StartDate: 2022-05-22 13:50:19+00:00 CpuId: 8x AMD (unknown model) [Zen 3], 7nm CommitSHA: fedce27c3a36d9031d1dc52189396fabd5aa852b CommitTime: 2022-05-22 15:19:55 +0200 CommitAuthor: Ole Schütt CommitSubject: Add OpenMP to most of the tensor code Populating docker build cache... done. #################### Building Image cp2k-aiida #################### Dockerfile: /tools/docker/Dockerfile.test_aiida Build-Path: / Build-Args: GIT_COMMIT_SHA=fedce27c3a36d9031d1dc52189396fabd5aa852b Sending build context to Docker daemon 362.9MB Step 1/40 : FROM ubuntu:22.04 22.04: Pulling from library/ubuntu 125a6e411906: Already exists Digest: sha256:26c68657ccce2cb0a31b330cb0be2b5e108d467f641c62e13ab40cbec258c68d Status: Downloaded newer image for ubuntu:22.04 ---> d2e4e1f51132 Step 2/40 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> cd3e16853753 Step 3/40 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> 728f5bc7e816 Step 4/40 : RUN ./install_requirements.sh ubuntu:22.04 ---> Using cache ---> 43059c07ec04 Step 5/40 : RUN mkdir scripts ---> Using cache ---> 3d6e5dfe781e Step 6/40 : 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 ---> af8e8981a376 Step 7/40 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> ac48daa526d8 Step 8/40 : RUN ./install_cp2k_toolchain.sh --install-all --mpi-mode=mpich --with-gcc=system --dry-run ---> Using cache ---> 1438da342036 Step 9/40 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> Using cache ---> 29e17904f213 Step 10/40 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Using cache ---> 6d5910ba6de7 Step 11/40 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> Using cache ---> 600023e58c01 Step 12/40 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Using cache ---> 72516b544d5d Step 13/40 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> Using cache ---> ed8c13fc4ecc Step 14/40 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Using cache ---> ff0093495615 Step 15/40 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> Using cache ---> d237ee76aff1 Step 16/40 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Using cache ---> 777088228f39 Step 17/40 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> Using cache ---> 72a2ced0d6d8 Step 18/40 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Using cache ---> 33810a84eaaf Step 19/40 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> Using cache ---> 7802bc93c8b2 Step 20/40 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Using cache ---> fd3e821fbc83 Step 21/40 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> Using cache ---> 84be5a9ecf56 Step 22/40 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Using cache ---> 9f54ef16c51d Step 23/40 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> Using cache ---> f407d68b86c1 Step 24/40 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Using cache ---> 336cfcb36d24 Step 25/40 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> Using cache ---> 60ec79a328e1 Step 26/40 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Using cache ---> fe11e6ee9548 Step 27/40 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> Using cache ---> 4f135dc1b945 Step 28/40 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Using cache ---> 84638f9710b7 Step 29/40 : WORKDIR /opt/cp2k ---> Using cache ---> d1203857c5ed Step 30/40 : COPY ./Makefile . ---> Using cache ---> d4c31891804b Step 31/40 : COPY ./src ./src ---> Using cache ---> 67b427885c99 Step 32/40 : COPY ./exts ./exts ---> Using cache ---> d9daf822faa3 Step 33/40 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> fb7d701e0df0 Step 34/40 : RUN /bin/bash -c " mkdir -p arch && ln -vs /opt/cp2k-toolchain/install/arch/local.sdbg ./arch/ && echo 'Compiling cp2k...' && source /opt/cp2k-toolchain/install/setup && ( make -j ARCH=local VERSION=sdbg &> /dev/null || true )" ---> Using cache ---> 73db488940ef Step 35/40 : COPY ./data ./data ---> Using cache ---> b794ac20951a Step 36/40 : COPY ./tests ./tests ---> Using cache ---> e226741526dc Step 37/40 : COPY ./tools/regtesting ./tools/regtesting ---> Using cache ---> c661dee6506d Step 38/40 : COPY ./tools/docker/scripts/test_aiida.sh . ---> 102dcfd4245d Step 39/40 : RUN ./test_aiida.sh 2>&1 | tee report.log ---> Running in 044b64506569 ========== Compiling CP2K ========== Compiling cp2k... done. ========== Installing Dependencies ========== debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package cron. 