Added max-cpu-factor, max-mem-factor and --customTag #1
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GallVp
commented
Apr 15, 2025
| @@ -46,3 +50,17 @@ def __init__(self, config_file=_CONFIG_FILE): | |||
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| def parameters(self): | |||
| return self._parameters | |||
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| def max_cpu_factor(self): | |||
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These parameters make the profile behave similar to nf-float.
The maxFactors are very useful for finding spot instances when running lots of jobs of the same kind in parallel.
GallVp
commented
Apr 15, 2025
| @@ -69,6 +75,11 @@ def submit_job(self, job_file): | |||
| cmd.extend(['--job', job_file]) | |||
| cmd.extend(shlex.split(config_parameters.get('submit-extra', ''))) | |||
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| rule_name = job_properties.get('rule') | |||
| cmd.extend(['--customTag', f"nextflow-io-run-name:{job_prefix}"]) | |||
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This is sort of a hack of a hack to bundle the jobs into a workflow on MM Cloud OpCentre. I feel we should document this behaviour on https://docs.memverge.com/MMCloud/latest/. The nextflow-io bit can be misleading for the users, though.
GallVp
commented
Apr 15, 2025
| LOG_FILE = ( | ||
| '.snakemake/log/' | ||
| f"{os.environ.get('SNAKEMAKE_CLUSTER_SIDECAR_VARS', 'snakemake')}" | ||
| '.float.log' | ||
| ) | ||
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| log_level = os.environ.get('SNAKEMAKE_FLOAT_LOG_LEVEL', 'INFO') | ||
| match log_level: |
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This was not supported by Python 3.9 which is what verkko requires.
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Hi @edwinyyyu
cc. @sateeshperi
I am testing the profile with verkko and have made a couple of changes that I hope can be generally useful. Kindly see the changelog.