Open
Description
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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