4MRS__opm.pdb
[1024/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/2mcm_0001.pdb core/pack/2mcm_0001.pdb
[1025/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/RTMIN.u core/pack/RTMIN.u
[1026/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/4MRS__opm_0001.pdb core/pack/4MRS__opm_0001.pdb
[1027/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/peptoid_design_2.resfile core/pack/peptoid_design_2.resfile
[1028/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/peptoid_design_1.resfile core/pack/peptoid_design_1.resfile
[1029/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/peptoid_design_2.comp core/pack/peptoid_design_2.comp
[1030/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/RotamerTrials.u core/pack/RotamerTrials.u
[1031/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/test_in.pdb core/pack/test_in.pdb
[1032/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/SymmetricRotamerTrials.u core/pack/SymmetricRotamerTrials.u
[1033/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_bbMET_buriedASP.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_bbMET_buriedASP.pdb.gz
[1034/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/annealer/2akf.clipped.pdb core/pack/annealer/2akf.clipped.pdb
[1035/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/dunbrack/dummy_type.params core/pack/dunbrack/dummy_type.params
[1036/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_bbMET_buriedO.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_bbMET_buriedO.pdb.gz
[1037/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/APA.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/APA.pdb.gz
[1038/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/dunbrack/1UBQ_repack.pdb core/pack/dunbrack/1UBQ_repack.pdb
[1039/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_buriedASP.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/1ARG_buriedASP.pdb.gz
[1040/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/natural_corrections1.pdb core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/natural_corrections1.pdb
[1041/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/4SER_buriedASP.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/4SER_buriedASP.pdb.gz
[1042/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_asn.pdb core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_asn.pdb
[1043/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/thr_ser_to_bb.pdb core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/thr_ser_to_bb.pdb
[1044/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_super_NN.pdb core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_super_NN.pdb
[1045/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_NN.pdb core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/C3_NN.pdb
[1046/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase1_symm.pdb core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase1_symm.pdb
[1047/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/proline_nh_test.pdb.gz core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/proline_nh_test.pdb.gz
[1048/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/buried_unsat_penalty/C3.symm core/pack/guidance_scoreterms/buried_unsat_penalty/C3.symm
[1049/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase2.pdb core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase2.pdb
[1050/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase2_symm.pdb core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase2_symm.pdb
[1051/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/hbnet_energy/S4.symm core/pack/guidance_scoreterms/hbnet_energy/S4.symm
[1052/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase1.pdb core/pack/guidance_scoreterms/buried_unsat_penalty/graph/hbnet_testcase1.pdb
[1053/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/voids_penalty_energy/1ubq.pdb core/pack/guidance_scoreterms/voids_penalty_energy/1ubq.pdb
[1054/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/hbnet_energy/hbnet_energy_test1.pdb core/pack/guidance_scoreterms/hbnet_energy/hbnet_energy_test1.pdb
[1055/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/guidance_scoreterms/voids_penalty_energy/d2.symm core/pack/guidance_scoreterms/voids_penalty_energy/d2.symm
[1056/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/DAB_corrected_order.params core/pack/rotamers/DAB_corrected_order.params
[1057/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/interaction_graph/resfile core/pack/interaction_graph/resfile
[1058/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamer_set/glycerol.pdb core/pack/rotamer_set/glycerol.pdb
[1059/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/interaction_graph/fibril.silent core/pack/interaction_graph/fibril.silent
[1060/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamer_set/GOL.params core/pack/rotamer_set/GOL.params
[1061/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/6SA.params core/pack/rotamers/6SA.params
[1062/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/LEU_NCAA.params core/pack/rotamers/LEU_NCAA.params
[1063/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/test_in.pdb core/pack/task/test_in.pdb
[1064/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/LEU_NCAA_DUN02.params core/pack/rotamers/LEU_NCAA_DUN02.params
[1065/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamer_set/test_rotamer_sets.pdb core/pack/rotamer_set/test_rotamer_sets.pdb
[1066/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/B53_corrected.rotlib core/pack/rotamers/B53_corrected.rotlib
[1067/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/4tim.params core/pack/rotamers/4tim.params
[1068/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/ConnectRight.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/ConnectRight.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/ConnectRight.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/ConnectRight.cc
[1069/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/lx2.bbdep.rotamers.lib core/pack/rotamers/lx2.bbdep.rotamers.lib
[1070/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/4tim_confs.pdb core/pack/rotamers/4tim_confs.pdb
[1071/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/rotamers/lxx.bbdep.rotamers.lib core/pack/rotamers/lxx.bbdep.rotamers.lib
[1072/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/EX_test.resfile core/pack/task/EX_test.resfile
[1073/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/resfile_test.pdb core/pack/task/resfile_test.pdb
[1074/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/resfile_test_mut.pdb core/pack/task/resfile_test_mut.pdb
[1075/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/resfile_test.resfile core/pack/task/resfile_test.resfile
