Error when running through Slurm

sita · April 18, 2019, 09:17

Hi all,

I'm using OpenFOAM-5.x on a Scientific Linux cluster. Everything works fine, I can run simulations no problem, but when I try running a job through Slurm, I get this error:

Code:

/opt/OpenFOAM/OpenFOAM-5.x/etc/config.sh/bash_completion: line 6658: `_rm~all_': not a valid identifier

I noticed that this error has been reported as a bug, and fixed in both OpenFOAM-5.x and OpenFOAM-dev (https://bugs.openfoam.org/view.php?id=2823). Does anyone have any idea why it still pops up when using Slurm, and how to fix this?

Many thanks!
Sita

P.S. For now I've removed the _rm~all_ bit from bash_completion, which rids me of the error, but I'm not sure whether this will get me into trouble at some later point

wyldckat · April 25, 2019, 08:43

Quick answer: It looks like your OpenFOAM 5.x installation isn't based on the most recent commits, because the bug report you mentioned is implying that it was fixed in this commit: https://github.com/OpenFOAM/OpenFOAM...a32d2a2deca208 - in which, yes, the "rm~all" script was simply removed, along with the associated auto-completion entry.

sita · April 25, 2019, 12:49

Thanks! To be honest, I don't know what commit that OpenFOAM-5.x install was based on, as I didn't install that one myself. But it looks like I can safely do without this script, great.

wyldckat · April 25, 2019, 14:55

The help argument with any OpenFOAM application should give the build with version and commit that was used to build things, e.g.:

Code:

blockMesh -help | grep Build

With luck you get something like this:

Code:

Build: 5.x-68e8507efb72

but if it was downloaded as a ZIP package, you will only get something like this:

Code:

Build: 5.x

It should also appear on the header of the runs, e.g.:

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  5.x                                   |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 5.x-68e8507efb72
Exec   : blockMesh
Date   : Apr 25 2019
Time   : 18:55:30

sita · April 25, 2019, 15:51

Cool, never really noticed that before, I'll give it a try.
Thanks!
Sita

April 18, 2019, 09:17	Error when running through Slurm	#1
sita Senior Member Sita Drost Join Date: Mar 2009 Location: Arnhem, The Netherlands Posts: 227 Rep Power: 18	Hi all, I'm using OpenFOAM-5.x on a Scientific Linux cluster. Everything works fine, I can run simulations no problem, but when I try running a job through Slurm, I get this error: Code: /opt/OpenFOAM/OpenFOAM-5.x/etc/config.sh/bash_completion: line 6658: `_rm~all_': not a valid identifier I noticed that this error has been reported as a bug, and fixed in both OpenFOAM-5.x and OpenFOAM-dev (https://bugs.openfoam.org/view.php?id=2823). Does anyone have any idea why it still pops up when using Slurm, and how to fix this? Many thanks! Sita P.S. For now I've removed the _rm~all_ bit from bash_completion, which rids me of the error, but I'm not sure whether this will get me into trouble at some later point Last edited by sita; April 18, 2019 at 10:13. Reason: Added a P.S.

April 25, 2019, 08:43		#2
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	Quick answer: It looks like your OpenFOAM 5.x installation isn't based on the most recent commits, because the bug report you mentioned is implying that it was fixed in this commit: https://github.com/OpenFOAM/OpenFOAM...a32d2a2deca208 - in which, yes, the "rm~all" script was simply removed, along with the associated auto-completion entry. __________________ OpenFOAM: FAQ \| Getting started Forum: How to get help, to post code/output and forum guide Read this before sending me PM

April 25, 2019, 14:55		#4
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,981 Blog Entries: 45 Rep Power: 128	The help argument with any OpenFOAM application should give the build with version and commit that was used to build things, e.g.: Code: blockMesh -help \| grep Build With luck you get something like this: Code: Build: 5.x-68e8507efb72 but if it was downloaded as a ZIP package, you will only get something like this: Code: Build: 5.x It should also appear on the header of the runs, e.g.: Code: /---------------------------------------------------------------------------\ \| ========= \| \| \| \\ / F ield \| OpenFOAM: The Open Source CFD Toolbox \| \| \\ / O peration \| Version: 5.x \| \| \\ / A nd \| Web: www.OpenFOAM.org \| \| \\/ M anipulation \| \| \---------------------------------------------------------------------------/ Build : 5.x-68e8507efb72 Exec : blockMesh Date : Apr 25 2019 Time : 18:55:30

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April 25, 2019, 12:49		#3
sita Senior Member Sita Drost Join Date: Mar 2009 Location: Arnhem, The Netherlands Posts: 227 Rep Power: 18	Thanks! To be honest, I don't know what commit that OpenFOAM-5.x install was based on, as I didn't install that one myself. But it looks like I can safely do without this script, great.

April 25, 2019, 15:51		#5
sita Senior Member Sita Drost Join Date: Mar 2009 Location: Arnhem, The Netherlands Posts: 227 Rep Power: 18	Cool, never really noticed that before, I'll give it a try. Thanks! Sita