StartDate: 2024-03-02 06:04:41+00:00 CpuId: 32x AMD EPYC (3rd Gen) (Milan) [Zen 3], 7nm (SMT disabled) CommitSHA: 38a20dc40e43fd67c759b615b5d67ed9a4af4e32 CommitTime: 2024-03-01 15:45:08 +0100 CommitAuthor: Ole Schütt CommitSubject: Rename reference Graml2023 to Graml2024 #################### Building Image cp2k-aiida #################### Dockerfile: /tools/docker/Dockerfile.test_aiida Build-Path: / Build-Args: GIT_COMMIT_SHA=38a20dc40e43fd67c759b615b5d67ed9a4af4e32 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 393.7MB Step 1/41 : FROM ubuntu:22.04 22.04: Pulling from library/ubuntu 01007420e9b0: Pulling fs layer 01007420e9b0: Verifying Checksum 01007420e9b0: Download complete 01007420e9b0: Pull complete Digest: sha256:f9d633ff6640178c2d0525017174a688e2c1aef28f0a0130b26bd5554491f0da Status: Downloaded newer image for ubuntu:22.04 ---> 3db8720ecbf5 Step 2/41 : WORKDIR /opt/cp2k-toolchain ---> Using cache ---> c91877cf7c4f Step 3/41 : COPY ./tools/toolchain/install_requirements*.sh ./ ---> Using cache ---> 40cd32e951b0 Step 4/41 : RUN ./install_requirements.sh ubuntu:22.04 ---> Using cache ---> 0e0c260a973e Step 5/41 : RUN mkdir scripts ---> Using cache ---> c18ee2447245 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 ---> 50a53065b028 Step 7/41 : COPY ./tools/toolchain/install_cp2k_toolchain.sh . ---> Using cache ---> 410cc668ef16 Step 8/41 : RUN ./install_cp2k_toolchain.sh --install-all --with-gcc=system --dry-run ---> Using cache ---> ef458af826b9 Step 9/41 : COPY ./tools/toolchain/scripts/stage0/ ./scripts/stage0/ ---> Using cache ---> 5b5e2bc49cd5 Step 10/41 : RUN ./scripts/stage0/install_stage0.sh && rm -rf ./build ---> Using cache ---> b6701df80a4f Step 11/41 : COPY ./tools/toolchain/scripts/stage1/ ./scripts/stage1/ ---> Using cache ---> 65bb47d5e0be Step 12/41 : RUN ./scripts/stage1/install_stage1.sh && rm -rf ./build ---> Using cache ---> 3235032c243b Step 13/41 : COPY ./tools/toolchain/scripts/stage2/ ./scripts/stage2/ ---> Using cache ---> 9fdaac814822 Step 14/41 : RUN ./scripts/stage2/install_stage2.sh && rm -rf ./build ---> Using cache ---> 89a5d839f744 Step 15/41 : COPY ./tools/toolchain/scripts/stage3/ ./scripts/stage3/ ---> Using cache ---> d4181b8c9115 Step 16/41 : RUN ./scripts/stage3/install_stage3.sh && rm -rf ./build ---> Using cache ---> a200824ab62c Step 17/41 : COPY ./tools/toolchain/scripts/stage4/ ./scripts/stage4/ ---> Using cache ---> cf4e3530cfac Step 18/41 : RUN ./scripts/stage4/install_stage4.sh && rm -rf ./build ---> Using cache ---> b7543240dd55 Step 19/41 : COPY ./tools/toolchain/scripts/stage5/ ./scripts/stage5/ ---> Using cache ---> 7661f7b25b97 Step 20/41 : RUN ./scripts/stage5/install_stage5.sh && rm -rf ./build ---> Using cache ---> 2b02d0f56252 Step 21/41 : COPY ./tools/toolchain/scripts/stage6/ ./scripts/stage6/ ---> Using cache ---> c6fa05294c14 Step 22/41 : RUN ./scripts/stage6/install_stage6.sh && rm -rf ./build ---> Using cache ---> 57c0d372fca0 Step 23/41 : COPY ./tools/toolchain/scripts/stage7/ ./scripts/stage7/ ---> Using cache ---> c6bed1fbbe7e Step 24/41 : RUN ./scripts/stage7/install_stage7.sh && rm -rf ./build ---> Using cache ---> 3c67707a23a0 Step 25/41 : COPY ./tools/toolchain/scripts/stage8/ ./scripts/stage8/ ---> Using cache ---> b8ef848c5e78 Step 26/41 : RUN ./scripts/stage8/install_stage8.sh && rm -rf ./build ---> Using cache ---> 61b028d7894a Step 27/41 : COPY ./tools/toolchain/scripts/arch_base.tmpl ./tools/toolchain/scripts/generate_arch_files.sh ./scripts/ ---> Using cache ---> 7eda2a584141 Step 28/41 : RUN ./scripts/generate_arch_files.sh && rm -rf ./build ---> Using cache ---> 7ac6d70c4f6f Step 29/41 : WORKDIR /opt/cp2k ---> Using cache ---> 1c08b4b239c6 Step 30/41 : COPY ./Makefile . ---> Using cache ---> f0c5e49b29f4 Step 31/41 : COPY ./src ./src ---> Using cache ---> a20284117274 Step 32/41 : COPY ./exts ./exts ---> Using cache ---> e85132a87e6d Step 33/41 : COPY ./tools/build_utils ./tools/build_utils ---> Using cache ---> 22c1d51fad9d Step 34/41 : RUN /bin/bash -c " mkdir -p arch && ln -vs /opt/cp2k-toolchain/install/arch/local.sdbg ./arch/" ---> Using cache ---> 671b8ad5a4fe Step 35/41 : COPY ./data ./data ---> Using cache ---> 4b6e57a1363d Step 36/41 : COPY ./tests ./tests ---> Using cache ---> d82ffc3f8466 Step 37/41 : COPY ./tools/regtesting ./tools/regtesting ---> Using cache ---> 59554b07630f Step 38/41 : COPY ./tools/docker/scripts/test_aiida.sh . ---> 73ca103d2ce3 Step 39/41 : RUN ./test_aiida.sh 2>&1 | tee report.log ---> Running in b31b95537895 ========== 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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Selecting previously unselected package rabbitmq-server. Preparing to unpack .../62-rabbitmq-server_3.9.13-1ubuntu0.22.04.2_all.deb ... Unpacking rabbitmq-server (3.9.13-1ubuntu0.22.04.2) ... Setting up python3-pkg-resources (59.6.0-1.2ubuntu0.22.04.1) ... Setting up libpython3.10:amd64 (3.10.12-1~22.04.3) ... Setting up erlang-base (1:24.2.1+dfsg-1ubuntu0.1) ... Searching for services which depend on erlang and should be started... none found. Setting up python3-colorama (0.4.4-1) ... Setting up libcbor0.8:amd64 (0.8.0-2ubuntu1) ... Setting up erlang-xmerl (1:24.2.1+dfsg-1ubuntu0.1) ... 