[1076/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/short_his.pdb core/pack/task/short_his.pdb
[1077/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/test_in.resfile core/pack/task/test_in.resfile
[1078/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/test_in.silent core/pack/task/test_in.silent
[1079/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/operation/ALLAA_193.resfile core/pack/task/operation/ALLAA_193.resfile
[1080/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/operation/DisallowIfNonnativeTaskOperation.u core/pack/task/operation/DisallowIfNonnativeTaskOperation.u
[1081/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/operation/ClashBasedRepackShell.u core/pack/task/operation/ClashBasedRepackShell.u
[1082/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/operation/ReplicateTaskOperation.u core/pack/task/operation/ReplicateTaskOperation.u
[1083/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/NAD_from_1A80.params core/pack/task/residue_selector/NAD_from_1A80.params
[1084/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/1A80_with_NAD.pdb core/pack/task/residue_selector/1A80_with_NAD.pdb
[1085/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/2NXX.pdb core/pack/task/residue_selector/2NXX.pdb
[1086/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/no_clash.pdb core/pack/task/residue_selector/no_clash.pdb
[1087/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/sc_bb_clash.pdb core/pack/task/residue_selector/sc_bb_clash.pdb
[1088/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pack/task/residue_selector/sc_sc_clash.pdb core/pack/task/residue_selector/sc_sc_clash.pdb
[1089/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/onechain.pdb core/pose/onechain.pdb
[1090/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/pdbinfo_test_in.pdb core/pose/pdbinfo_test_in.pdb
[1091/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/multichain.pdb core/pose/multichain.pdb
[1092/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/reference_pose/1AFO_AB.pdb core/pose/reference_pose/1AFO_AB.pdb
[1093/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/2WDQ__tr.pdb core/pose/2WDQ__tr.pdb
[1094/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/2GB3.pdb core/scoring/2GB3.pdb
[1095/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/4dO8B.pdb core/scoring/4dO8B.pdb
[1096/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/pose/copydofs/excise_bp_7_14_min_again_relax_full_RNA_P_overlap_reR-hbond_sc_wildtype_bound.pdb core/pose/copydofs/excise_bp_7_14_min_again_relax_full_RNA_P_overlap_reR-hbond_sc_wildtype_bound.pdb
[1097/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/1pqc_0003.pdb core/scoring/1pqc_0003.pdb
[1098/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/1pqc_0001.pdb core/scoring/1pqc_0001.pdb
[1099/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/1pqc.params core/scoring/1pqc.params
[1100/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/4mmx_context_0001_renumbered_trimmed.pdb core/scoring/4mmx_context_0001_renumbered_trimmed.pdb
[1101/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/betapose.pdb core/scoring/betapose.pdb
[1102/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/atom_pair_constraint.data core/scoring/atom_pair_constraint.data
[1103/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aligned_for_rmstest.pdb core/scoring/aligned_for_rmstest.pdb
[1104/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/depc_test.txt core/scoring/depc_test.txt
[1105/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/ccs_imms_test.pdb core/scoring/ccs_imms_test.pdb
[1106/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dslf_ca_dih.u core/scoring/dslf_ca_dih.u
[1107/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dslf_cs_ang.u core/scoring/dslf_cs_ang.u
[1108/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/coordinate_constraint.data core/scoring/coordinate_constraint.data
[1109/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/cyclic_peptide.pdb core/scoring/cyclic_peptide.pdb
[1110/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dslf_ss_dst.u core/scoring/dslf_ss_dst.u
[1111/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dslf_ss_dih.u core/scoring/dslf_ss_dih.u
[1112/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_atr.data core/scoring/fa_atr.data
[1113/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_intra_atr.data core/scoring/fa_intra_atr.data
[1114/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_rep.data core/scoring/fa_rep.data
[1115/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_intra_rep.data core/scoring/fa_intra_rep.data
[1116/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_intra_sol.data core/scoring/fa_intra_sol.data
[1117/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_sol.data core/scoring/fa_sol.data
[1118/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fake_restype_with_tyr_backbone_aa.params core/scoring/fake_restype_with_tyr_backbone_aa.params
[1119/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fa_elec.data core/scoring/fa_elec.data
[1120/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hrf_test.txt core/scoring/hrf_test.txt
[1121/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbond_sr_bb.data core/scoring/hbond_sr_bb.data
[1122/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm_twist.data core/scoring/mm_twist.data
[1123/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hrf_dyn_test.pdb core/scoring/hrf_dyn_test.pdb
[1124/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/model-5.pdb core/scoring/model-5.pdb
[1125/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/rms_util.u core/scoring/rms_util.u
[1126/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nonideal_glycine.pdb core/scoring/nonideal_glycine.pdb
[1127/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/sc_NNQQNY.pdb core/scoring/sc_NNQQNY.pdb
[1128/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/native_for_rmstest.pdb core/scoring/native_for_rmstest.pdb
[1129/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/test.wts core/scoring/test.wts
[1130/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/test.wts_patch core/scoring/test.wts_patch
[1131/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/test_in.pdb core/scoring/test_in.pdb
[1132/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/twochain_cycpep.pdb core/scoring/twochain_cycpep.pdb
[1133/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fiber_diffraction/data/1IFP.mini.pdb core/scoring/fiber_diffraction/data/1IFP.mini.pdb
[1134/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/carbohydrates/dummy_params.data core/scoring/carbohydrates/dummy_params.data
