StartDate: 2025-11-14 06:04:11+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: c01e6a4e89d3b4b67a117c4170084206f8bd57c5 CommitTime: 2025-11-13 09:36:18 +0100 CommitAuthor: Hans Pabst CommitSubject: Fixed PACKAGE manifest #################### Building Image cp2k-phonopy #################### Dockerfile: /tools/docker/Dockerfile.test_phonopy Build-Path: / Build-Args: GIT_COMMIT_SHA=c01e6a4e89d3b4b67a117c4170084206f8bd57c5 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 407.9MB Step 1/43 : FROM ubuntu:24.04 24.04: Pulling from library/ubuntu 20043066d3d5: Pulling fs layer 20043066d3d5: Verifying Checksum 20043066d3d5: Download complete 20043066d3d5: Pull complete Digest: sha256:e96e81f410a9f9cae717e6cdd88cc2a499700ff0bb5061876ad24377fcc517d7 Status: Downloaded newer image for ubuntu:24.04 ---> c3a134f2ace4 Step 2/43 : WORKDIR /opt/cp2k-toolchain ---> Running in 0f4476f0fe85 ---> Removed intermediate container 0f4476f0fe85 ---> 7a92140bc53a Step 3/43 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> 59d184982977 Step 4/43 : RUN ./install_requirements.sh ubuntu:24.04 ---> Running in fb1cc0dcd2bb Installing Ubuntu packages... debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 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Preparing to unpack .../python3.12-minimal_3.12.3-1ubuntu0.8_amd64.deb ... Unpacking python3.12-minimal (3.12.3-1ubuntu0.8) ... Setting up libpython3.12-minimal:amd64 (3.12.3-1ubuntu0.8) ... Setting up libexpat1:amd64 (2.6.1-2ubuntu0.3) ... Setting up python3.12-minimal (3.12.3-1ubuntu0.8) ... Selecting previously unselected package python3-minimal. (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 ... 4700 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu2.1_amd64.deb ... Unpacking python3-minimal (3.12.3-0ubuntu2.1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-0ubuntu0.24.04.1_all.deb ... Unpacking tzdata (2025b-0ubuntu0.24.04.1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4build1_all.deb ... Unpacking readline-common (8.2-4build1) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4build1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4build1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.45.1-1ubuntu2.5_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.1-1ubuntu2.5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../7-libpython3.12-stdlib_3.12.3-1ubuntu0.8_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.3-1ubuntu0.8) ... Selecting previously unselected package python3.12. Preparing to unpack .../8-python3.12_3.12.3-1ubuntu0.8_amd64.deb ... Unpacking python3.12 (3.12.3-1ubuntu0.8) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.12.3-0ubuntu2.1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.3-0ubuntu2.1) ... Setting up python3-minimal (3.12.3-0ubuntu2.1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up libkrb5support0:amd64 (1.20.1-6ubuntu2.6) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu3.1) ... Setting up tzdata (2025b-0ubuntu0.24.04.1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Nov 14 06:06:53 UTC 2025. Universal Time is now: Fri Nov 14 06:06:53 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-2build1) ... Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... Setting up gcc-13-base:amd64 (13.3.0-6ubuntu2~24.04) ... Setting up make (4.3-4.1build2) ... Setting up libmpfr6:amd64 (4.2.1-1build1.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build7) ... Setting up perl-modules-5.38 (5.38.2-3.2ubuntu0.2) ... Setting up libquadmath0:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libmpc3:amd64 (1.3.1-1build1.1) ... Setting up libatomic1:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up patch (2.7.6-7build3) ... Setting up pkgconf-bin (1.8.1-2build1) ... Setting up libk5crypto3:amd64 (1.20.1-6ubuntu2.6) ... Setting up libgc1:amd64 (1:8.2.6-1build1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3.1) ... Setting up libgfortran5:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libubsan1:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libicu74:amd64 (74.2-1ubuntu3.1) ... Setting up nano (7.2-2ubuntu0.1) ... update-alternatives: using /bin/nano to provide /usr/bin/editor (editor) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/editor.1.gz