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 (14.11-0ubuntu0.22.04.1) ... Setting up erlang-syntax-tools (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up python3-click (8.0.3-1) ... Setting up locales (2.35-0ubuntu3.6) ... Generating locales (this might take a while)... Generation complete. Setting up tzdata (2024a-0ubuntu0.22.04) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 2 06:12:48 UTC 2024. Universal Time is now: Sat Mar 2 06:12:48 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up python3-six (1.16.0-3ubuntu1) ... Setting up erlang-parsetools (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up libexpat1-dev:amd64 (2.4.7-1ubuntu0.2) ... 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 (3.0.2-0ubuntu1.15) ... Setting up sudo (1.9.9-1ubuntu2.4) ... Setting up libpython3.10-dev:amd64 (3.10.12-1~22.04.3) ... Setting up ucf (3.0043) ... Setting up erlang-asn1 (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up erlang-tftp (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up python3.10-dev (3.10.12-1~22.04.3) ... Setting up libmd0:amd64 (1.0.4-1build1) ... Setting up libjson-perl (4.04000-1) ... Setting up libxslt1.1:amd64 (1.1.34-4ubuntu0.22.04.1) ... Setting up erlang-mnesia (1:24.2.1+dfsg-1ubuntu0.1) ... 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-1ubuntu0.1) ... Setting up libfido2-1:amd64 (1.10.0-1) ... Setting up libbsd0:amd64 (0.11.5-1) ... Setting up python3-lib2to3 (3.10.8-1~22.04) ... Setting up libjs-underscore (1.13.2~dfsg-2) ... Setting up libpopt0:amd64 (1.18-3build1) ... Setting up python3-distutils (3.10.8-1~22.04) ... Setting up logrotate (3.19.0-1ubuntu1.1) ... Setting up postgresql-client-common (238) ... Setting up libpython3-dev:amd64 (3.10.6-1~22.04) ... Setting up python3-setuptools (59.6.0-1.2ubuntu0.22.04.1) ... Setting up python3-reentry (1.3.2-1) ... Setting up erlang-runtime-tools (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up libedit2:amd64 (3.1-20210910-1build1) ... Setting up erlang-tools (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up libpq-dev (14.11-0ubuntu0.22.04.1) ... Setting up postgresql-client-14 (14.11-0ubuntu0.22.04.1) ... 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 (0.37.1-2ubuntu0.22.04.1) ... Setting up erlang-snmp (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up erlang-public-key (1:24.2.1+dfsg-1ubuntu0.1) ... 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-1ubuntu0.4) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up libllvm14:amd64 (1:14.0.0-1ubuntu1.1) ... Setting up erlang-ssl (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up postgresql-14 (14.11-0ubuntu0.22.04.1) ... 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 (1:8.9p1-3ubuntu0.6) ... 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-1ubuntu0.1) ... Setting up erlang-eldap (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up python3-dev (3.10.6-1~22.04) ... Setting up erlang-ftp (1:24.2.1+dfsg-1ubuntu0.1) ... Setting up postgresql (14+238) ... Setting up openssh-sftp-server (1:8.9p1-3ubuntu0.6) ... Setting up openssh-server (1:8.9p1-3ubuntu0.6) ... Creating config file /etc/ssh/sshd_config with new version Creating SSH2 RSA key; this may take some time ... 3072 SHA256:++qfez7wEhv47FpGM83WYTDFVNMzqQPQ0KSsKW91F4Y root@b31b95537895 (RSA) Creating SSH2 ECDSA key; this may take some time ... 256 SHA256:VTzTpuWg3Sw67KNuBdayuVA5481/wmzMJuyeB/ObKxQ root@b31b95537895 (ECDSA) Creating SSH2 ED25519 key; this may take some time ... 256 SHA256:vRSDkMDx9Fo89ZosRoioJBItpLBais5wXv1P3RIdEZI root@b31b95537895 (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-1ubuntu0.1) ... Setting up rabbitmq-server (3.9.13-1ubuntu0.22.04.2) ... 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 (1:8.9p1-3ubuntu0.6) ... Processing triggers for libc-bin (2.35-0ubuntu3.6) ... ./test_aiida.sh: line 42: 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 aiida-gaussian-datatypes Downloading aiida_gaussian_datatypes-0.5.1-py3-none-any.whl (25 kB) Collecting aiida-core<3.0.0,>=2.0.0 Downloading aiida_core-2.5.1-py3-none-any.whl (1.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3/1.3 MB 5.0 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 8.3 MB/s eta 0:00:00 Collecting ruamel.yaml>=0.16.5 Downloading 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Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting lexid Downloading lexid-2021.1006-py2.py3-none-any.whl (7.6 kB) Collecting pathlib2 Downloading pathlib2-2.3.7.post1-py2.py3-none-any.whl (18 kB) Requirement already satisfied: colorama>=0.4 in /usr/lib/python3/dist-packages (from bumpver==2022.1119->aiida-cp2k==2.0.0) (0.4.4) Requirement already satisfied: click in /usr/lib/python3/dist-packages (from bumpver==2022.1119->aiida-cp2k==2.0.0) (8.0.3) Requirement already satisfied: setuptools>=45.0.0 in /usr/lib/python3/dist-packages (from bumpver==2022.1119->aiida-cp2k==2.0.0) (59.6.0) Collecting docstring-parser Downloading docstring_parser-0.15-py3-none-any.whl (36 kB) Collecting numpy~=1.21 Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 55.8 MB/s eta 0:00:00 Collecting aio-pika~=6.6 Downloading aio_pika-6.8.2-py3-none-any.whl (42 kB) 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with status 'done' Collecting pytz~=2021.1 Downloading pytz-2021.3-py2.py3-none-any.whl (503 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 503.5/503.5 KB 65.6 MB/s eta 0:00:00 Collecting pydantic~=2.4 Downloading pydantic-2.6.3-py3-none-any.whl (395 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 395.2/395.2 KB 53.1 MB/s eta 0:00:00 Collecting graphviz~=0.19 Downloading graphviz-0.20.1-py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.0/47.0 KB 10.0 MB/s eta 0:00:00 Collecting wrapt~=1.11 Downloading wrapt-1.16.