ERROR: benchmark.py script terminated with non-zero exit-code, execution log:
Running Singularity container...
Command line: singularity exec --contain --cleanenv --no-home --bind /scratch/benchmark/nobu-4/w/.singularity.home:/home/benchmark --bind /home/benchmark/release:/home/benchmark/release_root --bind /home/benchmark/prefix/fragment_picking_database/2019.05.19:/home/benchmark/fragment_picking_database --bind /scratch/benchmark/nobu-4/w/T/commits-20716.855076.ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit.0:/home/benchmark/working_dir --bind /scratch/benchmark/nobu-4/w/rosetta/commits/rosetta:/home/benchmark/rosetta --bind /scratch/benchmark/nobu-4/w/prefix/ubuntu:/home/benchmark/prefix --hostname nobu-4 --workdir /scratch/benchmark/nobu-4/w/.singularity.tmpfs --pwd /home/benchmark/rosetta/tests/benchmark /scratch/benchmark/nobu-4/b3/back/../../w/.singularity.images/ubuntu.simg python3 ./benchmark.py --setup /home/benchmark/working_dir/.execution.setup.json <<<''
Loading test from: tests/PyRosetta.py, suite+test: 'PyRosetta.unit', test: 'unit'
Found test suite description in file: 'tests/PyRosetta.md'
Running PyRosetta unit tests: at working_dir='/home/benchmark/working_dir' with rosetta_dir=/home/benchmark/rosetta, platform={'compiler': 'clang', 'extras': ['cxx11thread', 'serialization'], 'os': 'ubuntu', 'python': '3.8'}, jobs=64, memory=256GB, hpc_driver=MultiCore_HPC_Driver<>...
Getting python configuration info...
unset __PYVENV_LAUNCHER__ && cd /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin && PATH=.:$PATH && /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8-config --prefix --includes
/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220
-I/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -I/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8
Getting PyRosetta build path...
cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8 build.py -j64 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 --python-lib=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib --multi-threaded --serialization --print-build-root
/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread
Building PyRosetta MinSizeRel...
cd /home/benchmark/rosetta/source/src/python/PyRosetta && /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/bin/python3.8 build.py -j64 --compiler clang --type MinSizeRel --python-include-dir=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 --python-lib=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib --multi-threaded --serialization
Creating PyRosetta in "MinSizeRel" mode in: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/clang-6.0.0/python-3.8/minsizerel.serialization.thread
Getting main repository root...
cd /home/benchmark/rosetta/source && git rev-parse --show-toplevel
/home/benchmark/rosetta
Updating Pybind11 Git submodule...
cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/external/pybind11
Updating Binder Git submodule...
cd /home/benchmark/rosetta/source/.. && git submodule update --init -- source/src/python/PyRosetta/binder
LLVM:6.0.1 + Binder install is detected at /home/benchmark/rosetta/source/build/prefix/llvm-6.0.1/llvm-6.0.1.Linux-5.4.0-84-generic-x86_64-with-glibc2.27.release, skipping LLVM installation and Binder building procedures...
Updating compilation submodules, version, options and residue-type-enum files...
cd /home/benchmark/rosetta/source && ./update_submodules.sh PyRosetta bcl zeromq && ./version.py && ./update_options.sh && ./update_ResidueType_enum_files.sh
...truncated...
Building wheel for blosc (pyproject.toml) ... [?25l- \ | / - \ | / - error
[1;31merror[0m: [1msubprocess-exited-with-error[0m
[31m×[0m [32mBuilding wheel for blosc [0m[1;32m([0m[32mpyproject.toml[0m[1;32m)[0m did not run successfully.
[31m│[0m exit code: [1;36m1[0m
[31m╰─>[0m [31m[113 lines of output][0m
[31m [0m
[31m [0m
[31m [0m --------------------------------------------------------------------------------
[31m [0m -- Trying 'Ninja' generator
[31m [0m --------------------------------
[31m [0m ---------------------------
[31m [0m ----------------------
[31m [0m -----------------
[31m [0m ------------
[31m [0m -------
[31m [0m --
[31m [0m CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
[31m [0m Compatibility with CMake < 3.10 will be removed from a future version of
[31m [0m CMake.