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Searching for services which depend on erlang and should be started... none found. Setting up libcbor0.8:amd64 (0.8.0-2ubuntu1) ... Setting up erlang-xmerl (1:24.2.1+dfsg-1) ... Setting up cron (3.0pl1-137ubuntu3) ... Adding group `crontab' (GID 102) ... Done. invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libpq5:amd64 (14.2-1ubuntu1) ... Setting up erlang-syntax-tools (1:24.2.1+dfsg-1) ... Setting up locales (2.35-0ubuntu3) ... Generating locales (this might take a while)... Generation complete. Setting up tzdata (2022a-0ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun May 22 13:52:59 UTC 2022. Universal Time is now: Sun May 22 13:52:59 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up erlang-parsetools (1:24.2.1+dfsg-1) ... Setting up libexpat1-dev:amd64 (2.4.7-1) ... Setting up libwrap0:amd64 (7.6.q-31build2) ... Setting up ssl-cert (1.1.2) ... Setting up socat (1.7.4.1-3ubuntu4) ... Setting up libssl-dev:amd64 (3.0.2-0ubuntu1.2) ... Setting up sudo (1.9.9-1ubuntu2) ... Setting up libpython3.10-dev:amd64 (3.10.4-3) ... Setting up ucf (3.0043) ... Setting up erlang-asn1 (1:24.2.1+dfsg-1) ... Setting up erlang-tftp (1:24.2.1+dfsg-1) ... Setting up python3.10-dev (3.10.4-3) ... Setting up libmd0:amd64 (1.0.4-1build1) ... Setting up libjson-perl (4.04000-1) ... Setting up libxslt1.1:amd64 (1.1.34-4build2) ... Setting up erlang-mnesia (1:24.2.1+dfsg-1) ... Setting up netbase (6.3) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up erlang-crypto (1:24.2.1+dfsg-1) ... Setting up libfido2-1:amd64 (1.10.0-1) ... Setting up libbsd0:amd64 (0.11.5-1) ... Setting up python3-lib2to3 (3.10.4-0ubuntu1) ... Setting up libjs-underscore (1.13.2~dfsg-2) ... Setting up libpopt0:amd64 (1.18-3build1) ... Setting up python3-distutils (3.10.4-0ubuntu1) ... Setting up logrotate (3.19.0-1ubuntu1) ... Setting up postgresql-client-common (238) ... Setting up libpython3-dev:amd64 (3.10.4-0ubuntu2) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up erlang-runtime-tools (1:24.2.1+dfsg-1) ... Setting up libedit2:amd64 (3.1-20210910-1build1) ... Setting up erlang-tools (1:24.2.1+dfsg-1) ... Setting up libpq-dev (14.2-1ubuntu1) ... Setting up postgresql-client-14 (14.2-1ubuntu1) ... update-alternatives: using /usr/share/postgresql/14/man/man1/psql.1.gz to provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode Setting up python3-wheel (0.37.1-2) ... Setting up erlang-snmp (1:24.2.1+dfsg-1) ... Setting up erlang-public-key (1:24.2.1+dfsg-1) ... Setting up postgresql-common (238) ... Adding user postgres to group ssl-cert Creating config file /etc/postgresql-common/createcluster.conf with new version Building PostgreSQL dictionaries from installed myspell/hunspell packages... Removing obsolete dictionary files: Setting up python3-pip (22.0.2+dfsg-1) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up libllvm14:amd64 (1:14.0.0-1ubuntu1) ... Setting up erlang-ssl (1:24.2.1+dfsg-1) ... Setting up postgresql-14 (14.2-1ubuntu1) ... Creating new PostgreSQL cluster 14/main ... /usr/lib/postgresql/14/bin/initdb -D /var/lib/postgresql/14/main --auth-local peer --auth-host scram-sha-256 --no-instructions The files belonging to this database system will be owned by user "postgres". This user must also own the server process. The database cluster will be initialized with locale "C.UTF-8". The default database encoding has accordingly been set to "UTF8". The default text search configuration will be set to "english". Data page checksums are disabled. fixing permissions on existing directory /var/lib/postgresql/14/main ... ok creating subdirectories ... ok selecting dynamic shared memory implementation ... posix selecting default max_connections ... 100 selecting default shared_buffers ... 