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[OpenFOAM.org] HPC setup error

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Old   July 26, 2022, 11:47
Default HPC setup error
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Good afternoon,

These days I have been facing an error during the installation of OpenFOAM in HPC. I had followed the instructions provided for my university; however, I have not been able to set up a case. The first was the creation of a workspace, which I did, and the second is the project setup. The code is the following ,and I am attaching the error as a picture Error message.jpg. If someone could help me I will be grateful.


#!/bin/bash

#SBATCH --time=72:00:00 # walltime
#SBATCH --ntasks=39 # number of processor cores (i.e. tasks)
#SBATCH --partition=haswell
#SBATCH --mem-per-cpu=2000M # memory per CPU core
#SBATCH -J "Test" # job name
#SBATCH -A p_test # project name
#SBATCH --mail-user=paca797c@tu-dresden.de # email address
#SBATCH --mail-type=ALL

OUTFILE="Output_Test"

module load OpenFOAM/8
source $FOAM_BASH
srun interFoam -parallel > "$OUTFILE"

exit 0
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Old   July 26, 2022, 23:34
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The first error message seems to be "attempt to run parallel on one processor". You have specified -parallel but did not write $NCORES.

The command should look something like this

srun -n $NCORES interFoam -parallel >& my_output_file
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Old   July 27, 2022, 12:47
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Thank you, Justin,

I successfully solved it, however, I have a different error, I checked the folder constant/polyMesh and the file "points" is there, then I do not know what could be the problem. The folder organization in my laptop using Ubuntu 20.04 works perfectly but running the model again in the HPC I am facing some errors. I am pretty new to Open FOAM, and I feel my errors are easy to solve, but I could not manage them properly.

[25] --> FOAM FATAL ERROR:
[25] Cannot find file "points" in directory "polyMesh" in times "0" down to constant
[25]
[25] From function virtual Foam::IOobject Foam::fileOperation::findInstance(const Foam::IOobject&, Foam::scalar, const Foam::word&) const
[25] in file global/fileOperations/fileOperation/fileOperation.C at line 871.
[25]
FOAM parallel run exiting


Thank you for your help!!

Kind Regards,
Pamela
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Old   July 27, 2022, 23:08
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This usually means your BlockMesh was not ran correctly.
Try to run BlockMesh, then CheckMesh -allTopology

and then see what the error is. I suggest to run your job interactively first to troubleshoot initial problems, rather than using a batch script right away.
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Old   July 28, 2022, 12:14
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Thank you, I will run it again. Thanks a lot!
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Old   August 3, 2022, 14:18
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Good afternoon,

I am writing to get some recommendations. I have to create a surface from a river channel and its respectively Mesh in HPC, for this aim I am using block Mesh, surfaceFeatureExtract, and snappyHexMesh. However, I have been facing some complications, at the beginning, I ran the model on my computer with a coarse Mesh with the commands mentioned before, and later I used interFOAM to process the boundary conditions, and everything worked. For my project, I need to refine the surface, which means I need to use HPC. I created the batch file that I am attaching here, but I got errors.

- The first error is this one:
"slurmstepd: error: execve(): surfaceFeatureExtract: No such file or directory"
run: error: taurusi6529: tasks 90-99: Exited with exit code 2

-The second error is this other:
"urmstepd: error: Detected 1 oom-kill event(s) in StepId=27549201.0 cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
srun: error: taurusi6305: task 11: Out Of Memory
slurmstepd: error: Detected 1 oom-kill event(s) in StepId=27549201.0 cgroup. Some of your processes may have been killed by the group out-of-memory handler."

After all, I checked my folders and even with those errors the "Coarse Mesh" is in the folder results.

I would like to know, maybe my batch file is not well developed or why is the reason of the errors and furthermore do these errors affect the outcome of my Mesh?

I appreciate your help!
Attached Images
File Type: jpg error3.jpg (159.4 KB, 4 views)
File Type: jpg error3.2.jpg (159.9 KB, 3 views)
Attached Files
File Type: txt error3.txt (15.0 KB, 0 views)
File Type: txt batchfile_blockMesh.txt (706 Bytes, 0 views)
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