conformance tests: failed checksum comparison (133)

[audrium]

Workflow finishes successfully, but

cwl ❯ cwltest --tool /home/amecioni/.virtualenvs/cwl/bin/reana-cwl-runner --test=conformance_test_v1.0.yaml -n133 --basedir /home/amecioni/Documents/tests/common-workflow-language/v1.0   --

Test [133/197] env_home_tmpdir_docker_complex: Test $HOME and $TMPDIR are set correctly in Docker without using return code
/home/amecioni/.virtualenvs/cwl/bin/reana-cwl-runner--outdir=/tmp/tmpnkz38c8s--quietv1.0/envvar3.cwlv1.0/empty.jsonTest 133 failed: /home/amecioni/.virtualenvs/cwl/bin/reana-cwl-runner --outdir=/tmp/tmpnkz38c8s --quiet v1.0/envvar3.cwl v1.0/empty.json
Test $HOME and $TMPDIR are set correctly in Docker without using return code
Compare failure expected: {
    "results": {
        "basename": "results",
        "checksum": "sha1$7d5ca8c0c03e883c56c4eb1ef6f6bb9bccad4d86",
        "class": "File",
        "size": 8
    }
}
got: {
    "results": {
        "basename": "results",
        "checksum": "sha1$957e6915fce641da594630569e806811b253b325",
        "class": "File",
        "http://commonwl.org/cwltool#generation": 0,
        "location": "file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/3bb2c6f5-e056-4d90-9f57-3e404a8692e1/outputs/results",
        "nameext": "",
        "nameroot": "results",
        "size": 8
    }
}
caused by: failed comparison for key 'results': expected: {
    "basename": "results",
    "checksum": "sha1$7d5ca8c0c03e883c56c4eb1ef6f6bb9bccad4d86",
    "class": "File",
    "size": 8
}
got: {
    "basename": "results",
    "checksum": "sha1$957e6915fce641da594630569e806811b253b325",
    "class": "File",
    "http://commonwl.org/cwltool#generation": 0,
    "location": "file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/3bb2c6f5-e056-4d90-9f57-3e404a8692e1/outputs/results",
    "nameext": "",
    "nameroot": "results",
    "size": 8
}
caused by: field 'checksum' failed comparison: expected: "sha1$7d5ca8c0c03e883c56c4eb1ef6f6bb9bccad4d86"
got: "sha1$957e6915fce641da594630569e806811b253b325"
0 tests passed, 1 failures, 0 unsupported features

[mr-c]

@audrium Can you share contents of the results file here?

[audrium]

@audrium Can you share contents of the results file here?

It consists of a single word: failure :)

I see that test workflow command executes something like this:

...
if [ "$HOME" = "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/0c80b005-87f3-4b3e-8a91-c361b14fec74/cwl/docker_outdir" ] && [ "$TMPDIR" = "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/0c80b005-87f3-4b3e-8a91-c361b14fec74/cwl/docker_tmpdir" ]
then
    echo success > results
else
    echo failure > results
...

Checked docker_outdir, there is identical results file there with failure in it as well

[tiborsimko]

Does cwltool itself pass all the reference test suite?

[mr-c]

Does cwltool itself pass all the reference test suite?

It does

[mr-c]

@audrium Are there execution logs available? How are you invoking the container? You can modify the test to print the values of $HOME and $TMPDIR to help with troubleshooting.

