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cwltool Freezes When Not Using Inputs in Scatter Parallelization #2031

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gen740 opened this issue Aug 8, 2024 · 0 comments
Open

cwltool Freezes When Not Using Inputs in Scatter Parallelization #2031

gen740 opened this issue Aug 8, 2024 · 0 comments

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@gen740
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gen740 commented Aug 8, 2024

Expected Behavior

Successfully runs.

Actual Behavior

cwltool freezes.

Workflow Code

cwlVersion: v1.2
class: Workflow
inputs:
  targets:
    type: string[]
requirements:
  ScatterFeatureRequirement: {}
steps:
  job:
    in:
      target: targets
    scatter: target
    scatterMethod: dotproduct
    run:
      inputs:
        target:
          type: string
      class: CommandLineTool
      baseCommand: ls
      outputs: []
    out: []
outputs: []
  • with cwltool --parallel --cachedir=./cache repro.cwl --targets "A" --targets "B"

Full Traceback

INFO /Users/gen/home/tmp/venv/bin/cwltool 3.1.20240708091337
INFO Resolved 'test.cwl' to 'file:///Users/gen/home/tmp/test.cwl'
WARNING Error checking CUDA version with nvidia-smi: [Errno 2] No such file or directory: 'nvidia-smi'
DEBUG Parsed job order from command line: {
    "__id": "test.cwl",
    "targets": [
        "A",
        "B"
    ]
}
DEBUG [workflow ] initialized from file:///Users/gen/home/tmp/test.cwl
DEBUG [workflow ] inputs {
    "targets": [
        "A",
        "B"
    ]
}
INFO [workflow ] starting step job
INFO [step job] start
DEBUG job: <cwltool.workflow_job.WorkflowJob object at 0x105162510>, runtime_context: <cwltool.context.RuntimeContext object at 0x102414610>, TMPDIR_LOCK: <unlocked _thread.lock object at 0x104cabc80>
INFO [workflow ] start
DEBUG [job job] keydictstr is {"cmdline":["ls"]} -> a09766136709aa2e858984e35fe3ca63
INFO [job job] Output of job will be cached in /Users/gen/home/tmp/.cache/a09766136709aa2e858984e35fe3ca63
DEBUG [job job] initializing from _:0b038dc5-e3da-45de-8f98-d4b5ce005d90 as part of step job
DEBUG [job job] {
    "target": "A"
}
DEBUG [job job] path mappings is {}
DEBUG [job job] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "ls"
    }
]
INFO [step job] start
DEBUG job: CommandLineJob(job), runtime_context: <cwltool.context.RuntimeContext object at 0x102414610>, TMPDIR_LOCK: <unlocked _thread.lock object at 0x104cabc80>
DEBUG [job job] initial work dir {}
INFO [job job] /Users/gen/home/tmp/.cache/a09766136709aa2e858984e35fe3ca63$ ls
DEBUG [job job_2] keydictstr is {"cmdline":["ls"]} -> a09766136709aa2e858984e35fe3ca63
DEBUG Could not collect memory usage, job ended before monitoring began.
INFO [job job] completed success
DEBUG [job job] outputs {}

Your Environment

  • cwltool version: /Users/gen/home/tmp/venv/bin/cwltool 3.1.20240708091337
  • macOS Sonoma 14.6.1
  • python 3.12.4, 3.11.9
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