StartDate: 2025-07-14 06:04:15+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: ede6ae935488a87899e1874758f0926d17abbb82 CommitTime: 2025-07-13 21:39:08 +0200 CommitAuthor: Hans Pabst CommitSubject: FFTW: removed distinction with MKL #################### Building Image cp2k-gromacs #################### Dockerfile: /tools/docker/Dockerfile.test_gromacs Build-Path: / Build-Args: GIT_COMMIT_SHA=ede6ae935488a87899e1874758f0926d17abbb82 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 405.6MB Step 1/41 : FROM ubuntu:24.04 24.04: Pulling from library/ubuntu b08e2ff4391e: Pulling fs layer b08e2ff4391e: Verifying Checksum b08e2ff4391e: Download complete b08e2ff4391e: Pull complete Digest: sha256:440dcf6a5640b2ae5c77724e68787a906afb8ddee98bf86db94eea8528c2c076 Status: Downloaded newer image for ubuntu:24.04 ---> f9248aac10f2 Step 2/41 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> 9f209947b5dd Step 3/41 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> 7a503e940187 Step 4/41 : RUN ./install_requirements.sh ubuntu:24.04 ---> Using cache ---> 51fb7d7d6c7a Step 5/41 : RUN mkdir scripts ---> Using cache ---> a6229555cac5 Step 6/41 : 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 ---> 26f495712ebc Step 7/41 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> 6806b8669701 Step 8/41 : RUN ./install_cp2k_toolchain.sh --install-all --mpi-mode=no --with-dbcsr --with-gcc=system --dry-run ---> Running in 1d121072613d Not using MPI, so ScaLAPACK is disabled. Not using MPI, so ELPA is disabled. Not using MPI, so PLUMED is disabled. Not using MPI, so libsmeagol is disabled. Not using MPI, so SIRIUS is disabled Not using MPI, so SpFFT is disabled Not using MPI, so SpLA is disabled Not using MPI, so COSMA is disabled Compiling with 32 processes for target native. WARNING: (./install_cp2k_toolchain.sh, line 371) No MPI installation detected (ignore this message in Cray Linux Environment or when MPI installation was requested). Wrote only configuration files (--dry-run). Removing intermediate container 1d121072613d ---> 42a0016e8cb7 Step 9/41 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> 8dfbc1bca92b Step 10/41 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Running in c1dee22c25bd ==================== Finding GCC from system paths ==================== path to gcc is /usr/bin/gcc path to g++ is /usr/bin/g++ path to gfortran is /usr/bin/gfortran GCC compiler version 13.3.0 found Found include directory /usr/include Step gcc took 0.00 seconds. Step intel took 0.00 seconds. Step amd took 0.00 seconds. ==================== Getting proc arch info using OpenBLAS tools ==================== wget --quiet https://www.cp2k.org/static/downloads/OpenBLAS-0.3.29.tar.gz -O OpenBLAS-0.3.29.tar.gz OpenBLAS-0.3.29.tar.gz: OK Checksum of OpenBLAS-0.3.29.tar.gz Ok /usr/bin/ld: warning: /tmp/cc0cY8QJ.o: missing .note.GNU-stack section implies executable stack /usr/bin/ld: NOTE: This behaviour is deprecated and will be removed in a future version of the linker OpenBLAS detected LIBCORE = zen OpenBLAS detected ARCH = x86_64 ==================== Installing CMake ==================== wget --quiet https://www.cp2k.org/static/downloads/cmake-3.31.7-linux-x86_64.sh -O cmake-3.31.7-linux-x86_64.sh cmake-3.31.7-linux-x86_64.sh: OK Checksum of cmake-3.31.7-linux-x86_64.sh Ok Installing from scratch into /opt/cp2k-toolchain/install/cmake-3.31.7 Step cmake took 5.00 seconds. ==================== Installing Ninja ==================== wget --quiet https://www.cp2k.org/static/downloads/ninja-v1.12.1.tar.gz -O ninja-v1.12.1.tar.gz ninja-v1.12.1.tar.gz: OK Checksum of ninja-v1.12.1.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/ninja-v1.12.1 Step ninja took 6.00 seconds. Removing intermediate container c1dee22c25bd ---> 705c34ea9a81 Step 11/41 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> c093f02ede07 Step 12/41 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Running in 0a7e0faf1cae Removing intermediate container 0a7e0faf1cae ---> f4e376e031c9 Step 13/41 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> f9eae2fef701 Step 14/41 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Running in c6fe7cdb78ec ==================== Installing OpenBLAS ==================== wget --quiet https://www.cp2k.org/static/downloads/OpenBLAS-0.3.29.tar.gz -O OpenBLAS-0.3.29.tar.gz OpenBLAS-0.3.29.tar.gz: OK Checksum of OpenBLAS-0.3.29.