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 80.3/80.3 KB 15.1 MB/s eta 0:00:00 Collecting tqdm~=4.45 Downloading tqdm-4.66.2-py3-none-any.whl (78 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 KB 16.3 MB/s eta 0:00:00 Collecting plumpy~=0.21.6 Downloading plumpy-0.21.10-py3-none-any.whl (74 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 74.4/74.4 KB 14.1 MB/s eta 0:00:00 Collecting psycopg2-binary~=2.8 Downloading psycopg2_binary-2.9.9-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 117.5 MB/s eta 0:00:00 Collecting pyyaml~=6.0 Downloading PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (705 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 705.5/705.5 KB 69.1 MB/s eta 0:00:00 Collecting disk-objectstore~=1.0 Downloading disk_objectstore-1.0.0-py3-none-any.whl (65 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 65.0/65.0 KB 11.0 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 paramiko>=2.7.2,~=2.7 Downloading paramiko-2.12.0-py2.py3-none-any.whl (213 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 213.1/213.1 KB 35.0 MB/s eta 0:00:00 Collecting ipython>=7 Downloading ipython-8.22.1-py3-none-any.whl (811 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 812.0/812.0 KB 78.8 MB/s eta 0:00:00 Collecting 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pyzmq>=17.0 Downloading pyzmq-25.1.2-cp310-cp310-manylinux_2_28_x86_64.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 16.1 MB/s eta 0:00:00 Collecting tornado>=5.0.2 Downloading tornado-6.4-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (435 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 435.4/435.4 KB 2.1 MB/s eta 0:00:00 Collecting transitions<0.10,>=0.7 Downloading transitions-0.9.0-py2.py3-none-any.whl (97 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.7/97.7 KB 666.4 kB/s eta 0:00:00 Collecting Pint<0.24,>=0.15 Downloading Pint-0.23-py3-none-any.whl (305 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 305.0/305.0 KB 3.9 MB/s eta 0:00:00 Collecting zipp>=0.5 Downloading zipp-3.17.0-py3-none-any.whl (7.4 kB) Collecting stack-data Downloading stack_data-0.6.3-py3-none-any.whl (24 kB) Collecting traitlets>=5.13.0 Downloading traitlets-5.14.1-py3-none-any.whl (85 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.4/85.4 KB 576.3 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pgsu: filename=pgsu-0.2.4-py3-none-any.whl size=8903 sha256=14dde83e3ec2168b1c0060d07860d34e16921e9a29bf9dfc500a906fe526a523 Stored in directory: /root/.cache/pip/wheels/05/d5/be/0041e03d4ab4bd55f731a084850a4188a8e832ea4536477fbc Successfully built aiida-cp2k pgsu Installing collected packages: wcwidth, upf_to_json, regex, pytz, pure-eval, ptyprocess, pamqp, distlib, click-spinner, asn1crypto, zipp, wrapt, urllib3, typing-extensions, transitions, traitlets, tqdm, tornado, toml, tabulate, shortuuid, scramp, ruamel.yaml.clib, pyzmq, pyyaml, python-dateutil, pyparsing, pygments, pycparser, py, psycopg2-binary, psutil, prompt-toolkit, pluggy, platformdirs, pillow, pexpect, pathlib2, parso, packaging, numpy, nodeenv, nest_asyncio, multidict, MarkupSafe, lexid, kiwisolver, iniconfig, idna, identify, greenlet, graphviz, fonttools, filelock, executing, exceptiongroup, docstring-parser, decorator, cycler, coverage, click, charset-normalizer, cfgv, certifi, bcrypt, attrs, async-generator, asttokens, archive-path, annotated-types, yarl, virtualenv, stack-data, sqlalchemy, scipy, ruamel.yaml, requests, pytest, pydantic-core, Pint, pgsu, pg8000, matplotlib-inline, Mako, jinja2, jedi, importlib-metadata, deprecation, cp2k-output-tools, contourpy, circus, cffi, bumpver, pytray, pytest-cov, pynacl, pydantic, pre-commit, pgtest, matplotlib, ipython, disk-objectstore, cryptography, alembic, aiormq, paramiko, kiwipy, cp2k-input-tools, ase, aio-pika, plumpy, aiida-core, aiida-gaussian-datatypes, aiida-cp2k Attempting uninstall: click Found existing installation: click 8.0.3 Not uninstalling click at /usr/lib/python3/dist-packages, outside environment /usr Can't uninstall 'click'. No files were found to uninstall. Successfully installed Mako-1.3.2 MarkupSafe-2.1.5 Pint-0.23 aiida-core-2.5.1 aiida-cp2k-2.0.0 aiida-gaussian-datatypes-0.5.1 aio-pika-6.8.1 aiormq-3.3.1 alembic-1.13.1 annotated-types-0.6.0 archive-path-0.4.2 ase-3.22.1 asn1crypto-1.5.1 asttokens-2.4.1 async-generator-1.10 attrs-23.2.0 bcrypt-4.1.2 bumpver-2022.1119 