[1135/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/unaligned_for_rmstest.pdb core/scoring/unaligned_for_rmstest.pdb
[1136/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/constraints/test_in.pdb core/scoring/constraints/test_in.pdb
[1137/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dunbrack/best_rotamer_energy.u core/scoring/dunbrack/best_rotamer_energy.u
[1138/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dunbrack/test_in_rotamers.dat core/scoring/dunbrack/test_in_rotamers.dat
[1139/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/dunbrack/test_in.pdb core/scoring/dunbrack/test_in.pdb
[1140/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/electron_density/1onc_8A.mrc core/scoring/electron_density/1onc_8A.mrc
[1141/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fiber_diffraction/data/1ifp.mini.dat core/scoring/fiber_diffraction/data/1ifp.mini.dat
[1142/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/func/GaussianFunc.u core/scoring/func/GaussianFunc.u
[1143/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/fiber_diffraction/data/helix_denovo.sdef core/scoring/fiber_diffraction/data/helix_denovo.sdef
[1144/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/hbond_compute_energy_sp2.u core/scoring/hbonds/hbond_compute_energy_sp2.u
[1145/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/hbond_compute_energy_sp2_specific_cases.u core/scoring/hbonds/hbond_compute_energy_sp2_specific_cases.u
[1146/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/1ubq_23_to_34.pdb core/scoring/hbonds/1ubq_23_to_34.pdb
[1147/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/bad_symm_hbonds.silent core/scoring/hbonds/bad_symm_hbonds.silent
[1148/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/hbond_compute_energy.u core/scoring/hbonds/hbond_compute_energy.u
[1149/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/read_polynomials_from_database.u core/scoring/hbonds/read_polynomials_from_database.u
[1150/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/hbond_type_manager.u core/scoring/hbonds/hbond_type_manager.u
[1151/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/aliphatic_not_pro.comp core/scoring/aa_composition_energy/aliphatic_not_pro.comp
[1152/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/hbonds/Polynomial_1d_model.u core/scoring/hbonds/Polynomial_1d_model.u
[1153/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/1afo_A.pdb core/scoring/membrane/1afo_A.pdb
[1154/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/1afo_A.span core/scoring/membrane/1afo_A.span
[1155/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/4O79_A.pdb core/scoring/membrane/4O79_A.pdb
[1156/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/2KSF_tr.span core/scoring/membrane/2KSF_tr.span
[1157/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/4O79_A.span core/scoring/membrane/4O79_A.span
[1158/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/1afo_A.embed core/scoring/membrane/1afo_A.embed
[1159/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/4O79_A.embed core/scoring/membrane/4O79_A.embed
[1160/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/membrane/2KSF_tr.pdb core/scoring/membrane/2KSF_tr.pdb
[1161/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/exactly_two_trportyr.comp core/scoring/aa_composition_energy/exactly_two_trportyr.comp
[1162/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/complex_booleans.comp core/scoring/aa_composition_energy/complex_booleans.comp
[1163/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/exactly_three_transACPC.comp core/scoring/aa_composition_energy/exactly_three_transACPC.comp
[1164/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/fractdelta.comp core/scoring/aa_composition_energy/fractdelta.comp
[1165/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/one_trp_one_tyr.comp core/scoring/aa_composition_energy/one_trp_one_tyr.comp
[1166/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/fractdelta_quadratic.comp core/scoring/aa_composition_energy/fractdelta_quadratic.comp
[1167/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/tailfunction_const.comp core/scoring/aa_composition_energy/tailfunction_const.comp
[1168/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/epr_deer/2lzm.pdb core/scoring/epr_deer/2lzm.pdb
[1169/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/tailfunction_linear.comp core/scoring/aa_composition_energy/tailfunction_linear.comp
[1170/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/tailfunction_quadratic.comp core/scoring/aa_composition_energy/tailfunction_quadratic.comp
[1171/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/aa_composition_energy/twenty_percent_pro_fract_ranges.comp core/scoring/aa_composition_energy/twenty_percent_pro_fract_ranges.comp
[1172/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/epr_deer/coords_file.txt core/scoring/epr_deer/coords_file.txt
[1173/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/epr_deer/input_file_epr_deer.txt core/scoring/epr_deer/input_file_epr_deer.txt
[1174/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/bound_seq_GC_SRL.fasta core/scoring/loop_graph/bound_seq_GC_SRL.fasta
[1175/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/P1.pdb core/scoring/loop_graph/P1.pdb
[1176/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/GC_pair.pdb core/scoring/loop_graph/GC_pair.pdb
[1177/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/P2_part1.pdb core/scoring/loop_graph/P2_part1.pdb
[1178/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/P2_part2.pdb core/scoring/loop_graph/P2_part2.pdb
[1179/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/P3.pdb core/scoring/loop_graph/P3.pdb
[1180/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/arg_cation_pi_examples.pdb core/scoring/methods/arg_cation_pi_examples.pdb
[1181/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/loop_graph/SRL_1JBT.pdb core/scoring/loop_graph/SRL_1JBT.pdb
[1182/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/cyclic_pep.pdb core/scoring/methods/cyclic_pep.pdb
[1183/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/HEM.fa.params core/scoring/methods/HEM.fa.params
[1184/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/MMBondAngleEnergyTests.u core/scoring/methods/MMBondAngleEnergyTests.u
[1185/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/HEM.fa.tors core/scoring/methods/HEM.fa.tors
[1186/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/externaldb.csv core/scoring/mhc_epitope_energy/externaldb.csv
[1187/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/test_in.pdb core/scoring/methods/test_in.pdb
[1188/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/c3.sym core/scoring/mhc_epitope_energy/c3.sym
[1189/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/external_db.mhc core/scoring/mhc_epitope_energy/external_db.mhc
