StartDate: 2025-08-21 06:04:04+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: bd63e738b4693bb27f7e9c9030a02afc36f2adcb CommitTime: 2025-08-20 12:48:12 +0200 CommitAuthor: Matthias Krack CommitSubject: Use RPM macro _lib #################### Building Image cp2k-phonopy #################### Dockerfile: /tools/docker/Dockerfile.test_phonopy Build-Path: / Build-Args: GIT_COMMIT_SHA=bd63e738b4693bb27f7e9c9030a02afc36f2adcb SPACK_CACHE=gs://cp2k-spack-cache Build-Cache: Yes Populating docker build cache... done. DEPRECATED: The legacy builder is deprecated and will be removed in a future release. BuildKit is currently disabled; enable it by removing the DOCKER_BUILDKIT=0 environment-variable. Sending build context to Docker daemon 405.9MB Step 1/43 : FROM ubuntu:24.04 24.04: Pulling from library/ubuntu b71466b94f26: Pulling fs layer b71466b94f26: Verifying Checksum b71466b94f26: Download complete b71466b94f26: Pull complete Digest: sha256:7c06e91f61fa88c08cc74f7e1b7c69ae24910d745357e0dfe1d2c0322aaf20f9 Status: Downloaded newer image for ubuntu:24.04 ---> e0f16e6366fe Step 2/43 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> e40e2312aaae Step 3/43 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> dea345367eaf Step 4/43 : RUN ./install_requirements.sh ubuntu:24.04 ---> Using cache ---> 782d57da719e Step 5/43 : RUN mkdir scripts ---> Using cache ---> 6ab744ae7a48 Step 6/43 : COPY ./tools/toolchain/scripts/VERSION ./tools/toolchain/scripts/parse_if.py ./tools/toolchain/scripts/tool_kit.sh ./tools/toolchain/scripts/common_vars.sh ./tools/toolchain/scripts/signal_trap.sh ./tools/toolchain/scripts/get_openblas_arch.sh ./scripts/ ---> Using cache ---> c4dd5c045b77 Step 7/43 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> 7fd7c86ff27b Step 8/43 : RUN ./install_cp2k_toolchain.sh --install-all --mpi-mode=no --with-dbcsr --with-gcc=system --dry-run ---> Using cache ---> 3849241ac700 Step 9/43 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> Using cache ---> 5652fb4a51ec Step 10/43 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Using cache ---> 96c195ff8b65 Step 11/43 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> Using cache ---> b13dbc8849f7 Step 12/43 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Using cache ---> 5947358ac850 Step 13/43 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> Using cache ---> ae7934bd6eae Step 14/43 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Using cache ---> 743003f9fd19 Step 15/43 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> Using cache ---> b4df5cee6d64 Step 16/43 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Using cache ---> 779651deac4c Step 17/43 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> Using cache ---> 9c69ec90db32 Step 18/43 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Using cache ---> 308b403eccd8 Step 19/43 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> Using cache ---> ecf49be825dd Step 20/43 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Using cache ---> e6c763257c1c Step 21/43 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> Using cache ---> 6f7d0717d4f9 Step 22/43 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Using cache ---> ce15fa134c52 Step 23/43 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> Using cache ---> dac0b1295b38 Step 24/43 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Using cache ---> 480aedb27338 Step 25/43 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> Using cache ---> 0fd90d89fa5f Step 26/43 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Using cache ---> c4e06252964e Step 27/43 : COPY ./tools/toolchain/scripts/stage9/ ./scripts/stage9/ ---> Using cache ---> 42e30d257abb Step 28/43 : RUN ./scripts/stage9/install_stage9.sh && rm -rf ./build ---> Using cache ---> a5d479deff88 Step 29/43 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> Using cache ---> 711975d65292 Step 30/43 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Using cache ---> 46e91eb88e0d Step 31/43 : WORKDIR /opt/cp2k ---> Using cache ---> b14f9bd22bdc Step 32/43 : COPY ./src ./src ---> Using cache ---> b8bb2ca385e9 Step 33/43 : COPY ./data ./data ---> Using cache ---> 1ba61b899601 Step 34/43 : COPY ./tests ./tests ---> Using cache ---> dc8e6a8c419e Step 35/43 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> 7d4bef199cb1 Step 36/43 : COPY ./cmake ./cmake ---> Using cache ---> 658362e7f0d1 Step 37/43 : COPY ./CMakeLists.txt . ---> Using cache ---> b3ebae2d349d Step 38/43 : COPY ./tools/docker/scripts/build_cp2k_cmake.sh . ---> Using cache ---> 273c65380768 Step 39/43 : RUN ./build_cp2k_cmake.sh toolchain ssmp ---> Running in acdea94f161e ==================== Building CP2K ==================== -- The Fortran compiler identification is GNU 13.3.0 -- The C compiler identification is GNU 13.3.0 -- The CXX compiler identification is GNU 13.3.0 -- Detecting Fortran compiler ABI info -- Detecting Fortran compiler ABI info - done -- Check for working Fortran compiler: /usr/bin/gfortran - skipped -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Python: /usr/bin/python3.12 (found version "3.12.3") found components: Interpreter -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Checking for module 'mpi-c' -- Package 'mpi-c', required by 'virtual:world', not found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Checking for module 'mpi-cxx' -- Package 'mpi-cxx', required by 'virtual:world', not found -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Checking for module 'mpi-fort' -- Package 'mpi-fort', required by 'virtual:world', not found -- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIB_NAMES MPI_Fortran_F77_HEADER_DIR MPI_Fortran_MODULE_DIR MPI_Fortran_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND CXX C Fortran) -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX C Fortran -- Could NOT find MKL (missing: CP2K_MKL_INCLUDE_DIRS) -- Checking for module 'openblas' -- Found openblas, version 0.3.30 -- Found OpenBLAS: /opt/cp2k-toolchain/install/openblas-0.3.30/include -- Found Blas: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so -- Found Lapack: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so -- Checking for module 'libxsmm-shared' -- Found libxsmm-shared, version 1.17.0 -- Checking for module 'libxsmmf-shared' -- Found libxsmmf-shared, version 1.17.0 -- Checking for module 'libxsmmext-shared' -- Found libxsmmext-shared, version 1.17.0 -- Checking for module 'libxsmmnoblas-shared' -- Found libxsmmnoblas-shared, version 1.17.0 -- Found LibXSMM: /opt/cp2k-toolchain/install/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec/include -- Using LIBXSMM for Small Matrix Multiplication ------------------------------------------------------------ - OPENMP - ------------------------------------------------------------ -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: Fortran C CXX ------------------------------------------------------------ - DBCSR - ------------------------------------------------------------ -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") ------------------------------------------------------------ - Other dependencies - ------------------------------------------------------------ -- Found HDF5: hdf5-shared;hdf5_fortran-shared (found version "1.14.6") found components: C Fortran -- Found LibVORI: /opt/cp2k-toolchain/install/libvori-220621/lib/libvori.a -- Checking for one of the modules 'fftw3' -- Checking for one of the modules 'fftw3f' -- Checking for one of the modules 'fftw3l' -- Checking for one of the modules 'fftw3q' -- Found Fftw: /opt/cp2k-toolchain/install/fftw-3.3.10/include -- Checking for module 'libint2' -- Found libint2, version 2.6.0 -- Found Libint2: /opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5/include;/opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5/include/libint2 -- Component omp of Spglib: NOT FOUND -- Component fortran of Spglib: FOUND (LIB_TYPE: static) -- Found package: Spglib -- Looking for Fortran sgemm -- Looking for Fortran sgemm - not found -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Found BLAS: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so -- mctc-lib: Find installed package -- multicharge: Find installed package -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- Found LAPACK: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so;-lm;-ldl -- Found ACE: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/include -- Found ACE: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libpace.a -- Found ACE: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libyaml-cpp-pace.a -- Found ACE: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libcnpy.a -- Checking for module 'mpi-c' -- Package 'mpi-c', required by 'virtual:world', not found -- Could NOT find MPI_C (missing: MPI_C_LIB_NAMES MPI_C_HEADER_DIR MPI_C_WORKS) -- Checking for module 'mpi-cxx' -- Package 'mpi-cxx', required by 'virtual:world', not found -- Could NOT find MPI_CXX (missing: MPI_CXX_LIB_NAMES MPI_CXX_HEADER_DIR MPI_CXX_WORKS) -- Checking for module 'mpi-fort' -- Package 