common-workflow-language / common-workflow-language/cwltest
Conformance tests failing on BSC MareNostrum5 due to home directories being symlinks to GPFS
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Descrizione
Hi,
I tried to run the CWL Conformance Tests with StreamFlow on BSC MareNostrum5, and nearly all tests failed with the same error.
```
FileNotFoundError: [Errno 2] No such file or directory: '/gpfs/home/bsc//cwl/streamflow/file:/home/bsc//cwl/streamflow/common-workflow-language-1c1f122f780075d910fdfdea7e15e46eef3c078d/v1.0/v1.0/no-inputs-wf.cwl'
```
@GlassOfWhiskey helped me troubleshoot it, and apparently cwltest has some code that fails to resolve symlinks, and instead concatenates two directories. Iacopo shared this code with me on Element, so copying it here in case it helps:
https://github.com/common-workflow-language/cwltest/blob/b13d814489f2268382e0917596fa5035ecab8f68/src/cwltest/utils.py#L407-L421
Some context: https://github.com/kinow/cwl-mpi/issues/20#issuecomment-4374332230
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