[FLASH-USERS] flash2.5 in kraken
John ZuHone
jzuhone at milkyway.gsfc.nasa.gov
Tue Jul 10 18:57:10 EDT 2012
Hi Diego,
Which compiler to use is mostly a matter of your choice, depending on if you need compiler-specific optimizations or not. pgi is the compiler loaded by default, and I have had no issues with it (though I don't run on Kraken anymore).
As I mentioned in my previous email, you need to have the hdf5-parallel module loaded:
module load hdf5-parallel
From what I remember the proper hdf5 library for your compiler will be automatically loaded.
Pasted below is an example batch script, which runs on 192 processors for 4 hours.
For more information on Kraken (including batch script options) please see http://nics.tennessee.edu/computing-resources/kraken.
Best,
John
#!/bin/bash
#PBS -A your allocation number
#PBS -l size=192,walltime=04:00:00
#PBS -N your_job_name
#PBS -j oe
# the previous line combines stdout and stderr
cd $PBS_O_WORKDIR
aprun -n 192 ./flash2 >> flash.out
On Jul 10, 2012, at 6:29 PM, Diego wrote:
> Hi John, two more question.
>
> Now that it compiled fine I don't understand how to indicate what compiler it should use: pgi, intel and gcc.
>
> Is there a module I should upload, like the hdf5 one?
>
> And finally, can you also send me a type of the batch script (ie the script with all the info for qsub)?
>
> Cheers.
>
> D
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