'mpi-fort', required by 'virtual:world', not found -- Could NOT find MPI_Fortran (missing: MPI_Fortran_LIB_NAMES MPI_Fortran_F77_HEADER_DIR MPI_Fortran_MODULE_DIR MPI_Fortran_WORKS) -- Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND MPI_Fortran_FOUND CXX C Fortran) -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_Fortran: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX C Fortran -- Found Torch: /opt/cp2k-toolchain/install/libtorch-2.7.1/lib/libtorch.so -- Torch setting CMAKE_CXX_STANDARD to 17 -- Checking for module 'trexio' -- Found trexio, version 2.5.0 -- Found TrexIO: /opt/cp2k-toolchain/install/trexio-2.5.0/include;/opt/cp2k-toolchain/install/hdf5-1.14.6/include -- Setting build type to 'Release' as none was specified. -- Performing Test f2008-norm2 -- Performing Test f2008-norm2 - Success -- Performing Test f2008-block_construct -- Performing Test f2008-block_construct - Success -- Performing Test f2008-contiguous -- Performing Test f2008-contiguous - Success -- Performing Test f95-reshape-order-allocatable -- Performing Test f95-reshape-order-allocatable - Success -- FYPP preprocessor found. -------------------------------------------------------------------- - - - Summary of enabled dependencies - - - -------------------------------------------------------------------- - BLAS - vendor: OpenBLAS - include directories: /opt/cp2k-toolchain/install/openblas-0.3.30/include - libraries: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so - LAPACK - include directories: /opt/cp2k-toolchain/install/openblas-0.3.30/include - libraries: /opt/cp2k-toolchain/install/openblas-0.3.30/lib/libopenblas.so - LibXC - version: 7.0.0 - include directories: /opt/cp2k-toolchain/install/libxc-7.0.0/include/ - libraries: /opt/cp2k-toolchain/install/libxc-7.0.0/lib/libxcf03.a;/opt/cp2k-toolchain/install/libxc-7.0.0/lib/libxc.a - Spglib - include directories: /opt/cp2k-toolchain/install/spglib-2.5.0/include - LibTorch - extra CXX flags: -D_GLIBCXX_USE_CXX11_ABI=1 - include directories: /opt/cp2k-toolchain/install/libtorch-2.7.1/include;/opt/cp2k-toolchain/install/libtorch-2.7.1/include/torch/csrc/api/include - libraries: /opt/cp2k-toolchain/install/libtorch-2.7.1/lib/libtorch.so - HDF5 - version: 1.14.6 - include directories: /opt/cp2k-toolchain/install/hdf5-1.14.6/include - libraries: hdf5-shared;hdf5_fortran-shared - FFTW3 - include directories: /opt/cp2k-toolchain/install/fftw-3.3.10/include - libraries: /opt/cp2k-toolchain/install/fftw-3.3.10/lib/libfftw3.a - LIBXSMM - include directories: /opt/cp2k-toolchain/install/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec/include - libraries: /opt/cp2k-toolchain/install/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec/lib/libxsmmext.so;:libxsmm.a;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libc.so;/opt/cp2k-toolchain/install/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec/lib/libxsmmf.so;:libxsmmext.a;:libxsmm.a;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/librt.a;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libc.so - DFTD4 - include directories : /opt/cp2k-toolchain/install/tblite-0.5.0/include;/opt/cp2k-toolchain/install/tblite-0.5.0/include/dftd4/GNU-13.3.0 - libraries : - DeePMD - ACE - include directories: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/include - libraries: /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libpace.a;/opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libyaml-cpp-pace.a;/opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2/lib/libcnpy.a - TBLITE : - include directories : /opt/cp2k-toolchain/install/tblite-0.5.0/include;/opt/cp2k-toolchain/install/tblite-0.5.0/include/tblite/GNU-13.3.0 - tblite libraries : - Libint2 - include directories: /opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5/include;/opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5/include/libint2 - libraries: /opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib/libint2.a - Libvori - libraries: /opt/cp2k-toolchain/install/libvori-220621/lib/libvori.a - GRPP - TREXIO - include directories: /opt/cp2k-toolchain/install/trexio-2.5.0/include;/opt/cp2k-toolchain/install/hdf5-1.14.6/include - libraries: /opt/cp2k-toolchain/install/trexio-2.5.0/lib/libtrexio.so;/opt/cp2k-toolchain/install/hdf5-1.14.6/lib/libhdf5.so - GreenX - include directories: /opt/cp2k-toolchain/install/greenX-2.2/include/modules - libraries: /opt/cp2k-toolchain/install/greenX-2.2/lib/libGXCommon.so.0.0.1;/opt/cp2k-toolchain/install/greenX-2.2/lib/libgx_minimax.so.0.0.1;/opt/cp2k-toolchain/install/greenX-2.2/lib/libgx_ac.so.0.0.1 -------------------------------------------------------------------- - - - List of dependencies not included in this build - - - -------------------------------------------------------------------- - MPI - PEXSI - SIRIUS - LibSMEAGOL - COSMA - SpLA - GPU acceleration is disabled - ELPA - DLA-Future - PLUMED To run the regtests you need to run the following commands cd .. export CP2K_DATA_DIR=/opt/cp2k/data/ ./tests/do_regtest.py /opt/cp2k/build/bin ssmp -- Configuring done (4.7s) -- Generating done (0.3s) -- Build files have been written to: /opt/cp2k/build Compiling CP2K ... done ---> Removed intermediate container acdea94f161e ---> f1b67b82c9db Step 40/43 : COPY ./tools/docker/scripts/test_phonopy.sh ./ ---> 90fde2fbb9a3 Step 41/43 : RUN ./test_phonopy.sh 2>&1 | tee report.log ---> Running in df88d5cefc01 ========== Installing Dependencies ========== debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package python3-pip-whl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15455 files and directories currently installed.) Preparing to unpack .../python3-pip-whl_24.0+dfsg-1ubuntu1.2_all.deb ... Unpacking python3-pip-whl (24.0+dfsg-1ubuntu1.2) ... Selecting previously unselected package python3-setuptools-whl. Preparing to unpack .../python3-setuptools-whl_68.1.2-2ubuntu1.2_all.deb ... Unpacking python3-setuptools-whl (68.1.2-2ubuntu1.2) ... Selecting previously unselected package python3.12-venv. Preparing to unpack .../python3.12-venv_3.12.3-1ubuntu0.7_amd64.deb ... Unpacking python3.12-venv (3.12.3-1ubuntu0.7) ... Selecting previously unselected package python3-venv. Preparing to unpack .../python3-venv_3.12.3-0ubuntu2_amd64.deb ... Unpacking python3-venv (3.12.3-0ubuntu2) ... Setting up python3-setuptools-whl (68.1.2-2ubuntu1.2) ... Setting up python3-pip-whl (24.0+dfsg-1ubuntu1.2) ... Setting up python3.12-venv (3.12.3-1ubuntu0.7) ... Setting up python3-venv (3.12.3-0ubuntu2) ... ========== Installing Phonopy ========== Processing /opt/phonopy Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy>=1.17.0 (from phonopy==0.1.dev1+g9ea257c1b) Using cached numpy-2.3.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB) Collecting PyYAML>=5.3 (from phonopy==0.1.dev1+g9ea257c1b) Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) Collecting matplotlib>=2.2.2 (from phonopy==0.1.dev1+g9ea257c1b) Downloading matplotlib-3.10.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB) Collecting h5py>=3.0 (from phonopy==0.1.dev1+g9ea257c1b) Downloading h5py-3.14.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.7 kB) Collecting spglib>=2.3 (from phonopy==0.1.dev1+g9ea257c1b) Downloading spglib-2.6.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.2 kB) Collecting symfc>=1.5 (from phonopy==0.1.dev1+g9ea257c1b) Downloading symfc-1.5.4-py3-none-any.whl.metadata (3.8 kB) Collecting cp2k-input-tools (from phonopy==0.1.dev1+g9ea257c1b) Downloading cp2k_input_tools-0.9.1-py3-none-any.whl.metadata (16 kB) Collecting contourpy>=1.0.1 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading contourpy-1.3.3-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (5.5 kB) Collecting cycler>=0.10 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) Collecting fonttools>=4.22.0 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading fonttools-4.59.1-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (108 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 108.9/108.9 kB 4.3 MB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading kiwisolver-1.4.9-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.3 kB) Collecting packaging>=20.0 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) Collecting pillow>=8 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading pillow-11.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) Collecting pyparsing>=2.3.1 (from matplotlib>=2.2.2->phonopy==0.1.dev1+g9ea257c1b) Downloading pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB) Collecting python-dateutil>=2.7 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typing_inspection-0.4.1-py3-none-any.whl (14 kB) Building wheels for collected packages: phonopy Building wheel for phonopy (pyproject.toml): started Building wheel for phonopy (pyproject.toml): finished with status 'done' Created wheel for phonopy: filename=phonopy-0.1.dev1+g9ea257c1b-cp312-cp312-linux_x86_64.whl size=518403 sha256=16e05e1be272e3c307dea9a83f701b05eb6951bcee1b32864ceeb936b9ab7189 Stored in directory: /tmp/pip-ephem-wheel-cache-u687bod7/wheels/2f/e0/05/5e668a749d74ad7aa1c06dd26b8d7a6452bb1b8ed66ae3c43d