Here's the result of running this test with plain cwltool and --debug

$ /home/michael/cwltool/env3.9/bin/cwltool --debug  v1.0/envvar3.cwl v1.0/empty.json
INFO /home/michael/cwltool/env3.9/bin/cwltool 3.1.20210816212154
INFO Resolved 'v1.0/envvar3.cwl' to 'file:///home/michael/common-workflow-language/v1.0/v1.0/envvar3.cwl'
DEBUG [job envvar3.cwl] initializing from file:///home/michael/common-workflow-language/v1.0/v1.0/envvar3.cwl
DEBUG [job envvar3.cwl] {}
DEBUG [job envvar3.cwl] path mappings is {}
DEBUG [job envvar3.cwl] command line bindings is [
    {
        "shellQuote": false,
        "valueFrom": "echo HOME=$HOME TMPDIR=$TMPDIR # > log\nif [ \"$HOME\" = \"$(runtime.outdir)\" ] && [ \"$TMPDIR\" = \"$(runtime.tmpdir)\" ]\nthen\n    echo success > results\nelse\n    echo failure > results\nfi\n",
        "position": [
            0,
            0
        ]
    }
]
DEBUG [job envvar3.cwl] initial work dir {}
WARNING [job envvar3.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance.
INFO [job envvar3.cwl] /tmp/jh7tnyyh$ docker \
    run \
    -i \
    --mount=type=bind,source=/tmp/jh7tnyyh,target=/cbourI \
    --mount=type=bind,source=/tmp/hr0jqg_z,target=/tmp \
    --workdir=/cbourI \
    --read-only=true \
    --user=1000:1000 \
    --rm \
    --cidfile=/tmp/5ke1nnmz/20210830192003-813113.cid \
    --env=TMPDIR=/tmp \
    --env=HOME=/cbourI \
    debian:stretch-slim \
    /bin/sh \
    -c \
    echo HOME=$HOME TMPDIR=$TMPDIR # > log
if [ "$HOME" = "/cbourI" ] && [ "$TMPDIR" = "/tmp" ]
then
    echo success > results
else
    echo failure > results
fi
HOME=/cbourI TMPDIR=/tmp
INFO [job envvar3.cwl] Max memory used: 0MiB
INFO [job envvar3.cwl] completed success
DEBUG [job envvar3.cwl] outputs {
    "results": {
        "location": "file:///tmp/jh7tnyyh/results",
        "basename": "results",
        "nameroot": "results",
        "nameext": "",
        "class": "File",
        "checksum": "sha1$7d5ca8c0c03e883c56c4eb1ef6f6bb9bccad4d86",
        "size": 8,
        "http://commonwl.org/cwltool#generation": 0
    }
}
DEBUG [job envvar3.cwl] Removing input staging directory /tmp/dfs78ozg
DEBUG [job envvar3.cwl] Removing temporary directory /tmp/hr0jqg_z
DEBUG Moving /tmp/jh7tnyyh/results to /home/michael/common-workflow-language/v1.0/results
{
    "results": {
        "location": "file:///home/michael/common-workflow-language/v1.0/results",
        "basename": "results",
        "class": "File",
        "checksum": "sha1$7d5ca8c0c03e883c56c4eb1ef6f6bb9bccad4d86",
        "size": 8,
        "path": "/home/michael/common-workflow-language/v1.0/results"
    }
}
INFO Final process status is success
(env3.9) michael@mrc-tux:~/common-workflow-language/v1.0$ cat results 
success

[audrium]

@audrium Are there execution logs available? How are you invoking the container? You can modify the test to print the values of $HOME and $TMPDIR to help with troubleshooting.

I'm running the tests in a following way:

reana-cwl-runner --outdir=/tmp/tmpjtdf817v --quiet v1.0/envvar3.cwl v1.0/empty.json

or

cwltest --tool /home/amecioni/.virtualenvs/cwl/bin/reana-cwl-runner --test=conformance_test_v1.0.yaml -n133 --basedir /home/amecioni/Documents/tests/common-workflow-language/v1.0   --

Here are the full logs:

reana ❯ rc logs -w cwl-test.9
==> Workflow engine logs
{'results': {'location': 'file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/outputs/results', 'basename': 'results', 'nameroot': 'results', 'nameext': '', 'class': 'File', 'checksum': 'sha1$957e6915fce641da594630569e806811b253b325', 'size': 8, 'http://commonwl.org/cwltool#generation': 0}}

