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TOPIC: command run on SLURM

command run on SLURM 4 years 10 months ago #35169

  • SDAC
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I'm moving over to a cluster that uses SLURM - previously I used qsub. I'm trying to update my config file to make sure it runs smoothly with the new job scheduler, but I'm having trouble updating this for SLURM:

hpc_cmdexec: chmod 755 <hpc_stdin>; qsub < <hpc_stdin>

hpc_cmdexec is the command to run Batch script. It worked fine for my previous job scheduler. I've tried other iterations (below) but none seem to work:

for example:

job submit <wdir>\<hpc_stdin>

cp HPC_STDIN ../'cd../sbatch < <hpc_stdin>

Is there something specific for for SBATCH I need to use?
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command run on SLURM 4 years 10 months ago #35172

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Hi,

You can have a look at systel.edf.cfg for an exmaple.
The configuration eole.* and gaia.* are using sbatch.
There are 10 types of people in the world: those who understand binary, and those who don't.
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command run on SLURM 4 years 10 months ago #35196

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Thankyou. I had a look at the examples but still couldn't get it to work. I think I'm misunderstanding the syntax for cmdexec. I assume it's to push the variable/data stream through by redirecting stdin?
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command run on SLURM 4 years 10 months ago #35197

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<hpc_stdin> will be replace by the HPC_STDIN file generated by telemac.
We are just giving that as input to sbatch.
In the example you gave the ; where missing this could be the issue. This should be the command:
cp HPC_STDIN ../;cd../;sbatch < <hpc_stdin>
What error are you getting ?
There are 10 types of people in the world: those who understand binary, and those who don't.
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command run on SLURM 4 years 10 months ago #35199

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Thanks! I corrected for that. The error I'm getting is the below:


error_2020-01-13.jpg
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command run on SLURM 4 years 10 months ago #35200

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Could you post your HPC_STDIN as well.
I think the issue is in there.
There are 10 types of people in the world: those who understand binary, and those who don't.
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command run on SLURM 4 years 10 months ago #35201

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Could you post your systel.cfg as well.
There are 10 types of people in the world: those who understand binary, and those who don't.
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command run on SLURM 4 years 10 months ago #35202

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Thanks. Both are attached.

I can't see anything else in the source files, compilation etc.


File Attachment:

File Name: systel.liv-v7p2r3.cfg
File Size: 2 KB
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command run on SLURM 4 years 10 months ago #35205

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I see the issue.
In your cfg file.
There seems to be a wrong character.
In the line:
#SBATCH -N 1 �n 6
Replace it by - and that should do it.
There are 10 types of people in the world: those who understand binary, and those who don't.
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command run on SLURM 4 years 10 months ago #35210

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Ah, yes. Thankyou. I was confused as to what the checked symbol indicated.

I've note that the error:

OPENING FILES FOR TELEMAC3D

POINT_TELEMAC3D: MEMORY ALLOCATION

ERREUR 1003 LORS DE L APPEL A CLOSE_MESH:GET_SRF_OBJ
TEXTE DE L'ERROR : HERMES_FILE_NOT_OPENED_ERR

And that there is little on the forum detailing it. Is there any information on how this might be resolved?
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