Running: /home/benchmark/prefix/nobu-4/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin cxx=gcc extras= -j64
scons: Reading SConscript files ...
Running versioning script ... Done. (0.1 seconds)
Number of option files updated: 0
Total 4682 options.
Updating submodules needed for compilation.
Finished updating ResidueProperty code
-- no changes needed
Finished updating VariantType code
-- no changes needed
scons: done reading SConscript files.
scons: Building targets ...
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AbinitioRelax.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/AbinitioRelax.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchorFinder.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/interface_design/anchored_design/AnchorFinder.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchoredDesign.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/interface_design/anchored_design/AnchoredDesign.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchoredPDBCreator.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/interface_design/anchored_design/AnchoredPDBCreator.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/BuildPeptide.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/flexpep_docking/BuildPeptide.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ComputeSAXSSpectrum.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/dgront/saxs/ComputeSAXSSpectrum.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/CstfileToTheozymePDB.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/enzdes/CstfileToTheozymePDB.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/Cyclize.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/doug/Cyclize.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/DARC.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/darc/DARC.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/DNA_methylation.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/post-translational_modification/DNA_methylation.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FiberDiffractionFreeSet.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/fiber_diffraction/FiberDiffractionFreeSet.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FiberDiffractionTest.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/wojtek/FiberDiffractionTest.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FlexPepDocking.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/flexpep_docking/FlexPepDocking.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FloppyTail.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/scenarios/FloppyTail.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/GlycanDock.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/carbohydrates/GlycanDock.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/HDXEnergy.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/HDXEnergy.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/InterfaceAnalyzer.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/InterfaceAnalyzer.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/LoopAnalyzer.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/smlewis/LoopAnalyzer.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MSA_design.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/ashworth/MSA_design.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MakeRotLib.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/ncaa_utilities/MakeRotLib.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MakeSegmentFile.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/pose_sewing/MakeSegmentFile.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/N-terminal_acetylation.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/post-translational_modification/N-terminal_acetylation.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/PDB_diagnostic.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/smlewis/ChemXRW/PDB_diagnostic.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/PeptideDeriver.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/PeptideDeriver.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/RescorePDDF.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/dgront/saxs/RescorePDDF.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/RescoreSAXS.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/dgront/saxs/RescoreSAXS.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ResidueDisorder.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/ResidueDisorder.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SID_ERMS_prediction.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/SID_ERMS_prediction.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SID_rescore.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/jtseffer/SID_rescore.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SymDock.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/SymDock.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_E2_thioester.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_Gp_CYD-CYD.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/scenarios/chemically_conjugated_docking/UBQ_Gp_CYD-CYD.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_Gp_LYX-Cterm.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/scenarios/chemically_conjugated_docking/UBQ_Gp_LYX-Cterm.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UnfoldedStateEnergyCalculator.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/analyze_base_pairing.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/rna/util/analyze_base_pairing.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/angle_recovery_stats.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/james/angle_recovery_stats.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_CR_paratope.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_CR_paratope.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_H3.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_H3.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_designer.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_designer.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_graft.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_graft.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_legacy.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_legacy.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_numbering_converter.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/antibody/antibody_numbering_converter.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/assemble_domains_jd2.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/james/assemble_domains_jd2.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/atom_energy_breakdown.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/atom_energy_breakdown.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/avrg_silent.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/comparative_modeling/avrg_silent.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backrub.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/backrub.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backrub_pilot.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/colin/backrub_pilot.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backside_hbond_finder.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/sewing/ligand_sewing_tools/backside_hbond_finder.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/basic_glycan_sampler.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/carbohydrates/basic_glycan_sampler.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/batch_distances.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/batch_distances.