certifi-2024.2.2 cffi-1.16.0 cfgv-3.4.0 charset-normalizer-3.3.2 circus-0.18.0 click-8.1.7 click-spinner-0.1.10 contourpy-1.2.0 coverage-7.4.3 cp2k-input-tools-0.9.1 cp2k-output-tools-0.5.0 cryptography-42.0.5 cycler-0.12.1 decorator-5.1.1 deprecation-2.1.0 disk-objectstore-1.0.0 distlib-0.3.8 docstring-parser-0.15 exceptiongroup-1.2.0 executing-2.0.1 filelock-3.13.1 fonttools-4.49.0 graphviz-0.20.1 greenlet-3.0.3 identify-2.5.35 idna-3.6 importlib-metadata-6.11.0 iniconfig-2.0.0 ipython-8.22.1 jedi-0.18.2 jinja2-3.1.3 kiwipy-0.7.8 kiwisolver-1.4.5 lexid-2021.1006 matplotlib-3.8.3 matplotlib-inline-0.1.6 multidict-6.0.5 nest_asyncio-1.6.0 nodeenv-1.8.0 numpy-1.26.4 packaging-23.2 pamqp-2.3.0 paramiko-2.12.0 parso-0.8.3 pathlib2-2.3.7.post1 pexpect-4.9.0 pg8000-1.30.5 pgsu-0.2.4 pgtest-1.3.2 pillow-10.2.0 platformdirs-4.2.0 pluggy-1.4.0 plumpy-0.21.10 pre-commit-2.21.0 prompt-toolkit-3.0.43 psutil-5.9.8 psycopg2-binary-2.9.9 ptyprocess-0.7.0 pure-eval-0.2.2 py-1.11.0 pycparser-2.21 pydantic-2.6.3 pydantic-core-2.16.3 pygments-2.17.2 pynacl-1.5.0 pyparsing-3.1.1 pytest-6.2.5 pytest-cov-2.11.1 python-dateutil-2.9.0.post0 pytray-0.3.4 pytz-2021.3 pyyaml-6.0.1 pyzmq-25.1.2 regex-2021.11.10 requests-2.31.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 scipy-1.12.0 scramp-1.4.4 shortuuid-1.0.12 sqlalchemy-2.0.27 stack-data-0.6.3 tabulate-0.8.10 toml-0.10.2 tornado-6.4 tqdm-4.66.2 traitlets-5.14.1 transitions-0.9.0 typing-extensions-4.10.0 upf_to_json-0.9.5 urllib3-2.2.1 virtualenv-20.25.1 wcwidth-0.2.13 wrapt-1.16.0 yarl-1.9.4 zipp-3.17.0 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 3.10.12, pytest-6.2.5, py-1.11.0, pluggy-1.4.0 rootdir: /opt/aiida-cp2k, configfile: pyproject.toml plugins: cov-2.11.1 collected 49 items examples/gaussian_datatypes/example_automatic.py . [ 2%] examples/gaussian_datatypes/example_explicit.py . [ 4%] examples/single_calculations/example_bands.py . [ 6%] examples/single_calculations/example_dft.py . [ 8%] examples/single_calculations/example_dft_atomic_kinds.py . [ 10%] examples/single_calculations/example_failure.py . [ 12%] examples/single_calculations/example_geopt.py . [ 14%] examples/single_calculations/example_max_error.py . [ 16%] examples/single_calculations/example_mm.py . [ 18%] examples/single_calculations/example_mm_md.py . [ 20%] examples/single_calculations/example_multiple_force_eval.py . [ 22%] examples/single_calculations/example_no_struct.py . [ 24%] examples/single_calculations/example_precision.py . [ 26%] examples/single_calculations/example_restart.py . [ 28%] examples/single_calculations/example_structure_through_file.py . [ 30%] examples/workchains/example_base_energy_restart.py . [ 32%] examples/workchains/example_base_failed_restart.py . [ 34%] examples/workchains/example_base_geoopt_restart.py F [ 36%] test/test_gaussian_datatypes.py ........ [ 53%] test/test_input_generator.py ......... [ 71%] test/test_parser.py ............. [ 97%] test/test_xyz.py . [100%] =================================== FAILURES =================================== _________________________________ example_base _________________________________ 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( { "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( {"restart_incomplete_calculation": {"enabled": 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) > if "EXT_RESTART" in calc["final_input_parameters"].dict: E KeyError: 'final_input_parameters' examples/workchains/example_base_geoopt_restart.py:121: KeyError ----------------------------- Captured stdout call ----------------------------- Testing CP2K ENERGY on H2O (DFT) through a workchain... Submitted calculation... ----------------------------- Captured stderr call ----------------------------- 03/02/2024 06:17:51 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<187> iteration #1 03/02/2024 06:18:14 AM <16407> aiida.scheduler.direct: [WARNING] Unrecognized job_state 't' for job id 44047 03/02/2024 06:18:14 AM <16407> aiida.orm.nodes.process.calculation.calcjob.CalcJobNode: [WARNING] output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. 03/02/2024 06:18:15 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|restart_incomplete_calculation]: The CP2K calculation wasn't completed. The restart of the calculation might be able to fix the problem. 03/02/2024 06:18:15 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<187> failed but a handler dealt with the problem, restarting 03/02/2024 06:18:16 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<197> iteration #2 03/02/2024 06:18:38 AM <16407> aiida.scheduler.direct: [WARNING] Unrecognized job_state 't' for job id 46234 03/02/2024 06:18:38 AM <16407> aiida.scheduler.direct: [WARNING] Unrecognized job_state 't' for job id 46234 03/02/2024 06:18:39 AM <16407> aiida.orm.nodes.process.calculation.calcjob.CalcJobNode: [WARNING] output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. 