[31m [0m
[31m [0m Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
[31m [0m to tell CMake that the project requires at least <min> but has been updated
[31m [0m to work with policies introduced by <max> or earlier.
[31m [0m
[31m [0m Not searching for unused variables given on the command line.
[31m [0m
[31m [0m -- The C compiler identification is GNU 7.5.0
[31m [0m -- Detecting C compiler ABI info
[31m [0m -- Detecting C compiler ABI info - done
[31m [0m -- Check for working C compiler: /usr/bin/cc - skipped
[31m [0m -- Detecting C compile features
[31m [0m -- Detecting C compile features - done
[31m [0m -- The CXX compiler identification is GNU 7.5.0
[31m [0m -- Detecting CXX compiler ABI info
[31m [0m -- Detecting CXX compiler ABI info - done
[31m [0m -- Check for working CXX compiler: /usr/bin/c++ - skipped
[31m [0m -- Detecting CXX compile features
[31m [0m -- Detecting CXX compile features - done
[31m [0m -- Configuring done (1.1s)
[31m [0m -- Generating done (0.0s)
[31m [0m -- Build files have been written to: /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149/_cmake_test_compile/build
[31m [0m --
[31m [0m -------
[31m [0m ------------
[31m [0m -----------------
[31m [0m ----------------------
[31m [0m ---------------------------
[31m [0m --------------------------------
[31m [0m -- Trying 'Ninja' generator - success
[31m [0m --------------------------------------------------------------------------------
[31m [0m
[31m [0m Configuring Project
[31m [0m Working directory:
[31m [0m /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149/_skbuild/linux-x86_64-3.8/cmake-build
[31m [0m Command:
[31m [0m /tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/cmake/data/bin/cmake /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149 -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_VERSION_STRING:STRING=3.8.14 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPYTHON_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DPYTHON_LIBRARY:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/libpython3.8.a -DPython_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPython_ROOT_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413 -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DPython3_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPython3_ROOT_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413 -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja -DBLOSC_DIR:PATH= -DDEACTIVATE_SSE2:BOOL=OFF -DDEACTIVATE_AVX2:BOOL=OFF -DDEACTIVATE_LZ4:BOOL=OFF -DDEACTIVATE_SNAPPY:BOOL=ON -DDEACTIVATE_ZLIB:BOOL=OFF -DDEACTIVATE_ZSTD:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
[31m [0m
[31m [0m Not searching for unused variables given on the command line.
[31m [0m -- The C compiler identification is GNU 7.5.0
[31m [0m -- The CXX compiler identification is GNU 7.5.0
[31m [0m -- Detecting C compiler ABI info
[31m [0m -- Detecting C compiler ABI info - done
[31m [0m -- Check for working C compiler: /usr/bin/cc - skipped
[31m [0m -- Detecting C compile features
[31m [0m -- Detecting C compile features - done
[31m [0m -- Detecting CXX compiler ABI info
[31m [0m -- Detecting CXX compiler ABI info - done
[31m [0m -- Check for working CXX compiler: /usr/bin/c++ - skipped
[31m [0m -- Detecting CXX compile features
[31m [0m -- Detecting CXX compile features - done
[31m [0m CMake Warning (dev) at /tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/resources/cmake/FindPythonExtensions.cmake:245 (find_package):
[31m [0m Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
[31m [0m are removed. Run "cmake --help-policy CMP0148" for policy details. Use
[31m [0m the cmake_policy command to set the policy and suppress this warning.
[31m [0m
[31m [0m Call Stack (most recent call first):
[31m [0m CMakeLists.txt:3 (find_package)
[31m [0m This warning is for project developers. Use -Wno-dev to suppress it.