[1190/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/nmer_svm.mhc core/scoring/mhc_epitope_energy/nmer_svm.mhc
[1191/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/nmer_unittest.mhc core/scoring/mhc_epitope_energy/nmer_unittest.mhc
[1192/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/externaldb.sql core/scoring/mhc_epitope_energy/externaldb.sql
[1193/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/nmer_rank_unittest.mhc core/scoring/mhc_epitope_energy/nmer_rank_unittest.mhc
[1194/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/preload_csv.mhc core/scoring/mhc_epitope_energy/preload_csv.mhc
[1195/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/extra_mm_scoring/mm_bond_angle_params.txt core/scoring/mm/extra_mm_scoring/mm_bond_angle_params.txt
[1196/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/methods/score3_in.silent_out core/scoring/methods/score3_in.silent_out
[1197/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mhc_epitope_energy/propred8_5.mhc core/scoring/mhc_epitope_energy/propred8_5.mhc
[1198/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/extra_mm_scoring/mm_bond_length_params.txt core/scoring/mm/extra_mm_scoring/mm_bond_length_params.txt
[1199/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/extra_mm_scoring/mm_torsion_params.txt core/scoring/mm/extra_mm_scoring/mm_torsion_params.txt
[1200/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/MMBondAngleScoreTests.u core/scoring/mm/MMBondAngleScoreTests.u
[1201/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/mm_torsion_params.txt core/scoring/mm/mm_torsion_params.txt
[1202/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/netcharge_energy/constant_tailfxns.charge core/scoring/netcharge_energy/constant_tailfxns.charge
[1203/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/netcharge_energy/negative_three.charge core/scoring/netcharge_energy/negative_three.charge
[1204/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_l56c_tb.txt core/scoring/nmr/pcs/sim_pcs_val_l56c_tb.txt
[1205/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/mm/par_all27_prot_na.prm core/scoring/mm/par_all27_prot_na.prm
[1206/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/netcharge_energy/quadratic_tailfxns.charge core/scoring/netcharge_energy/quadratic_tailfxns.charge
[1207/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_tb.txt core/scoring/nmr/pcs/sim_pcs_val_tb.txt
[1208/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/netcharge_energy/linear_tailfxns.charge core/scoring/netcharge_energy/linear_tailfxns.charge
[1209/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/1x0n_model1_renum.pdb core/scoring/nmr/pcs/1x0n_model1_renum.pdb
[1210/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_dy.txt core/scoring/nmr/pcs/sim_pcs_val_dy.txt
[1211/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_er.txt core/scoring/nmr/pcs/sim_pcs_val_er.txt
[1212/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_tm.txt core/scoring/nmr/pcs/sim_pcs_val_tm.txt
[1213/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_l56c_dy.txt core/scoring/nmr/pcs/sim_pcs_val_l56c_dy.txt
[1214/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_l56c_tm.txt core/scoring/nmr/pcs/sim_pcs_val_l56c_tm.txt
[1215/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ksy_chainA_renum.pdb core/scoring/nmr/pcs/2ksy_chainA_renum.pdb
[1216/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_i121c_yb.txt core/scoring/nmr/pcs/sim_pcs_val_i121c_yb.txt
[1217/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_l56c_yb.txt core/scoring/nmr/pcs/sim_pcs_val_l56c_yb.txt
[1218/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_s154c_tb.txt core/scoring/nmr/pcs/sim_pcs_val_s154c_tb.txt
[1219/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_i121c_tb.txt core/scoring/nmr/pcs/sim_pcs_val_i121c_tb.txt
[1220/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_i121c_dy.txt core/scoring/nmr/pcs/sim_pcs_val_i121c_dy.txt
[1221/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_s154c_yb.txt core/scoring/nmr/pcs/sim_pcs_val_s154c_yb.txt
[1222/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_s154c_dy.txt core/scoring/nmr/pcs/sim_pcs_val_s154c_dy.txt
[1223/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_i121c_tm.txt core/scoring/nmr/pcs/sim_pcs_val_i121c_tm.txt
[1224/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_s154c_tm.txt core/scoring/nmr/pcs/sim_pcs_val_s154c_tm.txt
[1225/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_v169c_dy.txt core/scoring/nmr/pcs/sim_pcs_val_v169c_dy.txt
[1226/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_v169c_yb.txt core/scoring/nmr/pcs/sim_pcs_val_v169c_yb.txt
[1227/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainAB_renum.symm core/scoring/nmr/pcs/2ilk_chainAB_renum.symm
[1228/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/pcs_data_2ksy_input_file.txt core/scoring/nmr/pcs/pcs_data_2ksy_input_file.txt
[1229/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainAB_renum.pdb core/scoring/nmr/pcs/2ilk_chainAB_renum.pdb
[1230/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_dy.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_dy.txt
[1231/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainA_renum.pdb core/scoring/nmr/pcs/2ilk_chainA_renum.pdb
[1232/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_tb.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_tb.txt
[1233/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_tm.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_2su_tm.txt
[1234/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_tb.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_tb.txt
[1235/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_dy.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_dy.txt
[1236/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_tm.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_renum_asu_tm.txt
[1237/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/pcs_data_2ilk_2su_input_file.txt core/scoring/nmr/pcs/pcs_data_2ilk_2su_input_file.txt
[1238/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_dy.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_dy.txt
[1239/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/pcs_data_2ilk_asu_input_file.txt core/scoring/nmr/pcs/pcs_data_2ilk_asu_input_file.txt
[1240/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainAB.pdb core/scoring/nmr/pcs/2ilk_chainAB.pdb
[1241/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainAB.symm core/scoring/nmr/pcs/2ilk_chainAB.symm
[1242/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/2ilk_chainA.pdb core/scoring/nmr/pcs/2ilk_chainA.pdb