03/02/2024 06:18:39 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<197> failed and error was not handled, restarting once more 03/02/2024 06:18:39 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<202> iteration #3 03/02/2024 06:19:02 AM <16407> aiida.scheduler.direct: [WARNING] Unrecognized job_state 't' for job id 48402 03/02/2024 06:19:03 AM <16407> aiida.orm.nodes.process.calculation.calcjob.CalcJobNode: [WARNING] output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. 03/02/2024 06:19:03 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<202> failed and error was not handled for the second consecutive time, aborting 03/02/2024 06:19:03 AM <16407> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [186|Cp2kBaseWorkChain|on_terminated]: remote folders will not be cleaned ------------------------------ Captured log call ------------------------------- REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<187> iteration #1 WARNING aiida.scheduler.direct:direct.py:242 Unrecognized job_state 't' for job id 44047 WARNING aiida.orm.nodes.process.calculation.calcjob.CalcJobNode:calcjob.py:677 output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|restart_incomplete_calculation]: The CP2K calculation wasn't completed. The restart of the calculation might be able to fix the problem. REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<187> failed but a handler dealt with the problem, restarting REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<197> iteration #2 WARNING aiida.scheduler.direct:direct.py:242 Unrecognized job_state 't' for job id 46234 WARNING aiida.scheduler.direct:direct.py:242 Unrecognized job_state 't' for job id 46234 WARNING aiida.orm.nodes.process.calculation.calcjob.CalcJobNode:calcjob.py:677 output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<197> failed and error was not handled, restarting once more REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|run_process]: launching Cp2kCalculation<202> iteration #3 WARNING aiida.scheduler.direct:direct.py:242 Unrecognized job_state 't' for job id 48402 WARNING aiida.orm.nodes.process.calculation.calcjob.CalcJobNode:calcjob.py:677 output parser returned exit code<400>: The calculation stopped prematurely because it ran out of walltime. REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|inspect_process]: Cp2kCalculation<202> failed and error was not handled for the second consecutive time, aborting REPORT aiida.orm.nodes.process.workflow.workchain.WorkChainNode:process.py:580 [186|Cp2kBaseWorkChain|on_terminated]: remote folders will not be cleaned =============================== warnings summary =============================== ../../usr/local/lib/python3.10/dist-packages/aiida/manage/configuration/settings.py:59 /usr/local/lib/python3.10/dist-packages/aiida/manage/configuration/settings.py:59: UserWarning: Creating AiiDA configuration folder `/home/ubuntu/.aiida`. warnings.warn(f'Creating AiiDA configuration folder `{path}`.') examples/gaussian_datatypes/example_automatic.py::example_gdt /usr/local/lib/python3.10/dist-packages/aiida/manage/configuration/settings.py:59: UserWarning: Creating AiiDA configuration folder `/tmp/pytest-of-ubuntu/pytest-0/config0/.aiida`. warnings.warn(f'Creating AiiDA configuration folder `{path}`.') examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning examples/single_calculations/example_bands.py: 1 warning examples/single_calculations/example_dft.py: 1 warning examples/single_calculations/example_dft_atomic_kinds.py: 1 warning examples/single_calculations/example_failure.py: 1 warning examples/single_calculations/example_geopt.py: 1 warning examples/single_calculations/example_max_error.py: 1 warning examples/single_calculations/example_mm.py: 1 warning examples/single_calculations/example_mm_md.py: 1 warning examples/single_calculations/example_multiple_force_eval.py: 1 warning examples/single_calculations/example_no_struct.py: 1 warning examples/single_calculations/example_precision.py: 1 warning examples/single_calculations/example_restart.py: 1 warning examples/single_calculations/example_structure_through_file.py: 1 warning examples/workchains/example_base_energy_restart.py: 1 warning examples/workchains/example_base_failed_restart.py: 1 warning examples/workchains/example_base_geoopt_restart.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida/orm/nodes/data/code/legacy.py:42: AiidaDeprecationWarning: The `Code` class is deprecated. To create an instance, use the `aiida.orm.nodes.data.code.installed.InstalledCode` or `aiida.orm.nodes.data.code.portable.PortableCode` for a "remote" or "local" code, respectively. If you are using this class to compare type, e.g. in `isinstance`, use `aiida.orm.nodes.data.code.abstract.AbstractCode`. (this will be removed in v3) warn_deprecation( examples/gaussian_datatypes/example_automatic.py: 4 warnings examples/gaussian_datatypes/example_explicit.py: 4 warnings test/test_gaussian_datatypes.py: 33 warnings /usr/local/lib/python3.10/dist-packages/pydantic/main.py:1024: PydanticDeprecatedSince20: The `dict` method is deprecated; use `model_dump` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.6/migration/ warnings.warn('The `dict` method is deprecated; use `model_dump` instead.', category=PydanticDeprecatedSince20) examples/gaussian_datatypes/example_automatic.py: 3 