128MB selecting default time zone ... Etc/UTC creating configuration files ... ok running bootstrap script ... ok performing post-bootstrap initialization ... ok syncing data to disk ... ok update-alternatives: using /usr/share/postgresql/14/man/man1/postmaster.1.gz to provide /usr/share/man/man1/postmaster.1.gz (postmaster.1.gz) in auto mode invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up openssh-client (1:8.9p1-3) ... update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/rsh.1.gz because associated file /usr/share/man/man1/ssh.1.gz (of link group rsh) doesn't exist update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/rlogin.1.gz because associated file /usr/share/man/man1/slogin.1.gz (of link group rlogin) doesn't exist update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/rcp.1.gz because associated file /usr/share/man/man1/scp.1.gz (of link group rcp) doesn't exist Setting up erlang-os-mon (1:24.2.1+dfsg-1) ... Setting up erlang-eldap (1:24.2.1+dfsg-1) ... Setting up python3-dev (3.10.4-0ubuntu2) ... Setting up erlang-ftp (1:24.2.1+dfsg-1) ... Setting up postgresql (14+238) ... Setting up openssh-sftp-server (1:8.9p1-3) ... Setting up openssh-server (1:8.9p1-3) ... Creating config file /etc/ssh/sshd_config with new version Creating SSH2 RSA key; this may take some time ... 3072 SHA256:hczOKASF8Fz2Jpfj1I8xd6zcglxk8XUqdWiQePx0crE root@044b64506569 (RSA) Creating SSH2 ECDSA key; this may take some time ... 256 SHA256:csOSfLuy0kHKhpNxns91XWQcHvu45P2hD78jjmhSuMY root@044b64506569 (ECDSA) Creating SSH2 ED25519 key; this may take some time ... 256 SHA256:9HeRGANoiPUmPJMrShsYaboDLPQXTar2vz1VvTSA+CU root@044b64506569 (ED25519) invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up erlang-inets (1:24.2.1+dfsg-1) ... Setting up rabbitmq-server (3.9.13-1) ... Adding group `rabbitmq' (GID 106) ... Done. Adding system user `rabbitmq' (UID 104) ... Adding new user `rabbitmq' (UID 104) with group `rabbitmq' ... Not creating home directory `/var/lib/rabbitmq'. invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up ssh (1:8.9p1-3) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... ./test_aiida.sh: line 39: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) /bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) Generating locales (this might take a while)... en_US.UTF-8... done Generation complete. Adding user `ubuntu' ... Adding new group `ubuntu' (1000) ... Adding new user `ubuntu' (1000) with group `ubuntu' ... Creating home directory `/home/ubuntu' ... Copying files from `/etc/skel' ... ========== Installing AiiDA-CP2K plugin ========== Processing /opt/aiida-cp2k 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting ruamel.yaml>=0.16.5 Downloading ruamel.yaml-0.17.21-py3-none-any.whl (109 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 109.5/109.5 KB 3.2 MB/s eta 0:00:00 Collecting aiida-core<2.0.0,>=1.1.0 Downloading aiida_core-1.6.8-py3-none-any.whl (1.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 8.7 MB/s eta 0:00:00 Collecting cp2k-output-tools Downloading cp2k_output_tools-0.5.0-py3-none-any.whl (22 kB) Collecting ase Downloading ase-3.22.1-py3-none-any.whl (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 15.4 MB/s eta 0:00:00 Collecting aiida-gaussian-datatypes Downloading aiida_gaussian_datatypes-0.5.0-py3-none-any.whl (24 kB) Collecting pgtest~=1.3 Downloading pgtest-1.3.2-py2.py3-none-any.whl (9.1 kB) Collecting pytest-cov~=2.11.1 Downloading pytest_cov-2.11.1-py2.py3-none-any.whl (20 kB) Collecting pytest~=6.0 Downloading pytest-6.2.5-py3-none-any.whl (280 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 280.7/280.7 KB 17.4 MB/s eta 0:00:00 Collecting coverage Downloading coverage-6.3.3-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (211 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 211.1/211.1 KB 18.8 MB/s eta 0:00:00 Collecting wrapt~=1.11.1 Downloading wrapt-1.11.2.tar.gz (27 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting aldjemy~=0.9.1 Downloading aldjemy-0.9.1-py3-none-any.whl (26 kB) Collecting sqlalchemy~=1.3.10 Downloading SQLAlchemy-1.3.24.tar.gz (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 31.5 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting tqdm~=4.45 Downloading tqdm-4.64.0-py2.py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.4/78.4 KB 16.5 MB/s eta 0:00:00 Collecting circus~=0.17.1 Downloading circus-0.17.1-py3-none-any.whl (182 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 182.7/182.7 KB 31.8 MB/s eta 0:00:00 Collecting click-spinner~=0.1.8 Downloading click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB) Collecting psycopg2-binary~=2.8.3 Downloading psycopg2-binary-2.8.6.tar.gz (384 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 384.7/384.7 KB 43.2 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting python-dateutil~=2.8 Downloading python_dateutil-2.8.2-py2.py3-none-any.whl (247 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 