[1243/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_tb.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_tb.txt
[1244/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_tm.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_2su_tm.txt
[1245/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_yb.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_yb.txt
[1246/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_tm.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_tm.txt
[1247/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_tb.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_tb.txt
[1248/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_dy.txt core/scoring/nmr/pcs/sim_pcs_val_2ilk_asu_dy.txt
[1249/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/pcs_data_1cdl_mtsl_input_file.txt core/scoring/nmr/pcs/pcs_data_1cdl_mtsl_input_file.txt
[1250/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_tb.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_tb.txt
[1251/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_dy.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_dy.txt
[1252/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_tm.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_13_tm.txt
[1253/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_dy.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_dy.txt
[1254/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_tb.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_tb.txt
[1255/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_yb.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_yb.txt
[1256/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_tm.txt core/scoring/nmr/pcs/sim_pcs_val_mtsl_83_tm.txt
[1257/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/1cdl.pdb core/scoring/nmr/1cdl.pdb
[1258/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_c13z_r1_15n.txt core/scoring/nmr/pre/sim_pre_c13z_r1_15n.txt
[1259/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_d46z_r2_15n.txt core/scoring/nmr/pre/sim_pre_d46z_r2_15n.txt
[1260/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_c13z_r2_15n.txt core/scoring/nmr/pre/sim_pre_c13z_r2_15n.txt
[1261/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_c13z_r1_1h.txt core/scoring/nmr/pre/sim_pre_c13z_r1_1h.txt
[1262/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_c13z_r2_1h.txt core/scoring/nmr/pre/sim_pre_c13z_r2_1h.txt
[1263/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_d46z_r2_1h.txt core/scoring/nmr/pre/sim_pre_d46z_r2_1h.txt
[1264/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_d46z_r1_15n.txt core/scoring/nmr/pre/sim_pre_d46z_r1_15n.txt
[1265/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_d46z_r1_1h.txt core/scoring/nmr/pre/sim_pre_d46z_r1_1h.txt
[1266/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e119z_r1_1h.txt core/scoring/nmr/pre/sim_pre_e119z_r1_1h.txt
[1267/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e119z_r2_1h.txt core/scoring/nmr/pre/sim_pre_e119z_r2_1h.txt
[1268/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e83z_r1_15n.txt core/scoring/nmr/pre/sim_pre_e83z_r1_15n.txt
[1269/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e119z_r1_15n.txt core/scoring/nmr/pre/sim_pre_e119z_r1_15n.txt
[1270/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e119z_r2_15n.txt core/scoring/nmr/pre/sim_pre_e119z_r2_15n.txt
[1271/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e83z_r2_15n.txt core/scoring/nmr/pre/sim_pre_e83z_r2_15n.txt
[1272/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e83z_r1_1h.txt core/scoring/nmr/pre/sim_pre_e83z_r1_1h.txt
[1273/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pre_e83z_r2_1h.txt core/scoring/nmr/pre/sim_pre_e83z_r2_1h.txt
[1274/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/pre_data_1cdl_input.txt core/scoring/nmr/pre/pre_data_1cdl_input.txt
[1275/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/pre_data_mid1_input.txt core/scoring/nmr/pre/pre_data_mid1_input.txt
[1276/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pres_cu2_1h_r1.txt core/scoring/nmr/pre/sim_pres_cu2_1h_r1.txt
[1277/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/3v1e_AB_Mn.pdb core/scoring/nmr/pre/3v1e_AB_Mn.pdb
[1278/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/3v1e_AB_Cu.pdb core/scoring/nmr/pre/3v1e_AB_Cu.pdb
[1279/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pres_cu2_1h_r2.txt core/scoring/nmr/pre/sim_pres_cu2_1h_r2.txt
[1280/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_nh_norm_toNH.txt core/scoring/nmr/rdc/bicelles_nh_norm_toNH.txt
[1281/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pres_mn2_1h_r1.txt core/scoring/nmr/pre/sim_pres_mn2_1h_r1.txt
[1282/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/gb1.pdb core/scoring/nmr/rdc/gb1.pdb
[1283/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/pre/sim_pres_mn2_1h_r2.txt core/scoring/nmr/pre/sim_pres_mn2_1h_r2.txt
[1284/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_nh.txt core/scoring/nmr/rdc/bicelles_nh.txt
[1285/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_hnc_norm_toNH.txt core/scoring/nmr/rdc/bicelles_hnc_norm_toNH.txt
[1286/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_nc_norm_toNH.txt core/scoring/nmr/rdc/bicelles_nc_norm_toNH.txt
[1287/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_nc.txt core/scoring/nmr/rdc/bicelles_nc.txt
[1288/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/bicelles_hnc.txt core/scoring/nmr/rdc/bicelles_hnc.txt
[1289/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_nh_norm_toNH.txt core/scoring/nmr/rdc/tmv107_nh_norm_toNH.txt
[1290/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_nc_norm_toNH.txt core/scoring/nmr/rdc/tmv107_nc_norm_toNH.txt
[1291/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_nh.txt core/scoring/nmr/rdc/tmv107_nh.txt
[1292/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_nc.txt core/scoring/nmr/rdc/tmv107_nc.txt
[1293/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_hnc.txt core/scoring/nmr/rdc/tmv107_hnc.txt
[1294/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_AB_model1_renum.symm core/scoring/nmr/rdc/2jwk_AB_model1_renum.symm
[1295/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/tmv107_hnc_norm_toNH.txt core/scoring/nmr/rdc/tmv107_hnc_norm_toNH.txt
[1296/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_AB_model1.symm core/scoring/nmr/rdc/2jwk_AB_model1.symm
[1297/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/rdc_data_g_input_file.txt core/scoring/nmr/rdc/rdc_data_g_input_file.txt
[1298/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_A_model1_renamed_INPUT.pdb core/scoring/nmr/rdc/2jwk_A_model1_renamed_INPUT.pdb
[1299/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caco_renum_asu.txt core/scoring/nmr/rdc/2jwk_caco_renum_asu.txt