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/openblas-0.3.29 Installing OpenBLAS library for target ZEN Step openblas took 105.00 seconds. ==================== Installing GMP ==================== wget --quiet https://www.cp2k.org/static/downloads/gmp-6.3.0.tar.gz -O gmp-6.3.0.tar.gz gmp-6.3.0.tar.gz: OK Checksum of gmp-6.3.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/gmp-6.3.0 Step gmp took 23.00 seconds. Removing intermediate container c6fe7cdb78ec ---> 4ab77cb9fba0 Step 15/41 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> a44bd5c7f9e3 Step 16/41 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Running in afb08969496c ==================== Installing FFTW ==================== wget --quiet https://www.cp2k.org/static/downloads/fftw-3.3.10.tar.gz -O fftw-3.3.10.tar.gz fftw-3.3.10.tar.gz: OK Checksum of fftw-3.3.10.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/fftw-3.3.10 Step fftw took 44.00 seconds. ==================== Installing LIBINT ==================== wget --quiet https://www.cp2k.org/static/downloads/libint-v2.6.0-cp2k-lmax-5.tgz -O libint-v2.6.0-cp2k-lmax-5.tgz libint-v2.6.0-cp2k-lmax-5.tgz: OK Checksum of libint-v2.6.0-cp2k-lmax-5.tgz Ok Installing from scratch into /opt/cp2k-toolchain/install/libint-v2.6.0-cp2k-lmax-5 Step libint took 276.00 seconds. ==================== Installing LIBXC ==================== wget --quiet https://www.cp2k.org/static/downloads/libxc-7.0.0.tar.bz2 -O libxc-7.0.0.tar.bz2 libxc-7.0.0.tar.bz2: OK Checksum of libxc-7.0.0.tar.bz2 Ok Installing from scratch into /opt/cp2k-toolchain/install/libxc-7.0.0 Step libxc took 330.00 seconds. ==================== Installing GreenX ==================== wget --quiet https://www.cp2k.org/static/downloads/greenX-2.2.tar.gz -O greenX-2.2.tar.gz greenX-2.2.tar.gz: OK Checksum of greenX-2.2.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/greenX-2.2 Step greenx took 5.00 seconds. ==================== Using libgrpp ==================== Step libgrpp took 0.00 seconds. Removing intermediate container afb08969496c ---> c62931d43a17 Step 17/41 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> 332f3c121367 Step 18/41 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Running in 9940034354bb ==================== Installing Libxsmm ==================== wget --quiet https://www.cp2k.org/static/downloads/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec.tar.gz -O libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec.tar.gz libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec.tar.gz: OK Checksum of libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/libxsmm-e0c4a2389afba36c453233ad7de07bd92c715bec Step libxsmm took 11.00 seconds. Step scalapack took 0.00 seconds. Step cosma took 0.00 seconds. Removing intermediate container 9940034354bb ---> 98b416d52aa5 Step 19/41 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> 799059ac4885 Step 20/41 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Running in 52ecef09be0d WARNING: (./scripts/stage5/install_elpa.sh, line 31) MPI is disabled, skipping ELPA installation Removing intermediate container 52ecef09be0d ---> 4341f1e8849f Step 21/41 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> 2b640f9d882e Step 22/41 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Running in 3e75035ba3ba ==================== Installing GSL ==================== wget --quiet https://www.cp2k.org/static/downloads/gsl-2.8.tar.gz -O gsl-2.8.tar.gz gsl-2.8.tar.gz: OK Checksum of gsl-2.8.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/gsl-2.8 Step gsl took 44.00 seconds. WARNING: (./scripts/stage6/install_plumed.sh, line 29) MPI is disabled, skipping PLUMED installation ==================== Installing libtorch ==================== wget --quiet https://www.cp2k.org/static/downloads/libtorch-cxx11-abi-shared-with-deps-2.7.1+cpu.zip -O libtorch-cxx11-abi-shared-with-deps-2.7.1+cpu.zip libtorch-cxx11-abi-shared-with-deps-2.7.1+cpu.zip: OK Checksum of libtorch-cxx11-abi-shared-with-deps-2.7.1+cpu.zip Ok Installing from scratch into /opt/cp2k-toolchain/install/libtorch-2.7.1 Step libtorch took 12.00 seconds. ==================== Installing DeePMD ==================== wget --quiet https://www.cp2k.org/static/downloads/deepmd-kit-3.0.2.tar.gz -O deepmd-kit-3.0.2.tar.gz deepmd-kit-3.0.2.tar.gz: OK Checksum of deepmd-kit-3.0.2.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/deepmd-kit-3.0.2 Step deepmd took 121.00 seconds. ==================== Installing Ace ======================= wget --quiet https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz -O lammps-user-pace-v.2023.11.25.fix2.tar.gz lammps-user-pace-v.2023.11.25.fix2.tar.gz: OK Checksum of lammps-user-pace-v.2023.11.25.fix2.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/lammps-user-pace-v.2023.11.25.fix2 Step ace took 18.00 seconds. Removing intermediate container 3e75035ba3ba ---> 3fb6f3761d0d Step 23/41 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> aa5cfc247030 Step 24/41 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Running in 70c00240ae77 ==================== Installing hdf5 ==================== wget --quiet https://www.cp2k.org/static/downloads/hdf5-1.14.5.tar.gz -O hdf5-1.14.5.tar.gz hdf5-1.14.5.tar.gz: OK Checksum of hdf5-1.14.5.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/hdf5-1.14.5 Step hdf5 took 52.00 seconds. ==================== Installing libvdwxc ==================== wget --quiet https://www.cp2k.org/static/downloads/libvdwxc-0.4.0.tar.gz -O libvdwxc-0.4.0.tar.gz libvdwxc-0.4.0.tar.gz: OK Checksum of libvdwxc-0.4.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/libvdwxc-0.4.0 Step libvdwxc took 8.00 seconds. ==================== Installing Spglib ==================== wget --quiet https://www.cp2k.org/static/downloads/spglib-2.5.0.tar.gz -O spglib-2.5.0.tar.gz spglib-2.5.0.tar.gz: OK Checksum of spglib-2.5.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/spglib-2.5.0 Step spglib took 3.00 seconds. ==================== Installing libvori ==================== wget --quiet https://www.cp2k.org/static/downloads/libvori-220621.tar.gz -O libvori-220621.tar.gz libvori-220621.tar.gz: OK Checksum of libvori-220621.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/libvori-220621 Step libvori took 15.00 seconds. WARNING: (./scripts/stage7/install_libsmeagol.sh, line 27) MPI is disabled, skipping libsmeagol installation Removing intermediate container 70c00240ae77 ---> b40eb15ebf38 Step 25/41 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> a506b528a440 Step 26/41 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Running in c427535d126e Step pugixml took 0.00 seconds. Step spfft took 0.00 seconds. Step spla took 0.00 seconds. WARNING: (./scripts/stage8/install_sirius.sh, line 19) MPI is disabled, skipping sirius installation Step dftd4 took 0.00 seconds. ==================== Installing TREXIO ==================== Installing from scratch into /opt/cp2k-toolchain/install/trexio-2.5.0 wget --quiet https://www.cp2k.org/static/downloads/trexio-2.5.0.tar.gz -O trexio-2.5.0.tar.gz trexio-2.5.0.tar.gz: OK Checksum of trexio-2.5.0.tar.gz Ok Step trexio took 23.00 seconds. ==================== Installing tblite ==================== wget --quiet https://www.cp2k.org/static/downloads/tblite-0.4.0.tar.gz -O tblite-0.4.0.tar.gz tblite-0.4.0.tar.gz: OK Checksum of tblite-0.4.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/tblite-0.4.0 Step tblite took 21.00 seconds. Removing intermediate container c427535d126e ---> 6c0b4aba2ecb Step 27/41 : COPY ./tools/toolchain/scripts/stage9/ ./scripts/stage9/ ---> 6ab7bccf0256 Step 28/41 : RUN ./scripts/stage9/install_stage9.sh && rm -rf ./build ---> Running in 6bf392cae2cc ==================== Installing DBCSR ==================== wget --quiet https://github.com/cp2k/dbcsr/releases/download/v2.8.0/dbcsr-2.8.0.tar.gz -O dbcsr-2.8.0.tar.gz dbcsr-2.8.0.tar.gz: OK Checksum of dbcsr-2.8.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/dbcsr-2.8.0 Step DBCSR took 34.00 seconds. Removing intermediate container 6bf392cae2cc ---> 483a29041b32 Step 29/41 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> 00f3db124336 Step 30/41 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Running in bca1aa2725a9 ==================== generating arch files ==================== arch files can be found in the /opt/cp2k-toolchain/install/arch subdirectory Wrote /opt/cp2k-toolchain/install/arch/local.ssmp Wrote /opt/cp2k-toolchain/install/arch/local_static.ssmp Wrote /opt/cp2k-toolchain/install/arch/local.sdbg Wrote /opt/cp2k-toolchain/install/arch/local_asan.ssmp Wrote /opt/cp2k-toolchain/install/arch/local_coverage.sdbg ========================== usage ========================= Done! Now copy: cp /opt/cp2k-toolchain/install/arch/* to the cp2k/arch/ directory To use the installed tools and libraries and cp2k version compiled with it you will first need to execute at the prompt: source /opt/cp2k-toolchain/install/setup To build CP2K you should change directory: cd cp2k/ make -j 32 ARCH=local VERSION="ssmp sdbg" arch files for GPU enabled CUDA versions are named "local_cuda.*" arch files for GPU enabled HIP versions are named "local_hip.*" arch files for OpenCL (GPU) versions are named "local_opencl.*" arch files for coverage versions are named "local_coverage.*" Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers. It is possible to use the provided CP2K arch files as guidance. Removing intermediate container bca1aa2725a9 ---> ba5bfd88a8af Step 31/41 : WORKDIR /opt/cp2k ---> Running in edb14430ac41 Removing intermediate container edb14430ac41 ---> a3d8a9d61f8e Step 32/41 : COPY ./src ./src ---> d41d42729a68 Step 33/41 : COPY ./data ./data ---> f4e618d307ce Step 34/41 : COPY ./tests ./tests ---> ca5bce5b28d9 Step 35/41 : COPY ./tools/build_utils ./tools/build_utils ---> 2d93ed36b2b6 Step 36/41 : COPY ./cmake ./cmake ---> 6e8c11c9f0fe Step 37/41 : COPY ./CMakeLists.txt . ---> 20aa14222f74 Step 38/41 : COPY ./tools/docker/scripts/build_cp2k_cmake.sh ./tools/docker/scripts/test_gromacs.sh ./ ---> cc224299548a Step 39/41 : RUN ./test_gromacs.sh 2>&1 | tee report.log ---> Running in c4d791040eaa ==================== 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 fatal: not a git repository (or any of the parent directories): .git -- 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 0.3.29 -- Found OpenBLAS: /opt/cp2k-toolchain/install/openblas-0.3.29/include -- Found Blas: /opt/cp2k-toolchain/install/openblas-0.3.29/lib/libopenblas.so -- Found Lapack: /opt/cp2k-toolchain/install/openblas-0.3.29/lib/libopenblas.so ------------------------------------------------------------ - 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 -- 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") -- Found HDF5: hdf5-shared;hdf5_fortran-shared (found version "1.14.5") 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-0.3.29/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-0.3.29/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/hdf5-1.14.5/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-0.3.29/include - libraries: /opt/cp2k-toolchain/install/openblas-0.3.29/lib/libopenblas.so - LAPACK - include directories: /opt/cp2k-toolchain/install/openblas-0.3.29/include - libraries: /opt/cp2k-toolchain/install/openblas-0.3.29/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: 1.14.5 - include directories: /opt/cp2k-toolchain/install/hdf5-1.14.5/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 - DFTD4 - include directories : /opt/cp2k-toolchain/install/tblite-0.4.0/include;/opt/cp2k-toolchain/install/tblite-0.4.0/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-0.4.0/include;/opt/cp2k-toolchain/install/tblite-0.4.0/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/hdf5-1.14.5/include - libraries: /opt/cp2k-toolchain/install/trexio-2.5.0/lib/libtrexio.so;/opt/cp2k-toolchain/install/hdf5-1.14.5/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 - LIBXSMM 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 (4.2s) -- Generating done (0.3s) -- Build files have been written to: /opt/cp2k/build Compiling CP2K ... done ========== Installing Dependencies ========== debconf: delaying package configuration, since apt-utils is not installed (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 .../git-man_1%3a2.43.0-1ubuntu7.3_all.deb ... Unpacking git-man (1:2.43.0-1ubuntu7.3) over (1:2.43.0-1ubuntu7.2) ... Preparing to unpack .../git_1%3a2.43.0-1ubuntu7.3_amd64.deb ... Unpacking git (1:2.43.0-1ubuntu7.3) over (1:2.43.0-1ubuntu7.2) ... Setting up git-man (1:2.43.0-1ubuntu7.3) ... Setting up git (1:2.43.0-1ubuntu7.3) ... ========== Building Gromacs v2025.2 ========== Cloning Gromacs repository ... Note: switching to '0eaa03516a73b79845322166192a412ba3ebfa35'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false