because associated file /usr/share/man/man1/nano.1.gz (of link group editor) doesn't exist update-alternatives: using /bin/nano to provide /usr/bin/pico (pico) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/pico.1.gz because associated file /usr/share/man/man1/nano.1.gz (of link group pico) doesn't exist Setting up libhwasan0:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4build1) ... Setting up libasan8:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up git-man (1:2.43.0-1ubuntu7.3) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-6ubuntu2.6) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2ubuntu0.2) ... Setting up libtsan2:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.42-4ubuntu2.6) ... Setting up libisl23:amd64 (0.26-3build1.1) ... Setting up libc-dev-bin (2.39-0ubuntu8.6) ... Setting up openssl (3.0.13-0ubuntu3.6) ... Setting up readline-common (8.2-4build1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3.6) ... Setting up libcc1-0:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8.2) ... Setting up liblsan0:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libitm1:amd64 (14.2.0-4ubuntu2~24.04) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libctf0:amd64 (2.42-4ubuntu2.6) ... Setting up wget (1.21.4-1ubuntu4.1) ... Setting up libopts25-dev:amd64 (1:5.18.16-5build1) ... Setting up cpp-13-x86-64-linux-gnu (13.3.0-6ubuntu2~24.04) ... Setting up pkgconf:amd64 (1.8.1-2build1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up perl (5.38.2-3.2ubuntu0.2) ... Setting up libgprofng0:amd64 (2.42-4ubuntu2.6) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2.6) ... Setting up pkg-config:amd64 (1.8.1-2build1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libssh-4:amd64 (0.10.6-2ubuntu0.2) ... Setting up autoconf (2.71-3) ... Setting up libreadline8t64:amd64 (8.2-4build1) ... Setting up libgcc-13-dev:amd64 (13.3.0-6ubuntu2~24.04) ... Setting up libc6-dev:amd64 (2.39-0ubuntu8.6) ... Setting up libgfortran-13-dev:amd64 (13.3.0-6ubuntu2~24.04) ... Setting up libstdc++-13-dev:amd64 (13.3.0-6ubuntu2~24.04) ... Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2.6) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/automake.1.gz because associated file /usr/share/man/man1/automake-1.16.1.gz (of link group automake) doesn't exist update-alternatives: warning: skip creation of /usr/share/man/man1/aclocal.1.gz because associated file /usr/share/man/man1/aclocal-1.16.1.gz (of link group automake) doesn't exist Setting up libpython3.12-stdlib:amd64 (3.12.3-1ubuntu0.8) ... Setting up cpp-13 (13.3.0-6ubuntu2~24.04) ... Setting up guile-3.0-libs:amd64 (3.0.9-1build2) ... Setting up gcc-13-x86-64-linux-gnu (13.3.0-6ubuntu2~24.04) ... Setting up python3.12 (3.12.3-1ubuntu0.8) ... Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu10.6) ... Setting up binutils (2.42-4ubuntu2.6) ... Setting up gfortran-13-x86-64-linux-gnu (13.3.0-6ubuntu2~24.04) ... Setting up autogen (1:5.18.16-5build1) ... Setting up liberror-perl (0.17029-2) ... Setting up libpython3.12t64:amd64 (3.12.3-1ubuntu0.8) ... Setting up libexpat1-dev:amd64 (2.6.1-2ubuntu0.3) ... Setting up gcc-13 (13.3.0-6ubuntu2~24.04) ... Setting up git (1:2.43.0-1ubuntu7.3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu2.1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libpython3-stdlib:amd64 (3.12.3-0ubuntu2.1) ... Setting up g++-13-x86-64-linux-gnu (13.3.0-6ubuntu2~24.04) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtool (2.4.7-7build1) ... Setting up python3 (3.12.3-0ubuntu2.1) ... Setting up libpython3.12-dev:amd64 (3.12.3-1ubuntu0.8) ... Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up python3-wheel (0.42.0-2) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up gfortran-13 (13.3.0-6ubuntu2~24.04) ... Setting up python3.12-dev (3.12.3-1ubuntu0.8) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1.2) ... Setting up g++-13 (13.3.0-6ubuntu2~24.04) ... Setting up libtool-bin (2.4.7-7build1) ... Setting up libpython3-dev:amd64 (3.12.3-0ubuntu2.1) ... Setting up python3-setuptools (68.1.2-2ubuntu1.2) ... Setting up gfortran (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f95.