[1300/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_A_model1_renum_renamed_INPUT.pdb core/scoring/nmr/rdc/2jwk_A_model1_renum_renamed_INPUT.pdb
[1301/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caco_renum_all_su.txt core/scoring/nmr/rdc/2jwk_caco_renum_all_su.txt
[1302/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caha_renum_all_su.txt core/scoring/nmr/rdc/2jwk_caha_renum_all_su.txt
[1303/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caco_all_su.txt core/scoring/nmr/rdc/2jwk_caco_all_su.txt
[1304/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caha_renum_asu.txt core/scoring/nmr/rdc/2jwk_caha_renum_asu.txt
[1305/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caco_asu.txt core/scoring/nmr/rdc/2jwk_caco_asu.txt
[1306/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nco_renum_all_su.txt core/scoring/nmr/rdc/2jwk_nco_renum_all_su.txt
[1307/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caha_all_su.txt core/scoring/nmr/rdc/2jwk_caha_all_su.txt
[1308/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_caha_asu.txt core/scoring/nmr/rdc/2jwk_caha_asu.txt
[1309/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nco_renum_asu.txt core/scoring/nmr/rdc/2jwk_nco_renum_asu.txt
[1310/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nh_renum_all_su.txt core/scoring/nmr/rdc/2jwk_nh_renum_all_su.txt
[1311/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nco_asu.txt core/scoring/nmr/rdc/2jwk_nco_asu.txt
[1312/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nco_all_su.txt core/scoring/nmr/rdc/2jwk_nco_all_su.txt
[1313/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nh_renum_asu.txt core/scoring/nmr/rdc/2jwk_nh_renum_asu.txt
[1314/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nh_all_su.txt core/scoring/nmr/rdc/2jwk_nh_all_su.txt
[1315/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/2akf.pdb core/scoring/symmetry/2akf.pdb
[1316/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/2jwk_nh_asu.txt core/scoring/nmr/rdc/2jwk_nh_asu.txt
[1317/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/rdc_data_2jwk_all_su_input_file.txt core/scoring/nmr/rdc/rdc_data_2jwk_all_su_input_file.txt
[1318/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/atom_pair_constraint.data core/scoring/symmetry/atom_pair_constraint.data
[1319/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/nmr/rdc/rdc_data_2jwk_asu_input_file.txt core/scoring/nmr/rdc/rdc_data_2jwk_asu_input_file.txt
[1320/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/coordinate_constraint.data core/scoring/symmetry/coordinate_constraint.data
[1321/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/C3.symm core/scoring/symmetry/C3.symm
[1322/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/test.aln core/sequence/test.aln
[1323/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_intra_sol.data core/scoring/symmetry/fa_intra_sol.data
[1324/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_atr.data core/scoring/symmetry/fa_atr.data
[1325/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_intra_atr.data core/scoring/symmetry/fa_intra_atr.data
[1326/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_intra_rep.data core/scoring/symmetry/fa_intra_rep.data
[1327/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_rep.data core/scoring/symmetry/fa_rep.data
[1328/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fibril_in.pdb core/scoring/symmetry/fibril_in.pdb
[1329/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_elec.data core/scoring/symmetry/fa_elec.data
[1330/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fa_sol.data core/scoring/symmetry/fa_sol.data
[1331/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/fibril_symm.dat core/scoring/symmetry/fibril_symm.dat
[1332/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/sym_def.dat core/scoring/symmetry/sym_def.dat
[1333/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/mm_twist.data core/scoring/symmetry/mm_twist.data
[1334/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/hbond_sr_bb.data core/scoring/symmetry/hbond_sr_bb.data
[1335/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/symm_test.pdb core/scoring/symmetry/symm_test.pdb
[1336/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/scoring/symmetry/test_in.pdb core/scoring/symmetry/test_in.pdb
[1337/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/1aho_.fasta.pssm core/sequence/1aho_.fasta.pssm
[1338/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/abego_test.pdb core/sequence/abego_test.pdb
[1339/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/1aho_hom.fasta.pssm core/sequence/1aho_hom.fasta.pssm
[1340/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Emperor.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Emperor.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Emperor.cc.o -c /home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Emperor.cc
[1341/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/util/2c9v_stripped.pdb core/util/2c9v_stripped.pdb
[1342/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/test.grishin_aln core/sequence/test.grishin_aln
[1343/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/sequence/test.general_aln core/sequence/test.general_aln
[1344/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/simple_metrics/2r0l_1_1.pdb core/simple_metrics/2r0l_1_1.pdb
[1345/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/simple_metrics/metrics/testpose.pdb core/simple_metrics/metrics/testpose.pdb
[1346/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/numeric/interpolation/Histogram_sample.hist numeric/interpolation/Histogram_sample.hist
[1347/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/numeric/mt19937.u numeric/mt19937.u
[1348/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/simple_metrics/2cl2_opt_waters2.pdb core/simple_metrics/2cl2_opt_waters2.pdb
[1349/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/core/simple_metrics/two_glycans.pdb core/simple_metrics/two_glycans.pdb
[1350/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/numeric/kinematic_closure/test_peptide.pdb numeric/kinematic_closure/test_peptide.pdb
[1351/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/numeric/sampling.prob numeric/sampling.prob
[1352/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/1EER_A.pdb devel/znhash/1EER_A.pdb
[1353/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/denovo_design/D2I.params devel/denovo_design/D2I.params
[1354/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/denovo_design/cat_residues.pdb devel/denovo_design/cat_residues.pdb
[1355/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/denovo_design/C5_Z.sym devel/denovo_design/C5_Z.sym
