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Re: Process is killed inside GNU Parallel on High Performance Computing
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From: |
Ole Tange |
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Subject: |
Re: Process is killed inside GNU Parallel on High Performance Computing system |
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Date: |
Sat, 27 Feb 2021 17:15:11 +0100 |
On Thu, Feb 25, 2021 at 6:55 PM Truong, Minh Thanh Buu - trumt001
<trumt001@mymail.unisa.edu.au> wrote:
> I have a problem with GNU parallel on the HPC, my code is:
>
> parallel --progress --joblog
> ${home}/data/hsc-admmt/Projects/log_a.sh -j 5 :::: a.sh
>
> It automatically stops the code inside the bash script and resulted in this
> error:
>
> /scratch/eu82/bt0689/data/hsc-admmt/Projects/sim_causal_mantel_generate.sh:
> line 54: 3050285 Killed $home/data/hsc-admmt/Tools/mtg2
> -plink plink_all${nsamp}${nsnp}_1 -simreal snp.lst1
>
>
> I wonder what problem is this and how to solve it? However, I can run
> normally the code without parallel
>
> The single line of code usually takes around 30 min to finish.
>
> Your help is really appreciated!
I do not see that anyone can respond to this based on the info you have given.
You will need to follow:
https://www.gnu.org/software/parallel/man.html#REPORTING-BUGS
I suspect the error is dependent on your environment or distribution,
so please read the section on that carefully.
/Ole