Rerun Toil Slurm batch mode with 9.5.0 and dev cwltest

[kinow]

Partially addresses #30

[kinow]

Current results for FT3 with toil 9.5.0 and dev cwltest.

vs. the thesis previous results with toil 9.4.1 and latest cwltest from PyPI.

[kinow]

On LUMI, the local and slurm tests passed similar to how they did in the thesis. But the batch tests failed.

I was trying to launch them in parallel, as the queues on LUMI are slower than on CESGA FT3. @mr-c found a regression in Toil 9.5.0 (newer version, that I was trying to use): DataBiosphere/toil#5581

With this regression, not specifying a job store caused Toil to fail. I got about 5, 10 success tests, and all remaining tests failing in CWL v1.0.

I replaced 9.5.0 by 9.4.1, and adjusted the job again. Unfortunately, now the jobs started failing due to timeout (10 minutes, 600 seconds). So I set the timeout to 1 hour.

The tests still failed, with KeyboardInterrupt. I think LUMI's Slurm is sending a SIGINT, but it might be a Slurm/LUMI error, and not necessarily another problem with cwltest or Toil. But it's quite hard to debug this without spending many hours.

So instead I will stash what I have, include only the updated CESGA FT3 tests, skip the MN5 + container tests, and do a final test on Fugaku with cwltest + cwltool.

[kinow]

Fugaku

$ ssh fugaku
$ python3.11 -m venv venv
$ source venv/bin/activate
$ pip install cwltool cwltest
$ cwltool --version
/vol0006/mdt1/home/USER/venv/bin/cwltool 3.2.20260720092025

I tested CWL v1.0 (latest main branch) only, as it has less tests. I used cwltool 3.2.20260720092025.

$ git clone https://github.com/common-workflow-language/common-workflow-language.git
$ cd common-workflow-language/
$ cd v1.0/
$ cwltest --test conformance_test_v1.0.yaml --tool=cwltool -j 4 --junit-verbose --junit-xml junit.xml -- --singularity --enable-dev
Test [1/197] cl_basic_generation: General test of command line generation
Test [2/197] nested_prefixes_arrays: Test nested prefixes with arrays
Test [3/197] nested_cl_bindings: Test nested command line bindings
...
...
...
All tests passed
$ hostname
fn01sv04

[kinow]

Righto. Going to merge this one once CICD passes, and then create a new PR for Fugaku.