done Configuring Gromacs ... done Compiling Gromacs... done. :-) GROMACS - gmx, 2025.2-dev-20250512-0eaa035-local (-: Executable: /opt/gromacs/build/./bin/gmx Data prefix: /opt/gromacs (source tree) Working dir: /opt/gromacs/build Command line: gmx --version GROMACS version: 2025.2-dev-20250512-0eaa035-local GIT SHA1 hash: 0eaa03516a73b79845322166192a412ba3ebfa35 Branched from: unknown Precision: mixed Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128) GPU support: disabled SIMD instructions: AVX2_256 CPU FFT library: fftw-3.3.10-sse2-avx-avx2-avx2_128 GPU FFT library: none Multi-GPU FFT: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /usr/bin/gcc GNU 13.3.0 C compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wpedantic -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -DNDEBUG C++ compiler: /usr/bin/g++ GNU 13.3.0 C++ compiler flags: -Wno-array-bounds -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wpedantic -Wundef -Wstringop-truncation -Wno-missing-field-initializers -D_GLIBCXX_USE_CXX11_ABI=1 -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG BLAS library: External - detected on the system LAPACK library: External - detected on the system ========== Running Gromacs QM/MM unit test ========== [==========] Running 21 tests from 5 test suites. [----------] Global test environment set-up. [----------] 3 tests from QMMMInputGeneratorTest [ RUN ] QMMMInputGeneratorTest.CanConstruct [ OK ] QMMMInputGeneratorTest.CanConstruct (0 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBENoLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBENoLink (0 ms) [ RUN ] QMMMInputGeneratorTest.TwoWatersPBEWithLink [ OK ] QMMMInputGeneratorTest.TwoWatersPBEWithLink (0 ms) [----------] 3 tests from QMMMInputGeneratorTest (0 ms total) [----------] 7 tests from QMMMTopologyPreprocessorTest [ RUN ] QMMMTopologyPreprocessorTest.CanConstruct [ OK ] QMMMTopologyPreprocessorTest.CanConstruct (0 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMNoLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to -285343789 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMNoLink (2 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersSeondAndForthQMNoLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to -41959521 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersSeondAndForthQMNoLink (2 ms) [ RUN ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 21.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_FourWatersFirstQMWithLink_4water.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to 1140834280 Generated 10 of the 10 non-bonded parameter combinations Generated 10 of the 10 1-4 parameter combinations Excluding 2 bonded neighbours molecule type 'SOL' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/4water.gro', all velocities are zero Analysing residue names: There are: 4 Water residues This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.FourWatersFirstQMWithLink (2 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 Number of degrees of freedom in T-Coupling group rest is 63.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 129.093 K for determining the Verlet buffer size NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksNoConstraints_alanine_vacuo.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to -1612222603 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/alanine_vacuo.gro' Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 129.093 K Calculated rlist for 1x1 atom pair-list as 1.021 nm, buffer size 0.021 nm Set rlist, assuming 4x4 atom pair-list, to 1.013 nm, buffer size 0.013 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksNoConstraints (6 ms) [ RUN ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Generating 1-4 interactions: fudge = 0.5 NOTE 2 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. NOTE 3 [file unknown]: For energy conservation with LINCS, lincs_iter should be 2 or larger. Number of degrees of freedom in T-Coupling group rest is 42.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 4 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: NVE simulation: will use the initial temperature of 193.640 K for determining the Verlet buffer size NOTE 5 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 5 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_AlanineDipeptideWithLinksWithConstraints_alanine_vacuo.