Discussion group for the ARIA software

[Benjamin Bardiaux <bardiaux AT pasteur.fr>]

Dear Benedikt,

If you're slurm setup allows submission from the node where you're running 
aria, you could use

      <host enabled="yes" command="sbatch --your.sbatch.options" 
executable="/.../programs/cns_solve_1.21/intel-x86_64bit-linux/bin/cns_solve" n_cpu="20" use_absolute_path="yes"/>
    </job_manager>


this means that each CNS calculation will be submitted independently via 
sbatch, hence running in parallel.

Best regards,

Benjamin


On 30/04/2021 11:19, Benedikt Soeldner wrote:
> Dear Aria discussion group,
>
> since a few months, I'm running my Aria calculations on a cluster managed
> with the Slurm scheduling system. Unfortunately, I didn't find out yet,
> how to run Aria, i.e., the CNS calculation processes, on multiple nodes in
> parallel. Does anyone of you know if and how this works?
>
> At the moment, I start my Aria calculations by submitting a job script,
> which looks like the following:
>
> #!/bin/bash -l
> #SBATCH --job-name=Aria-Project_run01
> #SBATCH --output=Aria-Project_run01.out
> #SBATCH --error=Aria-Project_run01.err
> #SBATCH --partition=short
> #SBATCH --ntasks=1
> #SBATCH --cpus-per-task=20
> #SBATCH --mem=8G
> module purge
> module load python/2.7.18
> cd /.../Aria-Project
> srun python -O /.../programs/aria2.3.2/aria2.py --output=run01msg.txt
> Aria-Project_run01.xml
>
> And in the Aria project file, the following lines are written:
>
>      <job_manager default_command="csh -f">
>        <host enabled="yes" command="csh -f"
> executable="/.../programs/cns_solve_1.21/intel-x86_64bit-linux/bin/cns_solve"
> n_cpu="20" use_absolute_path="yes"/>
>      </job_manager>
>
> When I increase the number of nodes (#SBATCH --nodes=... in the job
> script), the job still runs just on one node, as there is only one initial
> task. I guess, the lines above from the project file also need to be
> modified somehow and not only in the Slurm job script. Do you know, how
> these two files should look like? Or do I need to modify other files in
> addition?
>
> Thank you for your help!
>
> Best regards,
>
> Benedikt Söldner
>
> --------------------------------------
> Benedikt Söldner (PhD student)
> benedikt.soeldner AT tu-dortmund.de
> Technical University Dortmund, Germany
> Research group of Prof. Dr. Rasmus Linser


--
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Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
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