Successfully built phonopy Installing collected packages: typing-extensions, six, PyYAML, pyparsing, pillow, packaging, numpy, MarkupSafe, kiwisolver, fonttools, cycler, click, annotated-types, typing-inspection, transitions, spglib, scipy, python-dateutil, pydantic-core, Pint, Jinja2, h5py, contourpy, symfc, pydantic, matplotlib, phonopy, cp2k-input-tools Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.2 Pint-0.23 PyYAML-6.0.2 annotated-types-0.7.0 click-8.2.1 contourpy-1.3.3 cp2k-input-tools-0.9.1 cycler-0.12.1 fonttools-4.59.1 h5py-3.14.0 kiwisolver-1.4.9 matplotlib-3.10.5 numpy-2.3.2 packaging-25.0 phonopy-0.1.dev1+g9ea257c1b pillow-11.3.0 pydantic-2.11.7 pydantic-core-2.33.2 pyparsing-3.2.3 python-dateutil-2.9.0.post0 scipy-1.16.1 six-1.17.0 spglib-2.6.0 symfc-1.5.4 transitions-0.9.3 typing-extensions-4.14.1 typing-inspection-0.4.1 Collecting Pint==0.24.4 Downloading Pint-0.24.4-py3-none-any.whl.metadata (8.5 kB) Collecting platformdirs>=2.1.0 (from Pint==0.24.4) Downloading platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB) Requirement already satisfied: typing-extensions>=4.0.0 in /opt/venv/lib/python3.12/site-packages (from Pint==0.24.4) (4.14.1) Collecting flexcache>=0.3 (from Pint==0.24.4) Downloading flexcache-0.3-py3-none-any.whl.metadata (7.0 kB) Collecting flexparser>=0.4 (from Pint==0.24.4) Downloading flexparser-0.4-py3-none-any.whl.metadata (18 kB) Downloading Pint-0.24.4-py3-none-any.whl (302 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.0/302.0 kB 8.3 MB/s eta 0:00:00 Downloading flexcache-0.3-py3-none-any.whl (13 kB) Downloading flexparser-0.4-py3-none-any.whl (27 kB) Downloading platformdirs-4.3.8-py3-none-any.whl (18 kB) Installing collected packages: platformdirs, flexparser, flexcache, Pint Attempting uninstall: Pint Found existing installation: Pint 0.23 Uninstalling Pint-0.23: Successfully uninstalled Pint-0.23 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. cp2k-input-tools 0.9.1 requires Pint<0.24,>=0.15, but you have pint 0.24.4 which is incompatible. Successfully installed Pint-0.24.4 flexcache-0.3 flexparser-0.4 platformdirs-4.3.8 ========== Running Phonopy Test ========== _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.43.1 -------------------------[time 2025-08-21 06:16:56]------------------------- Compiled with OpenMP support (max 32 threads). Python version 3.12.3 Spglib version 2.6.0 Calculator interface: cp2k Crystal structure was read from "Si.inp". Unit of length: angstrom Displacements creation mode Systematic displacements Settings: Supercell: [2 2 2] Spacegroup: Fd-3m (227) Number of symmetry operations in supercell: 1536 Use -v option to watch primitive cell, unit cell, and supercell structures. Generated number of supercells: 1 ************************************************************************ Note: A better primitive cell can be chosen by using "--pa auto" option. ************************************************************************ "phonopy_disp.yaml" and supercells have been created. Summary of calculation was written in "phonopy_disp.yaml". -------------------------[time 2025-08-21 06:16:58]------------------------- _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.43.1 -------------------------[time 2025-08-21 06:17:37]------------------------- Compiled with OpenMP support (max 32 threads). Python version 3.12.3 Spglib version 2.6.0 Calculator interface: cp2k Displacements were read from "phonopy_disp.yaml". Number of supercell files: 1 Number of displacements in "phonopy_disp.yaml": 1 1. Drift force of "Si-supercell-001-forces-1_0.xyz" to be subtracted -0.00000000 0.00000000 -0.00000000 "FORCE_SETS" has been created. -------------------------[time 2025-08-21 06:17:37]------------------------- _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| Summary: Phonopy commit 9ea257c works fine. Status: OK ---> Removed intermediate container df88d5cefc01 ---> e85f694ad6ce Step 42/43 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 20085eadfd4d ---> Removed intermediate container 20085eadfd4d ---> afb371501dea Step 43/43 : ENTRYPOINT [] ---> Running in f4046bbe1336 ---> Removed intermediate container f4046bbe1336 ---> ae4cef3152af [Warning] One or more build-args [GIT_COMMIT_SHA SPACK_CACHE] were not consumed Successfully built ae4cef3152af Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-phonopy:master Pushing new image... done. #################### Running Image cp2k-phonopy #################### EndDate: 2025-08-21 06:19:03+00:00