Running OpenFOAM from Platform LSF

phinallydone · October 22, 2010, 12:54

Does anyone have any experience running OF from LSF? If so, could you share an example shell script to submit the job to bsub?

Many Thanks!

jdiorio · June 27, 2011, 14:25

Posting this in response to a PM from member Linse. Sorry if this info is posted elsewhere but maybe others will find it helpful.

The key is the LSF environment variable $LSB_HOSTS which is the lists of machines assigned for your job. Create two files e.g. "parjobscript" and the "runparjob"

#script parjobscript
rm machineFile
for i in $LSB_HOSTS
do echo $i >> machineFile
done
mpirun -n 20 --hostfile machineFile simpleFoam -parallel > foam.log

#script runparjob
bsub -q limit150 -n 20 -e error.%J.log -o output.%J.log < parjobscript

The -n option in each of these files should be followed by the number of processors you want. In "runparjob" I'm submitting to the LSF scheduler using bsub, followed by the queue name (in this case limit150) and again the number of processors. The -e and -o options specify the error and log files respectively (using %J gives you the current job number).

Executing "runparjob" should assign the assigned LSF machines to OpenFOAM.

Hope this helps.

James

Linse · June 28, 2011, 10:30

James, thank you very much for that information!
At the very least it points to ways how to solve the problems I have!

ehsankf · June 3, 2013, 16:10

Does anyone have any experience running OF from LSF with mpirun.lsf?

immortality · June 3, 2013, 16:52

Hi
what is LSF?

wyldckat · June 8, 2013, 17:22

Greetings to all!

Quote:

Originally Posted by ehsankf

Does anyone have any experience running OF from LSF with mpirun.lsf?

If you make a more specific question as to what problem you're having with LSF, it'll be easier for anyone to answer you.

Quote:

Originally Posted by immortality

Hi
what is LSF?

I'm not 100% certain, but I think it's this: http://en.wikipedia.org/wiki/Load_Sharing_Facility

Best regards,
Bruno

DominicTNC · July 21, 2017, 04:39

Hi all,

I am now facing the same problem. Would anyone give me some help?

With reference to James comment, I write the following script

<<<<<<<<<<<<<snappyHexMesh.sh>>>>>>>>>>>>>>
rm machineFile
for i in $LSB_HOSTS
do echo $i >> machineFile
done
mpirun -n 264 --hostfile machineFile snappyHexMesh -overwrite -parallel > foam.log

<<<<<<<<<<<<<run_snappyHexMesh.sh>>>>>>>>>>>>>>
bsub -q model_queue_high -n 264 -e error.%J.log -o output.%J.log < snappyHexMesh.sh

But it turns out that it fails to run.

Any comments are appreciated! Many Thanks!

Regards,
Dominic

October 22, 2010, 12:54	Running OpenFOAM from Platform LSF	#1
phinallydone New Member Join Date: Jul 2010 Posts: 11 Rep Power: 16	Does anyone have any experience running OF from LSF? If so, could you share an example shell script to submit the job to bsub? Many Thanks!

June 3, 2013, 16:52		#5
immortality Senior Member Ehsan Join Date: Oct 2012 Location: Iran Posts: 2,208 Rep Power: 27	Hi what is LSF? __________________ Injustice Anywhere is a Threat for Justice Everywhere.Martin Luther King. To Be or Not To Be,Thats the Question! The Only Stupid Question Is the One that Goes Unasked.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
CFX11 + Fortran compiler ?	Mohan	CFX	20	March 30, 2011 19:56
How to Install OpenFOAM on 64 Ubuntu 9.04	hansel	OpenFOAM Installation	62	March 19, 2010 15:43
Problem installing OpenFOAM 1.5 installation on RHEL 4.	vwsj84	OpenFOAM Installation	4	April 23, 2009 05:48
OpenFOAM Training in Europe and USA	hjasak	OpenFOAM	0	August 8, 2008 06:33
Kubuntu uses dash breaks All scripts in tutorials	platopus	OpenFOAM Bugs	8	April 15, 2008 08:52

June 27, 2011, 14:25		#2
jdiorio New Member Join Date: Jan 2010 Posts: 23 Rep Power: 16	Posting this in response to a PM from member Linse. Sorry if this info is posted elsewhere but maybe others will find it helpful. The key is the LSF environment variable $LSB_HOSTS which is the lists of machines assigned for your job. Create two files e.g. "parjobscript" and the "runparjob" #script parjobscript rm machineFile for i in $LSB_HOSTS do echo $i >> machineFile done mpirun -n 20 --hostfile machineFile simpleFoam -parallel > foam.log #script runparjob bsub -q limit150 -n 20 -e error.%J.log -o output.%J.log < parjobscript The -n option in each of these files should be followed by the number of processors you want. In "runparjob" I'm submitting to the LSF scheduler using bsub, followed by the queue name (in this case limit150) and again the number of processors. The -e and -o options specify the error and log files respectively (using %J gives you the current job number). Executing "runparjob" should assign the assigned LSF machines to OpenFOAM. Hope this helps. James

June 28, 2011, 10:30		#3
Linse Senior Member Bernhard Linseisen Join Date: May 2010 Location: Heilbronn Posts: 183 Blog Entries: 1 Rep Power: 16	James, thank you very much for that information! At the very least it points to ways how to solve the problems I have!

June 3, 2013, 16:10		#4
ehsankf Member ehk Join Date: Sep 2012 Posts: 30 Rep Power: 14	Does anyone have any experience running OF from LSF with mpirun.lsf?

July 21, 2017, 04:39		#7
DominicTNC Member Dominic Join Date: Jan 2017 Posts: 41 Rep Power: 9	Hi all, I am now facing the same problem. Would anyone give me some help? With reference to James comment, I write the following script <<<<<<<<<<<<<snappyHexMesh.sh>>>>>>>>>>>>>> rm machineFile for i in $LSB_HOSTS do echo $i >> machineFile done mpirun -n 264 --hostfile machineFile snappyHexMesh -overwrite -parallel > foam.log <<<<<<<<<<<<<run_snappyHexMesh.sh>>>>>>>>>>>>>> bsub -q model_queue_high -n 264 -e error.%J.log -o output.%J.log < snappyHexMesh.sh But it turns out that it fails to run. Any comments are appreciated! Many Thanks! Regards, Dominic