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings examples/single_calculations/example_bands.py: 1 warning examples/single_calculations/example_dft.py: 1 warning examples/single_calculations/example_dft_atomic_kinds.py: 1 warning examples/single_calculations/example_failure.py: 1 warning examples/single_calculations/example_geopt.py: 2 warnings examples/single_calculations/example_max_error.py: 1 warning examples/single_calculations/example_mm.py: 1 warning examples/single_calculations/example_mm_md.py: 2 warnings examples/single_calculations/example_multiple_force_eval.py: 1 warning examples/single_calculations/example_no_struct.py: 1 warning examples/single_calculations/example_precision.py: 2 warnings examples/single_calculations/example_restart.py: 3 warnings examples/single_calculations/example_structure_through_file.py: 1 warning examples/workchains/example_base_energy_restart.py: 2 warnings examples/workchains/example_base_failed_restart.py: 2 warnings examples/workchains/example_base_geoopt_restart.py: 8 warnings test/test_gaussian_datatypes.py: 13 warnings /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/backend.py:266: SAWarning: Object of type not in session, add operation along 'DbUser.dbnodes' will not proceed with session.begin_nested() as savepoint: examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:51: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("name", name) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:52: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("element", element) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:53: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("tags", tags) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:54: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("aliases", aliases) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:55: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("n_el", n_el) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:56: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("blocks", blocks) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:57: AiidaDeprecationWarning: `BasisSet.set_attribute` is deprecated, use `BasisSet.base.attributes.set` instead. (this will be removed in v3) self.set_attribute("version", version) examples/gaussian_datatypes/example_automatic.py: 5 warnings examples/gaussian_datatypes/example_explicit.py: 4 warnings test/test_gaussian_datatypes.py: 35 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:102: AiidaDeprecationWarning: `BasisSet.get_attribute` is deprecated, use `BasisSet.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("element", None) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:72: AiidaDeprecationWarning: `Pseudopotential.set_attribute` is deprecated, use `Pseudopotential.base.attributes.set` instead. (this will be removed in v3) self.set_attribute(attr, locals()[attr]) examples/gaussian_datatypes/example_automatic.py: 4 warnings examples/gaussian_datatypes/example_explicit.py: 4 warnings test/test_gaussian_datatypes.py: 29 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:117: AiidaDeprecationWarning: `Pseudopotential.get_attribute` is deprecated, use `Pseudopotential.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("element", None) examples/gaussian_datatypes/example_automatic.py: 3 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings examples/single_calculations/example_bands.py: 3 warnings examples/single_calculations/example_dft.py: 3 warnings examples/single_calculations/example_dft_atomic_kinds.py: 3 warnings examples/single_calculations/example_failure.py: 2 warnings examples/single_calculations/example_geopt.py: 4 warnings examples/single_calculations/example_max_error.py: 3 warnings examples/single_calculations/example_mm.py: 3 warnings examples/single_calculations/example_mm_md.py: 4 warnings examples/single_calculations/example_multiple_force_eval.py: 3 warnings examples/single_calculations/example_no_struct.py: 3 warnings examples/single_calculations/example_precision.py: 4 warnings examples/single_calculations/example_restart.py: 7 warnings examples/single_calculations/example_structure_through_file.py: 3 warnings examples/workchains/example_base_energy_restart.py: 3 warnings examples/workchains/example_base_failed_restart.py: 2 warnings examples/workchains/example_base_geoopt_restart.py: 9 warnings test/test_gaussian_datatypes.py: 18 warnings /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/orm/utils.py:83: SAWarning: Object of type not in session, add operation along 'DbUser.dbnodes' will not proceed (This warning originated from the Session 'autoflush' process, which was invoked automatically in response to a user-initiated operation.) return getattr(self._model, item) examples/gaussian_datatypes/example_automatic.py: 5 warnings examples/gaussian_datatypes/example_explicit.py: 4 warnings test/test_gaussian_datatypes.py: 36 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:111: AiidaDeprecationWarning: `BasisSet.get_attribute` is deprecated, use `BasisSet.