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f95) doesn't exist update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/f77.1.gz because associated file /usr/share/man/man1/gfortran.1.gz (of link group f77) doesn't exist Setting up python3-dev (3.12.3-0ubuntu2.1) ... Setting up python3-pip (24.0+dfsg-1ubuntu1.3) ... Setting up g++ (4:13.2.0-7ubuntu1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist Processing triggers for libc-bin (2.39-0ubuntu8.6) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. ---> Removed intermediate container fb1cc0dcd2bb ---> cdc0fc768ac6 Step 5/43 : RUN mkdir scripts ---> Running in 811f0627b51b ---> Removed intermediate container 811f0627b51b ---> cf8ae4f622ae 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/ ---> a25f59789239 Step 7/43 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> 8014cff622c0 Step 8/43 : RUN ./install_cp2k_toolchain.sh --install-all --mpi-mode=no --with-dbcsr --with-gcc=system --dry-run ---> Running in aca651563bd6 WARNING: (./install_cp2k_toolchain.sh, line 371) No MPI installation detected (ignore this message in Cray Linux Environment or when MPI installation was requested). 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. Wrote only configuration files (--dry-run). ---> Removed intermediate container aca651563bd6 ---> f43376069539 Step 9/43 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> 33279cbc7c8e Step 10/43 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Running in a144de471964 ==================== 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-0.3.30.tar.gz -O OpenBLAS-0.3.30.tar.gz OpenBLAS-0.3.30.tar.gz: OK Checksum of OpenBLAS-0.3.30.tar.gz Ok 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-v1.13.1.tar.gz -O ninja-v1.13.1.tar.gz ninja-v1.13.1.tar.gz: OK Checksum of ninja-v1.13.1.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/ninja-v1.13.1 Step ninja took 9.00 seconds. ---> Removed intermediate container a144de471964 ---> 20c68a5253e7 Step 11/43 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> 3aaad593f752 Step 12/43 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Running in b9053a219639 ---> Removed intermediate container b9053a219639 ---> dee48629324e Step 13/43 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> 6434f5d89682 Step 14/43 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Running in 4e2e968a02cb ==================== Installing OpenBLAS ==================== wget --quiet https://www.cp2k.org/static/downloads/OpenBLAS-0.3.30.tar.gz -O OpenBLAS-0.3.30.tar.gz OpenBLAS-0.3.30.tar.gz: OK Checksum of OpenBLAS-0.3.30.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/openblas-0.3.30 Installing OpenBLAS library for target ZEN Step openblas took 152.00 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 27.00 seconds. ---> Removed intermediate container 4e2e968a02cb ---> 92ef9820525b Step 15/43 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> 6a58a77bda4e Step 16/43 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Running in 8c7182563602 ==================== 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 61.00 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 770.00 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 1304.00 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 6.00 seconds. ==================== Using libgrpp ==================== Step libgrpp took 0.00 seconds. ---> Removed intermediate container 8c7182563602 ---> 70410f53c3f6 Step 17/43 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> 52d61e816cd3 Step 18/43 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Running in ee26ad55c264 ==================== 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 13.00 seconds. Step scalapack took 0.00 seconds. Step cosma took 0.00 seconds. ---> Removed intermediate container ee26ad55c264 ---> 8a26abddfc2f Step 19/43 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> 4605e6107782 Step 20/43 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Running in f3976c5c360d WARNING: (./scripts/stage5/install_elpa.sh, line 31) MPI is disabled, skipping ELPA installation  ---> Removed intermediate container f3976c5c360d ---> 49fa505d6a0c Step 21/43 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> acaf77bc1a68 Step 22/43 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Running in e47048600cc5 ==================== 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 49.00 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 13.00 seconds. ==================== Installing DeePMD ==================== wget --quiet https://www.cp2k.org/static/downloads/deepmd-kit-3.1.0.tar.gz -O deepmd-kit-3.1.0.tar.gz deepmd-kit-3.1.0.tar.gz: OK Checksum of deepmd-kit-3.1.