running workflow on context: {'publisher': <reana_commons.publisher.WorkflowStatusPublisher object at 0x7fc9c1bb8040>, 'rjc_api_client': <reana_commons.api_client.JobControllerAPIClient object at 0x7fc9c146d580>, 'workflow_uuid': '20a24f22-2c8a-4b6a-b40e-575c229173b9', 'workflow_workspace': '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9', 'workflow_json': {'arguments': [{'shellQuote': False, 'valueFrom': 'echo HOME="$HOME"\necho runtime.outdir="$(runtime.outdir)"\necho TMPDIR="$TMPDIR"\necho runtime.tmpdir="$(runtime.tmpdir)"\n\nif [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ]\nthen\n    echo success > results\nelse\n    echo failure > results\nfi\n'}], 'class': 'CommandLineTool', 'cwlVersion': 'v1.0', 'hints': [{'class': 'DockerRequirement', 'dockerPull': 'debian:stretch-slim'}, {'class': 'ResourceRequirement', 'ramMin': 8}], 'id': '#main', 'inputs': [], 'outputs': [{'id': '#main/results', 'outputBinding': {'glob': 'results'}, 'type': 'File'}], 'requirements': [{'class': 'ShellCommandRequirement'}]}, 'workflow_parameters': {}, 'operational_options': [], 'kwargs': {'workflow_file': 'None'}}
2021-08-31 08:21:52,830 | reana-workflow-engine-cwl | MainThread | INFO | running workflow on context: {'publisher': <reana_commons.publisher.WorkflowStatusPublisher object at 0x7fc9c1bb8040>, 'rjc_api_client': <reana_commons.api_client.JobControllerAPIClient object at 0x7fc9c146d580>, 'workflow_uuid': '20a24f22-2c8a-4b6a-b40e-575c229173b9', 'workflow_workspace': '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9', 'workflow_json': {'arguments': [{'shellQuote': False, 'valueFrom': 'echo HOME="$HOME"\necho runtime.outdir="$(runtime.outdir)"\necho TMPDIR="$TMPDIR"\necho runtime.tmpdir="$(runtime.tmpdir)"\n\nif [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ]\nthen\n    echo success > results\nelse\n    echo failure > results\nfi\n'}], 'class': 'CommandLineTool', 'cwlVersion': 'v1.0', 'hints': [{'class': 'DockerRequirement', 'dockerPull': 'debian:stretch-slim'}, {'class': 'ResourceRequirement', 'ramMin': 8}], 'id': '#main', 'inputs': [], 'outputs': [{'id': '#main/results', 'outputBinding': {'glob': 'results'}, 'type': 'File'}], 'requirements': [{'class': 'ShellCommandRequirement'}]}, 'workflow_parameters': {}, 'operational_options': [], 'kwargs': {'workflow_file': 'None'}}
Dumping workflow specification and input parameter files...
2021-08-31 08:21:52,830 | reana-workflow-engine-cwl | MainThread | INFO | Dumping workflow specification and input parameter files...
parsing arguments ...
2021-08-31 08:21:52,846 | reana-workflow-engine-cwl | MainThread | INFO | parsing arguments ...
starting the run..
2021-08-31 08:21:52,850 | reana-workflow-engine-cwl | MainThread | INFO | starting the run..
INFO /usr/local/bin/run-cwl-workflow 0.8.0a2 with cwltool 3.1.20210628163208
2021-08-31 08:21:52,857 | cwltool | MainThread | INFO | /usr/local/bin/run-cwl-workflow 0.8.0a2 with cwltool 3.1.20210628163208
INFO Resolved 'workflow.json#main' to 'file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/workflow.json#main'
2021-08-31 08:21:52,860 | cwltool | MainThread | INFO | Resolved 'workflow.json#main' to 'file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/workflow.json#main'
[job main] CREATED TASK MSG----------------------
2021-08-31 08:21:53,940 | reana-workflow-engine-cwl | MainThread | INFO | [job main] CREATED TASK MSG----------------------
{'cmd': "/bin/sh -c 'umask 2;export "
        'TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf";export '
        'HOME="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir";export '
        'PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir '
        '-p '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
        '&& cd '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
        '&& echo HOME="$HOME"\n'
        'echo '
        'runtime.outdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir"\n'
        'echo TMPDIR="$TMPDIR"\n'
        'echo '
        'runtime.tmpdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir"\n'
        '\n'
        'if [ "$HOME" = '
        '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir" '
        '] && [ "$TMPDIR" = '
        '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir" '
        ']\n'
        'then\n'
        '    echo success > results\n'
        'else\n'
        '    echo failure > results\n'
        'fi; cp -r '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir/* '
        "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/outdir/n183z_lx' ",
 'compute_backend': None,
 'cvmfs_mounts': 'false',
 'htcondor_accounting_group': None,
 'htcondor_max_runtime': None,
 'image': 'debian:stretch-slim',
 'job_name': 'main',
 'kerberos': None,
 'kubernetes_memory_limit': None,
 'kubernetes_uid': None,
 'prettified_cmd': "/bin/sh -c 'umask 2;export "
                   'TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf";export '
                   'HOME="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir";export '
                   'PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir '
                   '-p '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
                   '&& cd '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
                   '&& echo HOME="$HOME"\n'
                   'echo '
                   'runtime.outdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir"\n'
                   'echo TMPDIR="$TMPDIR"\n'
                   'echo '
                   'runtime.tmpdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir"\n'
                   '\n'
                   'if [ "$HOME" = '
                   '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir" '
                   '] && [ "$TMPDIR" = '
                   '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir" '
                   ']\n'
                   'then\n'
                   '    echo success > results\n'
                   'else\n'
                   '    echo failure > results\n'
                   'fi; cp -r '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir/* '
