Problems with Snakemake 5.6.0 standard resources

[holtgrewe]

Apparently, Snakemake >=5.6.0 defines

• mem_mb
• disk_mb
• tmpdir

by default, cf.

• https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#standard-resources

At least the standard value for mem_mb has a higher precedence when using the snakemake profile than mem.

E.g.,

rule foo:
  resources:
    mem='8G'

Will lead to using the mem_mb=1000 from the defaults.

[holtgrewe]

This also leads to mem_per_thread not being settable.

sbatch: fatal: --mem, --mem-per-cpu, and --mem-per-gpu are mutually exclusive.
Traceback (most recent call last):
  File "/etc/xdg/snakemake/cubi-v1/slurm-submit.py", line 82, in <module>
    jobid = slurm_utils.submit_job(jobscript, **sbatch_options)
  File "/etc/xdg/snakemake/cubi-v1/slurm_utils.py", line 182, in submit_job
    raise e
  File "/etc/xdg/snakemake/cubi-v1/slurm_utils.py", line 180, in submit_job
    res = sp.check_output(cmd)
  File "/data/gpfs-1/users/euskircp_c/work/miniconda/lib/python3.7/subprocess.py", line 411, in check_output
    **kwargs).stdout
  File "/data/gpfs-1/users/euskircp_c/work/miniconda/lib/python3.7/subprocess.py", line 512, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['sbatch', '--parsable', '--cluster=cubi', '--time=02:00:00', '--mem=5532', '--mem-per-cpu=6G', '--cpus-per-task=12',...

[percyfal]

I can reproduce this using snakemake>=7.0. The proper place to apply a patch I would guess is here

[bs-az]

My solution to this was to change the order of priority here and therefore run convert_job_properties() before applying any defaults from my cluster_config.json. When using the HPC profile I don't really want the resources from the Snakefile anyway since they would be tuned for local execution and not for SLURM, but I understand the order is based on preference.

Edit for clarity: I mean I don't want any resources from the Snakefile to take priority over those in __defaults__ if there is a name clash.

[johnstonmj]

I am also encountering inconsistent resource mapping in combination with Snakemake 7.6.2.

Setting

resources:
    mem_mb = 30000

Works with scontrol show jobid indicating 30000M memory.

But
mem = 30000
or
mem = "30G"

Only provide the default 1000M.