[31m [0m
[31m [0m -- Found PythonInterp: /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python (found version "3.8.14")
[31m [0m CMake Warning (dev) at /tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/resources/cmake/FindPythonExtensions.cmake:252 (find_package):
[31m [0m Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
[31m [0m are removed. Run "cmake --help-policy CMP0148" for policy details. Use
[31m [0m the cmake_policy command to set the policy and suppress this warning.
[31m [0m
[31m [0m Call Stack (most recent call first):
[31m [0m CMakeLists.txt:3 (find_package)
[31m [0m This warning is for project developers. Use -Wno-dev to suppress it.
[31m [0m
[31m [0m -- Found PythonLibs: /home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/libpython3.8.a (found version "3.8.14")
[31m [0m CMake Error at c-blosc/CMakeLists.txt:74 (cmake_minimum_required):
[31m [0m Compatibility with CMake < 3.5 has been removed from CMake.
[31m [0m
[31m [0m Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
[31m [0m to tell CMake that the project requires at least <min> but has been updated
[31m [0m to work with policies introduced by <max> or earlier.
[31m [0m
[31m [0m Or, add -DCMAKE_POLICY_VERSION_MINIMUM=3.5 to try configuring anyway.
[31m [0m
[31m [0m
[31m [0m -- Configuring incomplete, errors occurred!
[31m [0m /tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
[31m [0m warnings.warn(msg)
[31m [0m Traceback (most recent call last):
[31m [0m File "/tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 660, in setup
[31m [0m env = cmkr.configure(
[31m [0m File "/tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 354, in configure
[31m [0m raise SKBuildError(msg)
[31m [0m
[31m [0m An error occurred while configuring with CMake.
[31m [0m Command:
[31m [0m /tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/cmake/data/bin/cmake /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149 -G Ninja -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja --no-warn-unused-cli -DCMAKE_INSTALL_PREFIX:PATH=/tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_VERSION_STRING:STRING=3.8.14 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-qykba7td/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DPYTHON_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPYTHON_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DPYTHON_LIBRARY:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/lib/libpython3.8.a -DPython_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPython_ROOT_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413 -DPython_FIND_REGISTRY:STRING=NEVER -DPython_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DPython3_EXECUTABLE:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413/bin/python -DPython3_ROOT_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.8/39b436240c2f250098506a2adbd3b413 -DPython3_FIND_REGISTRY:STRING=NEVER -DPython3_INCLUDE_DIR:PATH=/home/benchmark/prefix/nobu-4/ubuntu/python-3.8.gcc/c366c4308e4154e0a853e031f172e220/include/python3.8 -DCMAKE_MAKE_PROGRAM:FILEPATH=ninja -DBLOSC_DIR:PATH= -DDEACTIVATE_SSE2:BOOL=OFF -DDEACTIVATE_AVX2:BOOL=OFF -DDEACTIVATE_LZ4:BOOL=OFF -DDEACTIVATE_SNAPPY:BOOL=ON -DDEACTIVATE_ZLIB:BOOL=OFF -DDEACTIVATE_ZSTD:BOOL=OFF -DCMAKE_BUILD_TYPE:STRING=Release
[31m [0m Source directory:
[31m [0m /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149
[31m [0m Working directory:
[31m [0m /tmp/pip-install-b1zk3syz/blosc_4d9974ad8fa94a5c8f66afaeb4441149/_skbuild/linux-x86_64-3.8/cmake-build
[31m [0m Please see CMake's output for more information.
[31m [0m
[31m [0m [31m[end of output][0m
[1;35mnote[0m: This error originates from a subprocess, and is likely not a problem with pip.
[31m ERROR: Failed building wheel for blosc[0m[31m
[0m[?25hFailed to build blosc
[31mERROR: Failed to build installable wheels for some pyproject.toml based projects (blosc)[0m[31m
[0m
ERROR: Benchmark back-end script terminates abnormally, marking test state as 'script failed'!