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("name", None) examples/gaussian_datatypes/example_automatic.py: 5 warnings examples/gaussian_datatypes/example_explicit.py: 4 warnings test/test_gaussian_datatypes.py: 34 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:126: AiidaDeprecationWarning: `Pseudopotential.get_attribute` is deprecated, use `Pseudopotential.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("name", None) examples/gaussian_datatypes/example_automatic.py: 1 warning examples/gaussian_datatypes/example_explicit.py: 1 warning examples/single_calculations/example_bands.py: 1 warning examples/single_calculations/example_dft.py: 1 warning examples/single_calculations/example_dft_atomic_kinds.py: 1 warning examples/single_calculations/example_failure.py: 1 warning examples/single_calculations/example_geopt.py: 1 warning examples/single_calculations/example_max_error.py: 1 warning examples/single_calculations/example_mm.py: 1 warning examples/single_calculations/example_mm_md.py: 1 warning examples/single_calculations/example_multiple_force_eval.py: 1 warning examples/single_calculations/example_no_struct.py: 1 warning examples/single_calculations/example_precision.py: 1 warning examples/single_calculations/example_restart.py: 2 warnings examples/single_calculations/example_structure_through_file.py: 1 warning examples/workchains/example_base_energy_restart.py: 1 warning examples/workchains/example_base_failed_restart.py: 1 warning examples/workchains/example_base_geoopt_restart.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/orm/querybuilder/main.py:139: SAWarning: Object of type not in session, add operation along 'DbUser.dbnodes' will not proceed (This warning originated from the Session 'autoflush' process, which was invoked automatically in response to a user-initiated operation.) result = build.query.count() examples/gaussian_datatypes/example_automatic.py: 3 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings test/test_gaussian_datatypes.py: 25 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:138: AiidaDeprecationWarning: `BasisSet.get_attribute` is deprecated, use `BasisSet.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("version", None) examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 2 warnings examples/single_calculations/example_bands.py: 1 warning examples/single_calculations/example_dft.py: 1 warning examples/single_calculations/example_dft_atomic_kinds.py: 1 warning examples/single_calculations/example_failure.py: 1 warning examples/single_calculations/example_geopt.py: 1 warning examples/single_calculations/example_max_error.py: 1 warning examples/single_calculations/example_mm.py: 1 warning examples/single_calculations/example_mm_md.py: 1 warning examples/single_calculations/example_multiple_force_eval.py: 1 warning examples/single_calculations/example_no_struct.py: 1 warning examples/single_calculations/example_precision.py: 1 warning examples/single_calculations/example_restart.py: 2 warnings examples/single_calculations/example_structure_through_file.py: 1 warning examples/workchains/example_base_energy_restart.py: 1 warning examples/workchains/example_base_failed_restart.py: 1 warning examples/workchains/example_base_geoopt_restart.py: 3 warnings test/test_gaussian_datatypes.py: 5 warnings /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/backend.py:266: SAWarning: Object of type not in session, add operation along 'DbComputer.dbnodes' will not proceed with session.begin_nested() as savepoint: examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 2 warnings test/test_gaussian_datatypes.py: 17 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:82: AiidaDeprecationWarning: `BasisSet.attributes` is deprecated, use `BasisSet.base.attributes.all` instead. (this will be removed in v3) _dict2basissetdata(self.attributes) examples/gaussian_datatypes/example_automatic.py: 8 warnings examples/gaussian_datatypes/example_explicit.py: 8 warnings test/test_gaussian_datatypes.py: 53 warnings /usr/local/lib/python3.10/dist-packages/pydantic/main.py:1069: PydanticDeprecatedSince20: The `parse_obj` method is deprecated; use `model_validate` instead. Deprecated in Pydantic V2.0 to be removed in V3.0. See Pydantic V2 Migration Guide at https://errors.pydantic.dev/2.6/migration/ warnings.warn( examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings test/test_gaussian_datatypes.py: 22 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:120: AiidaDeprecationWarning: `BasisSet.get_attribute` is deprecated, use `BasisSet.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("aliases", []) examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 2 warnings test/test_gaussian_datatypes.py: 17 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:129: AiidaDeprecationWarning: `BasisSet.get_attribute` is deprecated, use `BasisSet.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("tags", []) examples/gaussian_datatypes/example_automatic.py: 3 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings test/test_gaussian_datatypes.py: 24 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:153: AiidaDeprecationWarning: `Pseudopotential.get_attribute` is deprecated, use `Pseudopotential.