Running FDS on a LSF Linux Cluster

[steve...@gmail.com]

Hi everyone,

I would like to submit an FDS simulations on a LSF Linux cluster 

I am struggling to work out the right syntax for the .sh file I will need to submit the job
Is anyone willing to share an example I could use as starting point?

Many thanks

Ste

[Glenn Forney]

does your cluster have a queuing system (like PBS, Torque etc)?

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Glenn Forney

[steve...@gmail.com]

Yes it does

Torque 

thanks

ste

[Glenn Forney]

if you have the FDS-SMV repository on your Linux cluster, you could use the qfds.sh script in Utilities/Scripts to submit a job to a torque cluster.  qfds.sh generates a script that Torque uses to submit a job with qsub .  For example, the command

 qfds.sh  -p 8 -e ~/FDS/FDS6/bin/fds mplume5c8.fds

generates the following qsub script (which you run using qsub script_name where script_name is a file containing the script below).  You could adapt the following script for your cluster or use the above qfds.sh command.  Note the line containing /home/gforney/FDS/FDS6/bin/fds mplume5c8.fds appears on the same line as mpirun

#!/bin/bash

#PBS -N mplume5c8(MPI_IB)

#PBS -e /home/gforney/FDS-SMV/Verification/Visualization/mplume5c8.err

#PBS -o /home/gforney/FDS-SMV/Verification/Visualization/mplume5c8.log

#PBS -l nodes=4:ppn=2

#PBS

export OMP_NUM_THREADS=1

cd /home/gforney/FDS-SMV/Verification/Visualization

echo Start time: `date`

echo Running mplume5c8 on `hostname`

echo Directory: `pwd`

/shared/openmpi_64ib/bin/mpirun --report-bindings --bind-to socket --map-by socket -np 8 /home/gforney/FDS/FDS6/bin/fds mplume5c8.fds

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Glenn Forney

[steve...@gmail.com]

I will give ti a shot 

THanks Gleen

Ste

[Stefano Capra]

Hi Glenn,

I have been trying to test the qsub script running:

bash qfds.sh -p 48 -e /gpfs/stfc/local/apps/intel/FDS/6.2.0/bin/fds test.fds 

It generates the following output:

         Input file:test.fds

         Executable:/gpfs/stfc/local/apps/intel/FDS/6.2.0/bin/fds

              Queue:batch

              Nodes:24

          Processes:48

 Processes per node:2

But it is not writing down a qsub script 

Is there any way to set the number of cores per node?
Do I have to split the mesh beforehand in the same number of subdivision of the number of cores I am using?

Thanks

ste

[Randy McDermott]

We use -n [number of cores per node].  And, yes, you must have at least one mesh per core.

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[Stefano Capra]

Thanks Randy!

Should it write down the script before submitting it?

Thanks

ste

On Tuesday, May 19, 2015 at 12:11:00 PM UTC+1, Stefano Capra wrote:

[Randy McDermott]

Not sure I understand the question.  If you do this (note the -v at the end):

bash qfds.sh -p 48 -n 2 -e /gpfs/stfc/local/apps/intel/FDS/6.2.0/bin/fds test.fds -v

you should see the details of the script without actually submitting it.

I've never run qfds.sh outside our cluster, so I am not sure how that works.  Unfortunately, both Kevin and Glenn on out today.  Kevin is back tomorrow I think and may have better advice.

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[Glenn Forney]

The qfds script erases the qsub script after it runs it. You could edit qfds.sh to change that behavior.

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[Stefano Capra]

Hi Glenn and Randy,

the -v flag at the end didn't help, the script is still not running and not showing me the submission script 

I will look through the code today and try to modify it for my needs

thanks

ste

On Tuesday, May 19, 2015 at 12:11:00 PM UTC+1, Stefano Capra wrote:

[Glenn Forney]

The -v flag outputs script generated to stdout. Redirect output to a file, make any edits you want, then use qsub to run it.

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[Stefano Capra]

Hi everyone,

I sorted the problem writing a small script for the submission file generation.

I turned out to be quite different since I am running it on an LSF system

Thanks

ste

On Tuesday, May 19, 2015 at 12:11:00 PM UTC+1, Stefano Capra wrote: