Hi Jason,
Thanks for your quick response, the truth is I don't think it is a typo I have checked it in several occasions and it produces always the same result. I send you here the result of a test with -r in the last position and in other position, and the output file produced with the full content of the script. Is a short minimisation.
I would like to mention that I am in the process of buying amber14, since amber12 I couldn't use in several nodes, it could be a bad compilation or a wrong version.....
As said if -r min.rst is not the last flag, the default restrt file is produced. I know from a friend that he also thinks is a very weird behaviour, but it has always been like this in my cluster....
Thanks a lot,
Fabian
Here it is:
#!/bin/sh
#
# job name (default is the name of pbs script file)
#---------------------------------------------------
#PBS -N ETA_9_min
# Submit the job to the queue "queue_name"
#---------------------------------------------------
#PBS -q short_l_p
#-----------------------------------------------------------------
#PBS -M fglaser.technion.ac.il
#---------------------------------------------------
#PBS -mbea
#------------------------------------------------------------------
#PBS -l select=1:ncpus=12:mpiprocs=12
#
#
# specifying working directory
#------------------------------------------------------
cd $PBS_O_WORKDIR
# running MPI executable with M*N processes
#------------------------------------------------------
source /usr/local/intel12/setup.sh
#command
mpirun sander -O -i min.in -o min.out -p ../clec2_system_ETA_ETA_9.prmtop -c ../clec2_system_ETA_ETA_9.prmcrd -ref ../clec2_system_ETA_ETA_9.prmcrd -r min.rst
cd ../eq
qsub eq.q
_______________________________
Fabian Glaser, PhD
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
fglaser.technion.ac.il
Tel: +972 4 8293701
Fax: +972 4 8225153
> On Oct 29, 2014, at 7:17 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Wed, Oct 29, 2014 at 11:31 AM, Fabian Glaser <fabian.glaser.gmail.com>
> wrote:
>
>> Hi all,
>>
>> I noticed that in my amber installation, when using the PBS queue system,
>> the -r flag has to be in the last place of the mpirun command:
>>
>> mpirun pmemd.MPI -O -i eq3.in -o eq3.out -p
>> ../clec2_system_ETA_ETA_9.prmtop -c eq2.rst -ref
>> ../clec2_system_ETA_ETA_9.prmcrd -x eq3.nc -r eq3.rst
>>
>> Otherwise the restart file name produced is the default restrt name and
>> not as in the case above command eq3.rst
>>
>
> This doesn't make any sense to me, and I've never seen this happen before.
>
>
>>
>> Any idea why or if I can somehow overcome this problem in a simple way?
>>
>
> My guess is that there was a typo in the original command somewhere that
> caused this problem. If you can't figure out where the typo might be,
> provide the (full) contents of the script that displays this strange
> behavior
>
> and we may be able to help.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Nov 02 2014 - 06:00:03 PST
