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Re: GNU Parallel Bug Reports The bugid: swap_activity_file-r
From: |
Ole Tange |
Subject: |
Re: GNU Parallel Bug Reports The bugid: swap_activity_file-r |
Date: |
Mon, 11 Feb 2019 23:17:37 +0100 |
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
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