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("version", None) examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 2 warnings test/test_gaussian_datatypes.py: 16 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:97: AiidaDeprecationWarning: `Pseudopotential.attributes` is deprecated, use `Pseudopotential.base.attributes.all` instead. (this will be removed in v3) _dict2pseudodata(self.attributes) examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 3 warnings test/test_gaussian_datatypes.py: 20 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:135: AiidaDeprecationWarning: `Pseudopotential.get_attribute` is deprecated, use `Pseudopotential.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("aliases", []) examples/gaussian_datatypes/example_automatic.py: 2 warnings examples/gaussian_datatypes/example_explicit.py: 2 warnings test/test_gaussian_datatypes.py: 16 warnings /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:144: AiidaDeprecationWarning: `Pseudopotential.get_attribute` is deprecated, use `Pseudopotential.base.attributes.get` instead. (this will be removed in v3) return self.get_attribute("tags", []) examples/gaussian_datatypes/example_automatic.py::example_gdt examples/gaussian_datatypes/example_explicit.py::example_gdt test/test_gaussian_datatypes.py::test_validation test/test_gaussian_datatypes.py::test_validation_mfe test/test_gaussian_datatypes.py::test_without_kinds test/test_gaussian_datatypes.py::test_multiple_kinds test/test_gaussian_datatypes.py::test_multiple_kinds_auto /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/basisset/data.py:301: AiidaDeprecationWarning: `BasisSet.attributes` is deprecated, use `BasisSet.base.attributes.all` instead. (this will be removed in v3) for line in _dict2basissetdata(self.attributes).cp2k_format_line_iter(): examples/gaussian_datatypes/example_automatic.py::example_gdt examples/gaussian_datatypes/example_explicit.py::example_gdt test/test_gaussian_datatypes.py::test_validation test/test_gaussian_datatypes.py::test_validation_mfe test/test_gaussian_datatypes.py::test_without_kinds test/test_gaussian_datatypes.py::test_multiple_kinds test/test_gaussian_datatypes.py::test_multiple_kinds_auto /usr/local/lib/python3.10/dist-packages/aiida_gaussian_datatypes/pseudopotential/data.py:337: AiidaDeprecationWarning: `Pseudopotential.attributes` is deprecated, use `Pseudopotential.base.attributes.all` instead. (this will be removed in v3) for line in _dict2pseudodata(self.attributes).cp2k_format_line_iter(): examples/single_calculations/example_bands.py: 1 warning examples/single_calculations/example_dft.py: 1 warning examples/single_calculations/example_dft_atomic_kinds.py: 1 warning examples/single_calculations/example_failure.py: 1 warning examples/single_calculations/example_geopt.py: 1 warning examples/single_calculations/example_max_error.py: 1 warning examples/single_calculations/example_mm.py: 1 warning examples/single_calculations/example_mm_md.py: 1 warning examples/single_calculations/example_multiple_force_eval.py: 1 warning examples/single_calculations/example_no_struct.py: 1 warning examples/single_calculations/example_precision.py: 1 warning examples/single_calculations/example_restart.py: 2 warnings examples/single_calculations/example_structure_through_file.py: 1 warning test/test_gaussian_datatypes.py: 8 warnings /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/orm/nodes.py:223: SAWarning: Object of type not in session, add operation along 'DbComputer.dbnodes' will not proceed session.commit() examples/single_calculations/example_dft_atomic_kinds.py::example_dft_atomic_kinds examples/single_calculations/example_max_error.py::example_dft examples/single_calculations/example_restart.py::example_restart examples/workchains/example_base_geoopt_restart.py::example_base examples/workchains/example_base_geoopt_restart.py::example_base examples/workchains/example_base_geoopt_restart.py::example_base /usr/local/lib/python3.10/dist-packages/aiida/storage/psql_dos/orm/utils.py:118: SAWarning: Object of type not in session, add operation along 'DbUser.dbnodes' will not proceed self.session.commit() ../../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_geoopt_restart.py::example_base - Key... ============ 1 failed, 48 passed, 814 warnings in 367.73s (0:06:07) ============ Summary: Something is wrong with aiida-cp2k commit 01564a7. Status: FAILED Removing intermediate container b31b95537895 ---> 0e703b9c06e5 Step 40/41 : CMD cat $(find ./report.log -mmin +10) | sed '/^Summary:/ s/$/ (cached)/' ---> Running in 317146c16069 Removing intermediate container 317146c16069 ---> 02c34e0b5349 Step 41/41 : ENTRYPOINT [] ---> Running in 60b3d050dd43 Removing intermediate container 60b3d050dd43 ---> 04d0088aff23 [Warning] One or more build-args [GIT_COMMIT_SHA] were not consumed Successfully built 04d0088aff23 Successfully tagged us-central1-docker.pkg.dev/cp2k-org-project/cp2kci/img_cp2k-aiida:master Pushing new image... done. #################### Running Image cp2k-aiida #################### EndDate: 2024-03-02 06:23:01+00:00