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/deepmd-kit-3.1.0 Step deepmd took 138.00 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 21.00 seconds. ---> Removed intermediate container e47048600cc5 ---> bafaf7b31f5d Step 23/43 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> 76838c80e7d2 Step 24/43 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Running in 2df3fe5cba36 ==================== Installing hdf5 ==================== wget --quiet https://www.cp2k.org/static/downloads/hdf5-1.14.6.tar.gz -O hdf5-1.14.6.tar.gz hdf5-1.14.6.tar.gz: OK Checksum of hdf5-1.14.6.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/hdf5-1.14.6 Step hdf5 took 87.00 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 11.00 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 17.00 seconds. WARNING: (./scripts/stage7/install_libsmeagol.sh, line 27) MPI is disabled, skipping libsmeagol installation  ---> Removed intermediate container 2df3fe5cba36 ---> 338640eaf938 Step 25/43 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> 95b1bd681c32 Step 26/43 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Running in 91ae3f9ebba4 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 24.00 seconds. ==================== Installing tblite ==================== wget --quiet https://www.cp2k.org/static/downloads/tblite-0.5.0.tar.gz -O tblite-0.5.0.tar.gz tblite-0.5.0.tar.gz: OK Checksum of tblite-0.5.0.tar.gz Ok Installing from scratch into /opt/cp2k-toolchain/install/tblite-0.5.0 Step tblite took 34.00 seconds. ---> Removed intermediate container 91ae3f9ebba4 ---> beae2e98e02c Step 27/43 : COPY ./tools/toolchain/scripts/stage9/ ./scripts/stage9/ ---> 38dd22e2776d Step 28/43 : RUN ./scripts/stage9/install_stage9.sh && rm -rf ./build ---> Running in 27f694a894bd ==================== 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 36.00 seconds. ---> Removed intermediate container 27f694a894bd ---> 74d269805204 Step 29/43 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> 09e1cd6f08ce Step 30/43 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Running in 4d820fc8f88c ==================== 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. ---> Removed intermediate container 4d820fc8f88c ---> 89e7c81817ff Step 31/43 : WORKDIR /opt/cp2k ---> Running in a96b65fe1962 ---> Removed intermediate container a96b65fe1962 ---> bce3df0de7f6 Step 32/43 : COPY ./src ./src ---> 42667fa94887 Step 33/43 : COPY ./data ./data ---> 680d29328fd8 Step 34/43 : COPY ./tests ./tests ---> b9e7517c42d4 Step 35/43 : COPY ./tools/build_utils ./tools/build_utils ---> bdd22269994e Step 36/43 : COPY ./cmake ./cmake ---> 9bec1b8ac9fa Step 37/43 : COPY ./CMakeLists.txt . ---> e1ba21cef1e6 Step 38/43 : COPY ./tools/docker/scripts/build_cp2k_cmake.sh . ---> c55b975c87ca Step 39/43 : RUN ./build_cp2k_cmake.sh toolchain ssmp ---> Running in 2a5237c9f887 ==================== 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 (4.9s) -- Generating done (0.3s) -- Build files have been written to: /opt/cp2k/build Compiling CP2K ... done ---> Removed intermediate container 2a5237c9f887 ---> c739079d3e44 Step 40/43 : COPY ./tools/docker/scripts/test_phonopy.sh ./ ---> 7bb449a60d90 Step 41/43 : RUN ./test_phonopy.sh 2>&1 | tee report.log ---> Running in 3d01d76bb249 ========== 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-1ubuntu1.3_all.deb ... Unpacking python3-pip-whl (24.0+dfsg-1ubuntu1.3) ... 