[1356/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/UM_39_H104D100_28_1EER_A_ZNX_1.pdb devel/znhash/UM_39_H104D100_28_1EER_A_ZNX_1.pdb
[1357/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/denovo_design/test_input.pdb devel/denovo_design/test_input.pdb
[1358/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/1EER_cn4_0043.pdb devel/znhash/1EER_cn4_0043.pdb
[1359/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/UM_26_H100D103_1_1EER_A_ZNX_1.pdb devel/znhash/UM_26_H100D103_1_1EER_A_ZNX_1.pdb
[1360/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/match_cst_pairs.txt devel/znhash/match_cst_pairs.txt
[1361/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/UM_50_H14E10_32_1EER_A_ZNX_1.pdb devel/znhash/UM_50_H14E10_32_1EER_A_ZNX_1.pdb
[1362/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/denovo_design/test_foldability.pdb devel/denovo_design/test_foldability.pdb
[1363/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/UM_1_H5E11_95_1EER_A_ZNX_1.pdb devel/znhash/UM_1_H5E11_95_1EER_A_ZNX_1.pdb
[1364/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/UM_41_H13E17_3_1EER_A_ZNX_1.pdb devel/znhash/UM_41_H13E17_3_1EER_A_ZNX_1.pdb
[1365/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/ZNX.cst devel/znhash/ZNX.cst
[1366/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/ZNX.params devel/znhash/ZNX.params
[1367/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/devel/znhash/ZNX_1H_2DE.cst devel/znhash/ZNX_1H_2DE.cst
[1368/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/utility/UTracer_test.u utility/UTracer_test.u
[1369/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/utility/io/no_final_newline.txt utility/io/no_final_newline.txt
[1370/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/basic/options/options_1 basic/options/options_1
[1371/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/utility/io/simple_input_file.txt utility/io/simple_input_file.txt
[1372/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/utility/io/zipped_file.txt.gz utility/io/zipped_file.txt.gz
[1373/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/ZNx.params apps/public/ligand_docking/ZNx.params
[1374/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/7cpa.params apps/public/ligand_docking/7cpa.params
[1375/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/basic/options/options_2 basic/options/options_2
[1376/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/1dm2_1aq1_10poses.out apps/public/ligand_docking/1dm2_1aq1_10poses.out
[1377/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/7cpa_7cpa_input.pdb apps/public/ligand_docking/7cpa_7cpa_input.pdb
[1378/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/1aq1.params apps/public/ligand_docking/1aq1.params
[1379/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/7cpa_confs.pdb apps/public/ligand_docking/7cpa_confs.pdb
[1380/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/silent.out.ref apps/public/ligand_docking/silent.out.ref
[1381/4561] cd /home/benchmark/rosetta/source/cmake/build_debug && /usr/bin/cmake3 -E copy /home/benchmark/rosetta/source/test/apps/public/ligand_docking/7cpa_7cpa_native.pdb apps/public/ligand_docking/7cpa_7cpa_native.pdb
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[1401/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/DarcParticleSwarmMinimizer.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/DarcParticleSwarmMinimizer.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/DarcParticleSwarmMinimizer.cc.o -c /home/benchmark/rosetta/source/src/protocols/pockets/DarcParticleSwarmMinimizer.cc
[1402/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentRebuild.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentRebuild.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentRebuild.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/SegmentRebuild.cc
[1403/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/LoopHashSampler.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/LoopHashSampler.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/LoopHashSampler.cc.o -c /home/benchmark/rosetta/source/src/protocols/loophash/LoopHashSampler.cc
[1404/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentInsert.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentInsert.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/build/SegmentInsert.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/build/SegmentInsert.cc
[1405/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Master.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Master.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Master.cc.o -c /home/benchmark/rosetta/source/src/protocols/loophash/MPI_LoopHashRefine_Master.cc
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[1409/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/util.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/util.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/methods/util.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/methods/util.cc
[1410/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_6_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -c /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc
FAILED: CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o
/usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_6_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -MF CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o.d -o CMakeFiles/protocols_b.6.dir/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc.o -c /home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc: In member function ‘core::Size LigandDiscoverySearch::discover(std::string)’:
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:988:6: error: ‘str’ has not been declared
str::string pdb_name = "";
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:988:18: error: expected ‘;’ before ‘pdb_name’
str::string pdb_name = "";
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:993:54: error: ‘pdb_name’ was not declared in this scope
if(score_placed_ligand(minipose, original_pose, pdb_name, pdb_short_unique_name, comment_table_header, comment_table_data))
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1032:7: error: ‘pdb_name’ was not declared in this scope
pdb_name = pdb_name + "_motifs_" + std::to_string(motifs_made);
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1271:6: error: ‘pdb_name’ was not declared in this scope
pdb_name = pdb_name + ".pdb";
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1309:71: error: ‘delta_score’ was not declared in this scope
std::tuple<core::Real, core::pose::Pose, std::string> pose_tuple(delta_score, *working_pose_, pdb_name);
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:799:9: error: unused variable ‘ligand_added’ [-Werror=unused-variable]