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to 2002486526 Generated 2145 of the 2145 non-bonded parameter combinations Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'ALANINEDIPEPTIDE' turning all bonds into constraints... Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/alanine_vacuo.gro' Analysing residue names: There are: 3 Protein residues Analysing Protein... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 193.64 K Calculated rlist for 1x1 atom pair-list as 1.023 nm, buffer size 0.023 nm Set rlist, assuming 4x4 atom pair-list, to 1.015 nm, buffer size 0.015 nm Note that mdrun will redetermine rlist based on the actual pair-list setup This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.AlanineDipeptideWithLinksWithConstraints (6 ms) [ RUN ] QMMMTopologyPreprocessorTest.RemovingQMVsites NOTE 1 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates. Number of degrees of freedom in T-Coupling group rest is 45.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 2 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: NVE simulation with an initial temperature of zero: will use a Verlet buffer of 10%. Check your energy drift! NOTE 3 [file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 NOTEs Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Reading file /opt/gromacs/build/src/gromacs/applied_forces/qmmm/tests/Testing/Temporary/QMMMTopologyPreprocessorTest_RemovingQMVsites_vsite_test.tpr, VERSION 2025.2-dev-20250512-0eaa035-local (single precision) Setting the LD random seed to 1038972120 Generated 3 of the 6 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'VSTEST' Taking velocities from '/opt/gromacs/src/testutils/simulationdatabase/vsite_test.gro', all velocities are zero Cleaning up constraints and constant bonded interactions with virtual sites Analysing residue names: There are: 1 Other residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 0 Mb of data [ OK ] QMMMTopologyPreprocessorTest.RemovingQMVsites (2 ms) [----------] 7 tests from QMMMTopologyPreprocessorTest (21 ms total) [----------] 9 tests from QMMMOptionsTest [ RUN ] QMMMOptionsTest.DefaultParameters [ OK ] QMMMOptionsTest.DefaultParameters (0 ms) [ RUN ] QMMMOptionsTest.OptionSetsActive [ OK ] QMMMOptionsTest.OptionSetsActive (0 ms) [ RUN ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive [ OK ] QMMMOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms) [ RUN ] QMMMOptionsTest.OutputDefaultValuesWhenActive [ OK ] QMMMOptionsTest.OutputDefaultValuesWhenActive (0 ms) [ RUN ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.CanConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.NoQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup [ OK ] QMMMOptionsTest.EmptyQMGroupConvertGroupStringToIndexGroup (0 ms) [ RUN ] QMMMOptionsTest.InternalsToKvtAndBack [ OK ] QMMMOptionsTest.InternalsToKvtAndBack (0 ms) [ RUN ] QMMMOptionsTest.CP2KInputProcessing [ OK ] QMMMOptionsTest.CP2KInputProcessing (0 ms) [----------] 9 tests from QMMMOptionsTest (0 ms total) [----------] 1 test from QMMMForceProviderTest [ RUN ] QMMMForceProviderTest.CanConstructOrNot [ OK ] QMMMForceProviderTest.CanConstructOrNot (0 ms) [----------] 1 test from QMMMForceProviderTest (0 ms total) [----------] 1 test from QMMMTest [ RUN ] QMMMTest.ForceProviderLackingInputThrows [ OK ] QMMMTest.ForceProviderLackingInputThrows (0 ms) [----------] 1 test from QMMMTest (0 ms total) [----------] Global test environment tear-down [==========] 21 tests from 5 test suites ran. (22 ms total) [ PASSED ] 21 tests. Summary: Gromacs commit 0eaa035 works fine. Status: OK Removing intermediate container c4d791040eaa ---> 4a7bed67e4b8 Step 40/41 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 8b0311368e61 Removing intermediate container 8b0311368e61 ---> 5b678ecad505 Step 41/41 : ENTRYPOINT [] ---> Running in ad2e95db042c Removing intermediate container ad2e95db042c ---> b444461904d5 [Warning] One or more build-args [GIT_COMMIT_SHA SPACK_CACHE] were not consumed Successfully built b444461904d5 Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-gromacs:master Pushing new image... done. #################### Running Image cp2k-gromacs #################### EndDate: 2025-07-14 06:38:47+00:00