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_3.12.3-1ubuntu0.8_amd64.deb ... Unpacking python3.12-venv (3.12.3-1ubuntu0.8) ... Selecting previously unselected package python3-venv. Preparing to unpack .../python3-venv_3.12.3-0ubuntu2.1_amd64.deb ... Unpacking python3-venv (3.12.3-0ubuntu2.1) ... Setting up python3-setuptools-whl (68.1.2-2ubuntu1.2) ... Setting up python3-pip-whl (24.0+dfsg-1ubuntu1.3) ... Setting up python3.12-venv (3.12.3-1ubuntu0.8) ... Setting up python3-venv (3.12.3-0ubuntu2.1) ... ========== 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+gccfd5a4ec) Using cached numpy-2.3.4-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+gccfd5a4ec) Downloading pyyaml-6.0.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Collecting matplotlib>=2.2.2 (from phonopy==0.1.dev1+gccfd5a4ec) Downloading matplotlib-3.10.7-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (11 kB) Collecting h5py>=3.0 (from phonopy==0.1.dev1+gccfd5a4ec) Downloading h5py-3.15.1-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (3.0 kB) Collecting spglib>=2.3 (from phonopy==0.1.dev1+gccfd5a4ec) 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+gccfd5a4ec) Downloading symfc-1.5.4-py3-none-any.whl.metadata (3.8 kB) Collecting cp2k-input-tools (from phonopy==0.1.dev1+gccfd5a4ec) 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+gccfd5a4ec) 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+gccfd5a4ec) 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+gccfd5a4ec) Downloading fonttools-4.60.1-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (112 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 112.3/112.3 kB 5.4 MB/s eta 0:00:00 Collecting kiwisolver>=1.3.1 (from matplotlib>=2.2.2->phonopy==0.1.dev1+gccfd5a4ec) 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+gccfd5a4ec) 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+gccfd5a4ec) Downloading pillow-12.0.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB) Collecting pyparsing>=3 (from matplotlib>=2.2.2->phonopy==0.1.dev1+gccfd5a4ec) Downloading pyparsing-3.2.5-py3-none-any.whl.metadata (5.0 kB) Collecting python-dateutil>=2.7 (from 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typing_inspection-0.4.2-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+gccfd5a4ec-cp312-cp312-linux_x86_64.whl size=522954 sha256=5bbdffddfafbb6081f7d1249f2f719320354adbd587201126c119521b3c9bf07 Stored in directory: /tmp/pip-ephem-wheel-cache-u4sb77dn/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-3.0.3 Pint-0.23 PyYAML-6.0.3 annotated-types-0.7.0 click-8.3.0 contourpy-1.3.3 cp2k-input-tools-0.9.1 cycler-0.12.1 fonttools-4.60.1 h5py-3.15.1 kiwisolver-1.4.9 matplotlib-3.10.7 numpy-2.3.4 packaging-25.0 phonopy-0.1.dev1+gccfd5a4ec pillow-12.0.0 pydantic-2.12.4 pydantic-core-2.41.5 pyparsing-3.2.5 python-dateutil-2.9.0.post0 scipy-1.16.3 six-1.17.0 spglib-2.6.0 symfc-1.5.4 transitions-0.9.3 typing-extensions-4.15.0 typing-inspection-0.4.2 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-4.5.0-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) (4.15.0) 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 8.7 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-4.5.0-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-4.5.0 ========== Running Phonopy Test ========== _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.43.6 -------------------------[time 2025-11-14 07:03:55]------------------------- 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 2025-11-14 07:03:58]------------------------- _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.43.6 -------------------------[time 2025-11-14 07:04:39]------------------------- 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 2025-11-14 07:04:39]------------------------- _ ___ _ __ __| | / _ \ '_ \ / _` | | __/ | | | (_| | \___|_| |_|\__,_| Summary: Phonopy commit ccfd5a4 works fine. Status: OK ---> Removed intermediate container 3d01d76bb249 ---> c1c928589c1c Step 42/43 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 33b3101f63c6 ---> Removed intermediate container 33b3101f63c6 ---> 5131dbd86d55 Step 43/43 : ENTRYPOINT [] ---> Running in df827a6019bf ---> Removed intermediate container df827a6019bf ---> b1203a000e76 [Warning] One or more build-args [GIT_COMMIT_SHA SPACK_CACHE] were not consumed Successfully built b1203a000e76 Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-phonopy:master Pushing new image... done. #################### Running Image cp2k-phonopy #################### EndDate: 2025-11-14 07:06:19+00:00