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/batchrelax.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/mike/batchrelax.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/beta_peptide_modeling.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/design/beta_peptide_modeling.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/build_full_model.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/stepwise/build_full_model.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/burial_measure_centroid.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/maprahamian/burial_measure_centroid.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ca_to_allatom.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/scenarios/ca_to_allatom.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calc_nmr_tensor.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/nmr/calc_nmr_tensor.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calculate_sasa.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/calculate_sasa.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calibur.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/clustering/calibur.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cartesian_ddg.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/ddg/cartesian_ddg.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cl_complex_rescore.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/analysis/cl_complex_rescore.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cloud_app.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/pilot/olli/cloud_app.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lcppdb -lsqlite3 -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cluster.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/clustering/cluster.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
g++ -o build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cluster_alns.default.linuxgccdebug -Wl,--disable-new-dtags -Wl,-rpath=/home/benchmark/rosetta/source/build/src/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=/home/benchmark/rosetta/source/build/external/debug/linux/5.4/64/x86/gcc/4.8/default -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib build/src/debug/linux/5.4/64/x86/gcc/4.8/default/apps/public/comparative_modeling/cluster_alns.o -Lexternal/lib -Lbuild/src/debug/linux/5.4/64/x86/gcc/4.8/default -Lsrc -Lbuild/external/debug/linux/5.4/64/x86/gcc/4.8/default -Lexternal -L/usr/lib -L/usr/local/lib -ldevel -lprotocols.8 -lprotocols.7 -lprotocols_e.6 -lprotocols_d.6 -lprotocols_c.6 -lprotocols_b.6 -lprotocols_a.6 -lprotocols_h.5 -lprotocols_g.5 -lprotocols_f.5 -lprotocols_e.5 -lprotocols_d.5 -lprotocols_c.5 -lprotocols_b.5 -lprotocols_a.5 -lprotocols.4 -lprotocols.3 -lprotocols_b.2 -lprotocols_a.2 -lprotocols.1 -lcore.6 -lcore.5 -lcore.4 -lcore.3 -lcore.2 -lcore.1 -lbasic -lnumeric -lutility -lObjexxFCL -lz -lzlib -lcppdb -lsqlite3 -lcifparse -lxml2 -lzmq -lrdkit -lbcl -lcmaes
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AbinitioRelax.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchoredDesign.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchorFinder.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/AnchoredPDBCreator.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/BuildPeptide.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ComputeSAXSSpectrum.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/CstfileToTheozymePDB.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/Cyclize.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/DNA_methylation.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FiberDiffractionFreeSet.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/DARC.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FlexPepDocking.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FiberDiffractionTest.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/FloppyTail.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/GlycanDock.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/HDXEnergy.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/InterfaceAnalyzer.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/LoopAnalyzer.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MakeRotLib.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MSA_design.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/N-terminal_acetylation.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/PDB_diagnostic.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/MakeSegmentFile.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/PeptideDeriver.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/RescorePDDF.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/RescoreSAXS.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ResidueDisorder.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SymDock.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SID_ERMS_prediction.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/SID_rescore.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_Gp_LYX-Cterm.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_E2_thioester.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UBQ_Gp_CYD-CYD.default.linuxgccdebug] Error 1
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/UnfoldedStateEnergyCalculator.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/analyze_base_pairing.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/angle_recovery_stats.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_H3.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_CR_paratope.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_designer.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_graft.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_legacy.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/antibody_numbering_converter.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/assemble_domains_jd2.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/atom_energy_breakdown.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backrub.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/avrg_silent.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backrub_pilot.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/basic_glycan_sampler.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/batch_distances.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/batchrelax.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/backside_hbond_finder.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/beta_peptide_modeling.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/burial_measure_centroid.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/build_full_model.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calc_nmr_tensor.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/ca_to_allatom.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calculate_sasa.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/calibur.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cartesian_ddg.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cloud_app.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cluster_alns.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cl_complex_rescore.default.linuxgccdebug] Error 1
build/src/debug/linux/5.4/64/x86/gcc/4.8/default/libprotocols.3.so: undefined reference to `protocols::recon_design::get_candidate_AAs(utility::vector1<utility::vector1<std::string, std::allocator<std::string> >, std::allocator<utility::vector1<std::string, std::allocator<std::string> > > >, unsigned long)'
collect2: error: ld returned 1 exit status
scons: *** [build/src/debug/linux/5.4/64/x86/gcc/4.8/default/cluster.default.linuxgccdebug] Error 1
scons: building terminated because of errors.