Hi,
I am using the following PBS file to run sander
#PBS -l select=1:ncpus=12:mpiprocs=12
...
mpirun -hostfile $PBS_NODEFILE pmemd.MPI -O -i prod.in -p 3SO6_clean.prmtop -c 3SO6_clean_prod_1.rst -o 3SO6_clean_prod_2.out -x 3SO6_clean_prod_2.mdcrd -r 3SO6_clean_prod_2.rst
Which runs perfectly, at a rate of about ns/day = 3.67
But if I try to use more than one node, for example:
#PBS -l select=2:ncpus=12:mpiprocs=12
The job does not seem to start or at least output files are not writte...
Is there a way to use more than one node? Or any way to accelerate the process?
Thanks in advance,
Fabian
_______________________________
Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
On Nov 29, 2012, at 3:36 PM, Jason Swails wrote:
> On Thu, Nov 29, 2012 at 8:18 AM, Fabian Glaser <fglaser.technion.ac.il>wrote:
>
>> Thanks Jason, much more clear now...
>>
>> So the following command is fine?
>>
>> mpirun -np 12 -hostfile $PBS_NODEFILE pmemd.MPI -O .... etc.
>>
>
> The -np 12 is redundant if you are using $PBS_NODEFILE. In fact, if you
> omit the "-np 12", then you can simply change the line
>
> #PBS -l select=1:ppn=12
>
> line when you want to change the number of processors used (instead of also
> having to change the mpirun command as well).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sat Dec 15 2012 - 23:30:02 PST
