Too many arguments on the command line

CWL Questions
22

Oks then should I wait for a fix?
Unfortunately cwltool is not an option as I cant submit slurm jobs with it.
So I guess I will just to work around this issue in the workflow directly in the meantime.

23

Hi @matmanc, I’ve created a Toil issue: https://github.com/DataBiosphere/toil/issues/3358 and will work on providing a fix for you.

1 Like
24

While a fix is being developed, can you try this workaround first?

ulimit -s unlimited
1 Like
25

So close, that could work on a single node, but probably not when the jobs go to slurm. Unless there’s a way to set ulimits with slurm.

26
27

I think it is a reasonable request for a cluster admin.

28

@matmanc So that gives you something else to try, at least.

29

Thanks! I think I will wait for the fix. Meanwhile we rewrote the workflow to avoid these situations. Basically collecting the infos from the different directories first and the aggregating the files. This is obviously a temporary workaround. So I hope the fix will be available soon.

30

If you have been following along on github, the Toil team takes it seriously and they are working on it.

31

I have been having similar issues. I was trying to get around it by using InitialWorkDirRequirement to put all the input files into a directory.

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: some_dir # <- put all the input files into a dir
        writable: true
        entry: "$({class: 'Directory', listing: inputs.input_files})"

This seems to “fix” the Singularity CLI arg issues because when you do this, the only --bind arg that it uses is the one for the directory that you put all the files into.

However, I ended up running into this issue instead:

So, it appears that this solution might work well if you are sure that your input files /dirs all have unique basenames, but you will have problems if the names conflict.

1 Like
32

Also worth noting that Singularity might not immediately break from these issues with long command lines; I had cases where it would stall out completely, as reported in here; Singularity exec stops working when command line args are too long · Issue #5815 · hpcng/singularity · GitHub