bool ligand_added = false;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc: In member function ‘bool LigandDiscoverySearch::score_placed_ligand(core::pose::PoseOP&, core::pose::Pose, std::string&, std::string&, std::string&, std::string&)’:
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1404:5: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1416:5: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1426:5: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1430:4: error: ‘passed_placement_counter’ was not declared in this scope
++passed_placement_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1434:41: error: ‘ligresOP’ was not declared in this scope
working_pose_->append_residue_by_jump(*ligresOP, working_pose_->size(), "", "", true);
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1440:174: error: ‘trip_atom_1’ was not declared in this scope
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1440:254: error: ‘working_position’ was not declared in this scope
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_1, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_1 ), fx1 ) ) );
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1443:174: error: ‘trip_atom_2’ was not declared in this scope
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_2, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_2 ), fx2 ) ) );
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1446:174: error: ‘trip_atom_3’ was not declared in this scope
sc_cst_set->add_constraint( core::scoring::constraints::ConstraintCOP( utility::pointer::make_shared< core::scoring::constraints::CoordinateConstraint >( core::id::AtomID( trip_atom_3, working_pose_->size() ), core::id::AtomID( working_pose_->residue( working_position ).atom_index( "CA" ), 1 ), ligresOP->xyz( trip_atom_3 ), fx3 ) ) );
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1487:7: error: ‘ligand_added’ was not declared in this scope
if ( ligand_added == false ) {
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1501:31: error: ‘lig_mrt’ was not declared in this scope
rts->add_base_residue_type(lig_mrt);
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1569:6: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1588:6: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1626:5: error: ‘clashing_counter’ was not declared in this scope
++clashing_counter;
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1638:13: error: ‘output_prefix’ was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1638:89: error: ‘discovery_position_residue’ was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1638:143: error: ‘i’ was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
/home/benchmark/rosetta/source/src/protocols/motifs/LigandDiscoverySearch.cc:1638:185: error: ‘motifcop’ was not declared in this scope
pdb_name = output_prefix + "_ResPos_" + std::to_string(working_position) + "_ResID_" + discovery_position_residue + "_Trio" + std::to_string(i) + "_" + ligresOP->name() + "_motif_" + motifcop->remark();
^
cc1plus: all warnings being treated as errors
[1411/4561] : && /usr/bin/c++ -fPIC -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -shared -Wl,-soname,libutility.so -o libutility.so CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/Binary_Util.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/CSI_Sequence.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/LexicographicalIterator.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/SimulateMPI.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/VirtualBase.srlz.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/backtrace.cc.o CMakeFiles/utility.dir/home/benchmark/rosetta/source/src/utility/crash_report.cc.o 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[1426/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelLoopMover.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelLoopMover.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelLoopMover.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelLoopMover.cc
[1427/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/PocketGrid.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/PocketGrid.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/pockets/PocketGrid.cc.o -c /home/benchmark/rosetta/source/src/protocols/pockets/PocketGrid.cc
[1428/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_b_5_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelGlobalFrame.cc.o -MF CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelGlobalFrame.cc.o.d -o CMakeFiles/protocols_b.5.dir/home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelGlobalFrame.cc.o -c /home/benchmark/rosetta/source/src/protocols/forge/remodel/RemodelGlobalFrame.cc
[1429/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_8_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register3.cc.o -MF CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register3.cc.o.d -o CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register3.cc.o -c /home/benchmark/rosetta/source/src/protocols/init/register3.cc
[1430/4561] /usr/bin/c++ -DBOOST_DISABLE_THREADS -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DCPPDB_EXPORTS -DCPPDB_LIBRARY_PREFIX=\"lib\" -DCPPDB_LIBRARY_SUFFIX=\".so\" -DCPPDB_MAJOR=0 -DCPPDB_MINOR=3 -DCPPDB_PATCH=0 -DCPPDB_SOVERSION=\"0\" -DCPPDB_VERSION=\"0.3.0\" -DCPPDB_WITH_SQLITE3 -DCXX11 -DLINUX -DPTR_STD -DSQLITE_OMIT_DISABLE_LFS -DSQLITE_OMIT_LOAD_EXTENSION -DSQLITE_THREADSAFE=0 -D_DEBUG -D_GLIBCXX_DEBUG -Dprotocols_8_EXPORTS -I../.. -I../../src -I../../src/platform/linux -I../../test -isystem ../../external -isystem ../../external/include -isystem ../../external/dbio -isystem ../../external/rdkit -isystem ../../external/boost_submod -isystem ../../external/cxxtest -isystem ../../external/dbio/sqlite3 -isystem ../../external/libxml2/include -std=c++11 -pipe -ffor-scope -ftemplate-depth-256 -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -I /usr/include -I /usr/local/include -I src -I external/include -I src/platform/linux -O0 -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -g -ggdb -ffloat-store -g -fPIC -MD -MT CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register4.cc.o -MF CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register4.cc.o.d -o CMakeFiles/protocols.8.dir/home/benchmark/rosetta/source/src/protocols/init/register4.cc.o -c /home/benchmark/rosetta/source/src/protocols/init/register4.cc
ninja: build stopped: subcommand failed.
Traceback (most recent call last):
File "./ninja_build.py", line 132, in <module>
subprocess.check_call(ninja_command)
File "/usr/local/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['ninja', '-C', '/home/benchmark/rosetta/source/cmake/build_debug', '-j', '64', '-v']' returned non-zero exit status 1.