247.7/247.7 KB 34.8 MB/s eta 0:00:00 Collecting graphviz~=0.13 Downloading graphviz-0.20-py3-none-any.whl (46 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 KB 10.2 MB/s eta 0:00:00 Collecting pamqp~=2.3 Downloading pamqp-2.3.0-py2.py3-none-any.whl (28 kB) Collecting psutil~=5.6 Downloading psutil-5.9.1-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (282 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 282.0/282.0 KB 38.4 MB/s eta 0:00:00 Collecting jinja2~=2.10 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 125.7/125.7 KB 16.0 MB/s eta 0:00:00 Collecting jsonschema~=3.0 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.3/56.3 KB 11.8 MB/s eta 0:00:00 Collecting pytz~=2019.3 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 509.2/509.2 KB 43.7 MB/s eta 0:00:00 Collecting pgsu~=0.2.0 Downloading pgsu-0.2.2.tar.gz (8.5 kB) 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting numpy~=1.17 Downloading numpy-1.22.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.8/16.8 MB 56.6 MB/s eta 0:00:00 Collecting ipython~=7.20 Downloading ipython-7.33.0-py3-none-any.whl (793 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 793.8/793.8 KB 67.7 MB/s eta 0:00:00 Collecting tabulate~=0.8.5 Downloading tabulate-0.8.9-py3-none-any.whl (25 kB) Collecting click-config-file~=0.6.0 Downloading click_config_file-0.6.0-py2.py3-none-any.whl (6.0 kB) Collecting reentry~=1.3 Downloading reentry-1.3.3-py3-none-any.whl (17 kB) Collecting pyyaml~=5.4 Downloading PyYAML-5.4.1.tar.gz (175 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 175.1/175.1 KB 31.2 MB/s eta 0:00:00 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' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting simplejson~=3.16 Downloading simplejson-3.17.6-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (137 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 137.1/137.1 KB 26.2 MB/s eta 0:00:00 Collecting markupsafe<2.1 Downloading MarkupSafe-2.0.1-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (30 kB) Collecting paramiko>=2.7.2,~=2.7 Downloading paramiko-2.11.0-py2.py3-none-any.whl (212 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 212.9/212.9 KB 36.5 MB/s eta 0:00:00 Collecting upf-to-json~=0.9.2 Downloading upf_to_json-0.9.5-py3-none-any.whl (12 kB) Collecting alembic~=1.2 Downloading alembic-1.7.7-py3-none-any.whl (210 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 210.7/210.7 KB 36.5 MB/s eta 0:00:00 Collecting tzlocal~=2.0 Downloading tzlocal-2.1-py2.py3-none-any.whl (16 kB) Collecting plumpy~=0.20.0 Downloading plumpy-0.20.0-py3-none-any.whl (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 KB 13.6 MB/s eta 0:00:00 Collecting click-completion~=0.5.1 Downloading click-completion-0.5.2.tar.gz (10 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting aio-pika~=6.6 Downloading aio_pika-6.8.2-py3-none-any.whl (42 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.3/42.3 KB 9.0 MB/s eta 0:00:00 Collecting click~=7.1 Downloading click-7.1.2-py2.py3-none-any.whl (82 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 82.8/82.8 KB 18.7 MB/s eta 0:00:00 Collecting django~=2.2 Downloading Django-2.2.28-py3-none-any.whl (7.5 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.5/7.5 MB 96.2 MB/s eta 0:00:00 Collecting kiwipy[rmq]~=0.7.5 Downloading kiwipy-0.7.5-py3-none-any.whl (29 kB) Collecting ete3~=3.1 Downloading ete3-3.1.2.tar.gz (4.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 115.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sqlalchemy-utils~=0.36.0 Downloading SQLAlchemy-Utils-0.36.5.tar.gz (131 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 131.2/131.2 KB 26.9 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting archive-path~=0.2.1 Downloading archive_path-0.2.1-py3-none-any.whl (17 kB) Collecting pg8000>=1.10 Downloading pg8000-1.29.0-py3-none-any.whl (34 kB) Collecting packaging Downloading packaging-21.3-py3-none-any.whl (40 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 KB 9.2 MB/s eta 0:00:00 Collecting pluggy<2.0,>=0.12 Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB) Collecting 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size=27057 sha256=98c8ea6f10d1667f12ffc962a9c5b70325ebb21ea66b892b0d6f27c391e804a2 Stored in directory: /root/.cache/pip/wheels/f5/4d/c5/96aec96e5895bbad36e5a2f8f744774ccd9991aebbc95ebb6f Building wheel for