Re: GNU Parallel Bug Reports The bugid: swap_activity_file-r

[Ole Tange]

On Wed, Jan 30, 2019 at 7:58 PM Dhawal Jain <address@hidden> wrote:
:
> However, often times, I get the following error when I run the job on Harvard 
> computing cluster with slurm scheduler:
:
> * The bugid: swap_activity_file-r

This is due to --noswap.

> The command I use is:
> samtools view $input | time parallel --resume-failed --no-run-if-empty 
> --memfree 10G --joblog parseGNU.log --tmpdir $tempdir --noswap --pipe --block 
> 1995M perl parse.pl -bam - -outprefix part_{#} -wd "$workdir" -clip 
> "$alignment_score"
> (here -bam, -outprefix, -wd and -clip are the inputs for my perl script 
> parse.pl)
>
> The bug is not reproducible. Sometimes a file runs completely fine but other 
> times I get the error. Also, this bug is only reported for larger files. 
> Smaller files such as ones <10G work absolutely fine. I tried increasing 
> --memfree to 20G but still the bug is reported.

If you use --memfree you really do not need --noswap.

Also --no-run-if-empty would make no sense when using --pipe.

The problem is due to not being able to open
~/.parallel/tmp/sshlogin/<<sshlogin>>/swap_activity. For some reason
your system has the file but it cannot be opened.

What file system is /tmp? What filesystem is
~/.parallel/tmp/sshlogin/? Is one of them a network file system?

/Ole