                   "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/outdir/n183z_lx' ",
 'unpacked_img': None,
 'voms_proxy': None,
 'workflow_uuid': '20a24f22-2c8a-4b6a-b40e-575c229173b9',
 'workflow_workspace': '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9'}
2021-08-31 08:21:53,941 | reana-workflow-engine-cwl | MainThread | INFO | {'cmd': "/bin/sh -c 'umask 2;export "
        'TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf";export '
        'HOME="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir";export '
        'PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir '
        '-p '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
        '&& cd '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
        '&& echo HOME="$HOME"\n'
        'echo '
        'runtime.outdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir"\n'
        'echo TMPDIR="$TMPDIR"\n'
        'echo '
        'runtime.tmpdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir"\n'
        '\n'
        'if [ "$HOME" = '
        '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir" '
        '] && [ "$TMPDIR" = '
        '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir" '
        ']\n'
        'then\n'
        '    echo success > results\n'
        'else\n'
        '    echo failure > results\n'
        'fi; cp -r '
        '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir/* '
        "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/outdir/n183z_lx' ",
 'compute_backend': None,
 'cvmfs_mounts': 'false',
 'htcondor_accounting_group': None,
 'htcondor_max_runtime': None,
 'image': 'debian:stretch-slim',
 'job_name': 'main',
 'kerberos': None,
 'kubernetes_memory_limit': None,
 'kubernetes_uid': None,
 'prettified_cmd': "/bin/sh -c 'umask 2;export "
                   'TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf";export '
                   'HOME="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir";export '
                   'PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir '
                   '-p '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
                   '&& cd '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir '
                   '&& echo HOME="$HOME"\n'
                   'echo '
                   'runtime.outdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir"\n'
                   'echo TMPDIR="$TMPDIR"\n'
                   'echo '
                   'runtime.tmpdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir"\n'
                   '\n'
                   'if [ "$HOME" = '
                   '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir" '
                   '] && [ "$TMPDIR" = '
                   '"/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir" '
                   ']\n'
                   'then\n'
                   '    echo success > results\n'
                   'else\n'
                   '    echo failure > results\n'
                   'fi; cp -r '
                   '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir/* '
                   "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/outdir/n183z_lx' ",
 'unpacked_img': None,
 'voms_proxy': None,
 'workflow_uuid': '20a24f22-2c8a-4b6a-b40e-575c229173b9',
 'workflow_workspace': '/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9'}
[job main] SUBMITTED TASK --------------------
2021-08-31 08:21:54,220 | reana-workflow-engine-cwl | MainThread | INFO | [job main] SUBMITTED TASK --------------------
[job main] task id: f40d5488-3793-49f4-bc48-1a3b69581d92
2021-08-31 08:21:54,220 | reana-workflow-engine-cwl | MainThread | INFO | [job main] task id: f40d5488-3793-49f4-bc48-1a3b69581d92
[job main] FINAL JOB STATE: finished ------------------
2021-08-31 08:21:59,247 | reana-workflow-engine-cwl | main | INFO | [job main] FINAL JOB STATE: finished ------------------
[job main] task id: f40d5488-3793-49f4-bc48-1a3b69581d92
2021-08-31 08:21:59,268 | reana-workflow-engine-cwl | main | ERROR | [job main] task id: f40d5488-3793-49f4-bc48-1a3b69581d92
[job main] OUTPUTS ------------------
2021-08-31 08:21:59,320 | reana-workflow-engine-cwl | main | INFO | [job main] OUTPUTS ------------------
FinalOutput{'results': {'location': 'file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/outputs/results', 'basename': 'results', 'nameroot': 'results', 'nameext': '', 'class': 'File', 'checksum': 'sha1$957e6915fce641da594630569e806811b253b325', 'size': 8, 'http://commonwl.org/cwltool#generation': 0}}FinalOutput
2021-08-31 08:21:59,393 | reana-workflow-engine-cwl | MainThread | INFO | FinalOutput{'results': {'location': 'file:///var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/outputs/results', 'basename': 'results', 'nameroot': 'results', 'nameext': '', 'class': 'File', 'checksum': 'sha1$957e6915fce641da594630569e806811b253b325', 'size': 8, 'http://commonwl.org/cwltool#generation': 0}}FinalOutput
INFO Final process status is success
2021-08-31 08:21:59,393 | cwltool | MainThread | INFO | Final process status is success
workflow done
2021-08-31 08:21:59,394 | reana-workflow-engine-cwl | MainThread | INFO | workflow done
2021-08-31 08:21:59,394 | root | MainThread | INFO | Workflow 20a24f22-2c8a-4b6a-b40e-575c229173b9 finished. Files available at /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9.
workflow_spec: {'arguments': [{'shellQuote': False, 'valueFrom': 'echo HOME="$HOME"\necho runtime.outdir="$(runtime.outdir)"\necho TMPDIR="$TMPDIR"\necho runtime.tmpdir="$(runtime.tmpdir)"\n\nif [ "$HOME" = "$(runtime.outdir)" ] && [ "$TMPDIR" = "$(runtime.tmpdir)" ]\nthen\n    echo success > results\nelse\n    echo failure > results\nfi\n'}], 'class': 'CommandLineTool', 'cwlVersion': 'v1.0', 'hints': [{'class': 'DockerRequirement', 'dockerPull': 'debian:stretch-slim'}, {'class': 'ResourceRequirement', 'ramMin': 8}], 'id': '#main', 'inputs': [], 'outputs': [{'id': '#main/results', 'outputBinding': {'glob': 'results'}, 'type': 'File'}], 'requirements': [{'class': 'ShellCommandRequirement'}]}