click-completion (setup.py): started Building wheel for click-completion (setup.py): finished with status 'done' Created wheel for click-completion: filename=click_completion-0.5.2-py3-none-any.whl size=11202 sha256=717bf968aff0b9adc548a60bdbe911f1594b0b17f41db82fe8b0082b6d56958b Stored in directory: /root/.cache/pip/wheels/05/cf/ad/28cfa7e4767d4884bb1ddfda4326acbc804b0d837505ff1dc7 Building wheel for ete3 (setup.py): started Building wheel for ete3 (setup.py): finished with status 'done' Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2273013 sha256=c5c75c58025c6314bb942d41a45e24e041d438dcd85ecdeaec194a9434351e8f Stored in directory: /root/.cache/pip/wheels/2d/57/b0/e3203a462a984f3eed3cedea122a9fe3f23ed67b2b7d7df2bf Building wheel for pgsu (pyproject.toml): started Building wheel for pgsu (pyproject.toml): finished with status 'done' Created wheel for pgsu: filename=pgsu-0.2.2-py3-none-any.whl size=8850 sha256=280c353039cadfb9fd3149642268010d959e8969acc9e7b34989f96a9515b6f5 Stored in directory: /root/.cache/pip/wheels/29/99/fc/1401b3a039664d4c0bf7ed25b69a5e3426137cf6017df45412 Building wheel for psycopg2-binary (setup.py): started Building wheel for psycopg2-binary (setup.py): finished with status 'done' Created wheel for psycopg2-binary: filename=psycopg2_binary-2.8.6-cp310-cp310-linux_x86_64.whl size=445140 sha256=2d2ab8404bb22c04293dbd14a30a5b5016605c95315bc1bea5804d62629d77ab Stored in directory: /root/.cache/pip/wheels/00/3d/07/c49775291721edb6168d276d38b8b83cc152c011de3e48d6f0 Building wheel for pyyaml (pyproject.toml): started Building wheel for pyyaml (pyproject.toml): finished with status 'done' Created wheel for pyyaml: filename=PyYAML-5.4.1-cp310-cp310-linux_x86_64.whl size=45657 sha256=f748a1bd8d0d26b2617404222998e5c7c96d92f8a62b1648337633d5d402cdad Stored in directory: /root/.cache/pip/wheels/c7/0d/22/696ee92245ad710f506eee79bb05c740d8abccd3ecdb778683 Building wheel for regex (setup.py): started Building wheel for regex (setup.py): finished with status 'done' Created wheel for regex: filename=regex-2020.11.13-cp310-cp310-linux_x86_64.whl size=725121 sha256=559160f4d6a19b1bd8ccbda07ffafff99c219b60d84fee2a7135aaa83f500c68 Stored in directory: /root/.cache/pip/wheels/b7/3a/15/2a9c535e101ab0d2e2440b54fc409178b1fba48aaeabe62097 Building wheel for sqlalchemy (setup.py): started Building wheel for sqlalchemy (setup.py): finished with status 'done' Created wheel for sqlalchemy: filename=SQLAlchemy-1.3.24-cp310-cp310-linux_x86_64.whl size=1253969 sha256=e2292fb424980531375f039038a776c4a659ae99a7284cecc046cfb88faf97fa Stored in directory: /root/.cache/pip/wheels/27/51/b3/3481e88d5a5ba95dd4aafedc9316774d941c4ba61cfb93add8 Building wheel for sqlalchemy-utils (setup.py): started Building wheel for sqlalchemy-utils (setup.py): finished with status 'done' Created wheel for sqlalchemy-utils: filename=SQLAlchemy_Utils-0.36.5-py2.py3-none-any.whl size=93147 sha256=d4164bd2682e02b3249eb468d18a6f06ae5b16a99e557984817266408318a619 Stored in directory: /root/.cache/pip/wheels/6f/fc/39/370f72b980d5642b8f7e0fdd0dceba400e1d015e9c30468ce8 Building wheel for wrapt (setup.py): started Building wheel for wrapt (setup.py): finished with status 'done' Created wheel for wrapt: filename=wrapt-1.11.2-cp310-cp310-linux_x86_64.whl size=71550 sha256=01e297b7cb757e3b33509beb0acfe41386032a204db1a89faf56b5a554b619ec Stored in directory: /root/.cache/pip/wheels/52/c4/b2/401bb0f4c0e950a9066cbc424cc87c6e771a781bcb05a1683b Building wheel for configobj (setup.py): started Building wheel for configobj (setup.py): finished with status 'done' Created wheel for configobj: filename=configobj-5.0.6-py3-none-any.whl size=34547 sha256=f974400079c582d436d5a23839c5e6c3db4d52f2be9453044f8def84128efb08 Stored in directory: /root/.cache/pip/wheels/90/cd/58/816b023d3eb0e2c9c6e0cd834a10a53e932e29d7c719298216 Building wheel for tornado (setup.py): started Building wheel for tornado (setup.py): finished with status 'done' Created wheel for tornado: filename=tornado-6.1-cp310-cp310-linux_x86_64.whl size=422307 sha256=44d75bfcbe6b93dd1f5e044215310545e9f2bb70269e324e29963dec4eacdf51 Stored in directory: /root/.cache/pip/wheels/80/32/8d/21cf0fa6ee4e083f6530e5b83dfdfa9489a3890d320803f4c7 Successfully built aiida-cp2k click-completion ete3 pgsu psycopg2-binary pyyaml regex sqlalchemy sqlalchemy-utils wrapt configobj tornado Installing collected packages: wrapt, wcwidth, upf-to-json, tabulate, regex, pytz, ptyprocess, pickleshare, pamqp, iniconfig, ete3, click-spinner, backcall, asn1crypto, tzlocal, typing-extensions, traitlets, tqdm, tornado, toml, sqlparse, sqlalchemy, six, simplejson, shortuuid, shellingham, scramp, ruamel.yaml.clib, pyzmq, pyyaml, pyrsistent, pyparsing, pygments, pycparser, py, psycopg2-binary, psutil, prompt-toolkit, pluggy, pillow, pexpect, parso, numpy, nest-asyncio, multidict, markupsafe, kiwisolver, idna, graphviz, fonttools, decorator, cycler, coverage, click, attrs, async-generator, archive-path, yarl, transitions, sqlalchemy-utils, scipy, ruamel.yaml, reentry, python-dateutil, pydantic, pgsu, pg8000, packaging, matplotlib-inline, Mako, jsonschema, jinja2, jedi, django, cp2k-output-tools, configobj, circus, cffi, aldjemy, pytest, pynacl, pint, pgtest, matplotlib, ipython, deprecation, cryptography, click-config-file, click-completion, bcrypt, alembic, aiormq, pytray, pytest-cov, paramiko, cp2k-input-tools, ase, aio-pika, kiwipy, plumpy, aiida-core, aiida-gaussian-datatypes, aiida-cp2k Successfully installed Mako-1.2.0 aiida-core-1.6.8 aiida-cp2k-1.4.1 aiida-gaussian-datatypes-0.5.0 aio-pika-6.8.2 aiormq-3.3.1 aldjemy-0.9.1 alembic-1.7.7 archive-path-0.2.1 ase-3.22.1 asn1crypto-1.5.1 async-generator-1.10 attrs-21.4.0 backcall-0.2.0 bcrypt-3.2.2 cffi-1.15.0 circus-0.17.1 click-7.1.2 click-completion-0.5.2 click-config-file-0.6.0 click-spinner-0.1.10 configobj-5.0.6 coverage-6.3.3 cp2k-input-tools-0.8.2 cp2k-output-tools-0.3.1 cryptography-37.0.2 cycler-0.11.0 decorator-5.1.1 deprecation-2.1.0 django-2.2.28 ete3-3.1.2 fonttools-4.33.3 graphviz-0.20 idna-3.3 iniconfig-1.1.1 ipython-7.33.0 jedi-0.18.1 jinja2-2.11.3 jsonschema-3.2.0 kiwipy-0.7.5 kiwisolver-1.4.2 markupsafe-2.0.1 matplotlib-3.5.2 matplotlib-inline-0.1.3 multidict-6.0.2 nest-asyncio-1.4.3 numpy-1.22.4 packaging-21.3 pamqp-2.3.0 paramiko-2.11.0 parso-0.8.3 pexpect-4.8.0 pg8000-1.29.0 pgsu-0.2.2 pgtest-1.3.2 pickleshare-0.7.5 pillow-9.1.1 pint-0.17 pluggy-1.0.0 plumpy-0.20.0 prompt-toolkit-3.0.29 psutil-5.9.1 psycopg2-binary-2.8.6 ptyprocess-0.7.0 py-1.11.0 pycparser-2.21 pydantic-1.9.1 pygments-2.12.0 pynacl-1.5.0 pyparsing-3.0.9 pyrsistent-0.18.1 pytest-6.2.5 pytest-cov-2.11.1 python-dateutil-2.8.2 pytray-0.3.2 pytz-2019.3 pyyaml-5.4.1 pyzmq-23.0.0 reentry-1.3.3 regex-2020.11.13 ruamel.yaml-0.17.21 ruamel.yaml.clib-0.2.6 scipy-1.8.1 scramp-1.4.1 shellingham-1.4.0 shortuuid-1.0.9 simplejson-3.17.6 six-1.16.0 sqlalchemy-1.3.24 sqlalchemy-utils-0.36.5 sqlparse-0.4.2 tabulate-0.8.9 toml-0.10.2 tornado-6.1 tqdm-4.64.0 traitlets-5.2.1.post0 transitions-0.7.2 typing-extensions-4.2.0 tzlocal-2.1 upf-to-json-0.9.5 wcwidth-0.2.5 wrapt-1.11.2 yarl-1.7.2 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv ========== Configuring AiiDA ========== * Starting RabbitMQ Messaging Server rabbitmq-server ...done. * Starting PostgreSQL 14 database server ...done. ========== Running AiiDA-CP2K Tests ========== ============================= test session starts ============================== platform linux -- Python 3.10.4, pytest-6.2.5, py-1.11.0, pluggy-1.0.0 rootdir: /opt/aiida-cp2k, configfile: pyproject.toml plugins: cov-2.11.1 collected 37 items examples/gaussian_datatypes/example_automatic.py . [ 2%] examples/gaussian_datatypes/example_explicit.py . [ 5%] examples/single_calculations/example_bands.py . [ 8%] examples/single_calculations/example_dft.py . [ 10%] examples/single_calculations/example_dft_atomic_kinds.py . [ 13%] examples/single_calculations/example_failure.py . [ 16%] examples/single_calculations/example_geopt.py . [ 18%] examples/single_calculations/example_mm.py . [ 21%] examples/single_calculations/example_multiple_force_eval.py . [ 24%] examples/single_calculations/example_no_struct.py . [ 27%] examples/single_calculations/example_precision.py . [ 29%] examples/single_calculations/example_restart.py . [ 32%] examples/single_calculations/example_structure_through_file.py . [ 35%] examples/workchains/example_base_failed_restart.py . [ 37%] examples/workchains/example_base_restart.py F [ 40%] test/test_gaussian_datatypes.py ........ [ 62%] test/test_input_generator.py ......... [ 86%] test/test_parser.py ... [ 94%] test/test_version_agreement.py . [ 97%] test/test_xyz.py . [100%] =================================== FAILURES =================================== _________________________________ example_base _________________________________ self = calc = @process_handler(priority=400, enabled=False) def resubmit_unconverged_geometry(self, calc): """Resubmit a calculation it is not converged, but can be recovered.""" self.report("Checking the geometry convergence.") content_string = calc.outputs.retrieved.get_object_content(calc.get_attribute('output_filename')) time_not_exceeded = "PROGRAM ENDED AT" time_exceeded = "exceeded requested execution time" one_step_done = "Max. gradient =" self.ctx.inputs.parent_calc_folder = calc.outputs.remote_folder params = self.ctx.inputs.parameters # If the problem is recoverable then do restart if (time_not_exceeded not in content_string or time_exceeded in content_string) and one_step_done in content_string: # pylint: disable=line-too-long try: # Firts check if all the restart keys are present in the input dictionary > wf_rest_fname_pointer = params['FORCE_EVAL']['DFT']['RESTART_FILE_NAME'] E KeyError: 'RESTART_FILE_NAME' aiida_cp2k/workchains/base.py:75: KeyError During handling of the above exception, another exception occurred: cp2k_code = def example_base(cp2k_code): """Run simple DFT calculation through a workchain.""" thisdir = os.path.dirname(os.path.realpath(__file__)) print("Testing CP2K ENERGY on H2O (DFT) through a workchain...") # Basis set. basis_file = SinglefileData(file=os.path.join(thisdir, "..", "files", "BASIS_MOLOPT")) # Pseudopotentials. pseudo_file = SinglefileData(file=os.path.join(thisdir, "..", "files", "GTH_POTENTIALS")) # Structure. structure = StructureData(ase=ase.io.read(os.path.join(thisdir, "..", "files", "h2o.xyz"))) # Parameters. parameters = Dict( dict={ 'GLOBAL': { 'RUN_TYPE': 'GEO_OPT', 'WALLTIME': '00:00:20', # too short }, 'FORCE_EVAL': { 'METHOD': 'Quickstep', 'DFT': { 'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT', 'POTENTIAL_FILE_NAME': 'GTH_POTENTIALS', 'QS': { 'EPS_DEFAULT': 1.0e-12, 'WF_INTERPOLATION': 'ps', 'EXTRAPOLATION_ORDER': 3, }, 'MGRID': { 'NGRIDS': 4, 'CUTOFF': 280, 'REL_CUTOFF': 30, }, 'XC': { 'XC_FUNCTIONAL': { '_': 'LDA', }, }, 'POISSON': { 'PERIODIC': 'none', 'PSOLVER': 'MT', }, 'SCF': { 'PRINT': { 'RESTART': { '_': 'ON' } } }, }, 'SUBSYS': { 'KIND': [ { '_': 'O', 'BASIS_SET': 'DZVP-MOLOPT-SR-GTH', 'POTENTIAL': 'GTH-LDA-q6' }, { '_': 'H', 'BASIS_SET': 'DZVP-MOLOPT-SR-GTH', 'POTENTIAL': 'GTH-LDA-q1' }, ], }, } }) # Construct process builder. builder = Cp2kBaseWorkChain.get_builder() # Switch on resubmit_unconverged_geometry disabled by default. builder.handler_overrides = Dict(dict={'resubmit_unconverged_geometry': True}) # Input structure. builder.cp2k.structure = structure builder.cp2k.parameters = parameters builder.cp2k.code = cp2k_code builder.cp2k.file = { 'basis': basis_file, 'pseudo': pseudo_file, } builder.cp2k.metadata.options.resources = { "num_machines": 1, "num_mpiprocs_per_machine": 1, } builder.cp2k.metadata.options.max_wallclock_seconds = 1 * 3 * 60 print("Submitted calculation...") > calc = run(builder) examples/workchains/example_base_restart.py:118: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/local/lib/python3.10/dist-packages/aiida/engine/launch.py:41: in run return runner.run(process, *args, **inputs) /usr/local/lib/python3.10/dist-packages/aiida/engine/runners.py:266: in run result, _ = self._run(process, *args, **inputs) /usr/local/lib/python3.10/dist-packages/aiida/engine/runners.py:250: in _run process_inited.execute() /usr/local/lib/python3.10/dist-packages/plumpy/processes.py:81: in func_wrapper return func(self, *args, **kwargs) /usr/local/lib/python3.10/dist-packages/plumpy/processes.py:1166: in execute return self.future().result() /usr/local/lib/python3.10/dist-packages/plumpy/process_states.py:231: in execute result = self.run_fn(*self.args, **self.kwargs) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/workchains/workchain.py:214: in _do_step finished, stepper_result = self._stepper.step() /usr/local/lib/python3.10/dist-packages/plumpy/workchains.py:299: in step finished, result = self._child_stepper.step() /usr/local/lib/python3.10/dist-packages/plumpy/workchains.py:532: in step finished, result = self._child_stepper.step() /usr/local/lib/python3.10/dist-packages/plumpy/workchains.py:299: in step finished, result = self._child_stepper.step() /usr/local/lib/python3.10/dist-packages/plumpy/workchains.py:250: in step return True, self._fn(self._workchain) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/workchains/restart.py:238: in inspect_process report = handler(self, node) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/workchains/utils.py:119: in wrapper result = wrapped(*args, **kwargs) aiida_cp2k/workchains/base.py:89: in resubmit_unconverged_geometry params = add_restart_sections(params) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/functions.py:179: in decorated_function result, _ = run_get_node(*args, **kwargs) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/functions.py:152: in run_get_node result = process.execute() /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/functions.py:351: in execute result = super().execute() /usr/local/lib/python3.10/dist-packages/plumpy/processes.py:81: in func_wrapper return func(self, *args, **kwargs) /usr/local/lib/python3.10/dist-packages/plumpy/processes.py:1166: in execute return self.future().result() /usr/local/lib/python3.10/dist-packages/plumpy/process_states.py:231: in execute result = self.run_fn(*self.args, **self.kwargs) /usr/local/lib/python3.10/dist-packages/aiida/engine/processes/functions.py:395: in run result = self._func(*args, **kwargs) aiida_cp2k/utils/input_generator.py:193: in add_restart_sections merge_dict(params, restart_wfn_dict) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dct = {'FORCE_EVAL': {'DFT': {'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT', 'MGRID': {'CUTOFF': 280, 'NGRIDS': 4, 'REL_CUTOFF': 30}...ZVP-MOLOPT-SR-GTH', 'POTENTIAL': 'GTH-LDA-q1', '_': 'H'}]}}, 'GLOBAL': {'RUN_TYPE': 'GEO_OPT', 'WALLTIME': '00:00:20'}} merge_dct = {'FORCE_EVAL': {'DFT': {'RESTART_FILE_NAME': './parent_calc/aiida-RESTART.wfn', 'SCF': {'SCF_GUESS': 'RESTART'}}}} def merge_dict(dct, merge_dct): """ Taken from https://gist.github.com/angstwad/bf22d1822c38a92ec0a9 Recursive dict merge. Inspired by :meth:``dict.update()``, instead of updating only top-level keys, merge_dict recurses down into dicts nested to an arbitrary depth, updating keys. The ``merge_dct`` is merged into ``dct``. :param dct: dict onto which the merge is executed :param merge_dct: dct merged into dct (overwrites dct data if in both) :return: None """ import collections for k, _ in merge_dct.items(): # it was .iteritems() in python2 > if (k in dct and isinstance(dct[k], dict) and isinstance(merge_dct[k], collections.Mapping)): E AttributeError: module 'collections' has no attribute 'Mapping' aiida_cp2k/utils/workchains.py:32: AttributeError ----------------------------- Captured stdout call ----------------------------- Testing CP2K ENERGY on H2O (DFT) through a workchain... Submitted calculation... =============================== warnings summary =============================== ../../usr/local/lib/python3.10/dist-packages/_pytest/cacheprovider.py:428 /usr/local/lib/python3.10/dist-packages/_pytest/cacheprovider.py:428: PytestCacheWarning: could not create cache path /opt/aiida-cp2k/.pytest_cache/v/cache/nodeids config.cache.set("cache/nodeids", sorted(self.cached_nodeids)) ../../usr/local/lib/python3.10/dist-packages/_pytest/cacheprovider.py:382 /usr/local/lib/python3.10/dist-packages/_pytest/cacheprovider.py:382: PytestCacheWarning: could not create cache path /opt/aiida-cp2k/.pytest_cache/v/cache/lastfailed config.cache.set("cache/lastfailed", self.lastfailed) ../../usr/local/lib/python3.10/dist-packages/_pytest/stepwise.py:49 /usr/local/lib/python3.10/dist-packages/_pytest/stepwise.py:49: PytestCacheWarning: could not create cache path /opt/aiida-cp2k/.pytest_cache/v/cache/stepwise session.config.cache.set(STEPWISE_CACHE_DIR, []) -- Docs: https://docs.pytest.org/en/stable/warnings.html =========================== short test summary info ============================ FAILED examples/workchains/example_base_restart.py::example_base - AttributeE... ============= 1 failed, 36 passed, 3 warnings in 187.10s (0:03:07) ============= Summary: Something is wrong with aiida-cp2k commit 0916da4. Status: FAILED Removing intermediate container 044b64506569 ---> 0d99e638bb32 Step 40/40 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in a9af1af39b9a Removing intermediate container a9af1af39b9a ---> d948ba54e181 [Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed Successfully built d948ba54e181 Successfully tagged gcr.io/cp2k-org-project/img_cp2k-aiida-arch-668:master Pushing new image... done. #################### Running Image cp2k-aiida #################### EndDate: 2022-05-22 13:58:43+00:00