==> Job logs
==> Step: main
==> Workflow ID: 20a24f22-2c8a-4b6a-b40e-575c229173b9
==> Compute backend: Kubernetes
==> Job ID: reana-run-job-22965abd-0b91-4911-9998-3a813a0428f1
==> Docker image: debian:stretch-slim
==> Command: /bin/sh -c 'umask 2;export TMPDIR="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf";export HOME="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir";export PATH="/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin";mkdir -p /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir && cd /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir && echo HOME="$HOME"
echo runtime.outdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir"
echo TMPDIR="$TMPDIR"
echo runtime.tmpdir="/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir"

if [ "$HOME" = "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir" ] && [ "$TMPDIR" = "/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir" ]
then
    echo success > results
else
    echo failure > results
fi; cp -r /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir/* /var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/outdir/n183z_lx'
==> Status: finished
==> Started: 2021-08-31T08:21:54
==> Finished: 2021-08-31T08:21:59
==> Logs:
job: :
 HOME=/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir
runtime.outdir=/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_outdir
TMPDIR=/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/tmpdir/o3ag03xf
runtime.tmpdir=/var/reana/users/00000000-0000-0000-0000-000000000000/workflows/20a24f22-2c8a-4b6a-b40e-575c229173b9/cwl/docker_tmpdir

I've modified the test output a bit to print the values of $HOME, runtime.outdir, $TMPDIR and runtime.tmpdir (in the very end) and as you can see the test fail because runtime.tmpdir does not match TMPDIR. Any ideas why this could happen?

[mr-c]

Any ideas why this could happen?

Something specific to reana-workflow-engine-cwl I presume