On Fri, 2013-11-22 at 12:36 +0530, anu chandra wrote:
> Dear Jason,
>
> Thanks for the reply and sorry the late reply. I have pmemd.cuda installed
> in ' /home/user1/amber12/bin/ ' and I am running pmemd.cuda from the folder
> " /home/anu/ " using the following script
No you are not.
>
> *********************************************************************************************
> #!/bin/csh
> #PBS -N PDP
> #PBS -l nodes=1:ppn=4:gpus=1
> #PBS -l walltime=24:00:00
> #PBS -e error.log
>
> cd /home/user1/amber12/bin
With this command you change to the directory /home/user1/amber12/bin
>
> pmemd.cuda -O -i /home/anu/md.in \
> -c /home/anu/eq.rst \
> -p /home/anu/PDP.top \
> -ref /home/anu/PDP.crd \
> -o /home/anu/md.out \
> -r /home/anu/md.rst \
> -x /home/anu/md.crd \
> -inf /home/anu/md.info
You are now running pmemd.cuda _inside_ /home/user1/amber12/bin. This
is unusual. In general, you do NOT have to run programs in the same
folder that they are installed in. This is the relevant part of your
input file:
DISANG=angle_pbc.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
You tell pmemd.cuda that your restraint file is "angle_pbc.RST", so it
tries to open "angle_pbc.RST". Since your current directory
is /home/user1/amber12/bin, it tries to open the
file /home/user1/amber12/bin/angle_pbc.RST -- a file that does not
exist. This file is actually in /home/anu. You can either specify the
full path of angle_pbc.RST inside md.in or go to /home/anu/ and run the
simulation from there. This is the PBS script that I would use [1]:
*********************************************************************************************
#!/bin/csh
#PBS -N PDP
#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l walltime=24:00:00
#PBS -e error.log
cd /home/anu
pmemd.cuda -O -i md.in \
-c eq.rst \
-p PDP.top \
-ref PDP.crd \
-o md.out \
-r md.rst \
-x md.crd \
-inf md.info
*********************************************************************************************
Understanding what happened here and why you got your error should help
you debug problems in the future.
Good luck,
Jason
[1] Actually, the first lines of my PBS scripts look something like
this:
************************************
#!/bin/csh
#PBS -N PDP
#PBS -l nodes=1:ppn=4:gpus=1
#PBS -l walltime=24:00:00
#PBS -e error.log
cd $PBS_O_WORKDIR
************************************
This command automatically changes to the directory from which you
submitted the script. My Wiki has a helpful page about more advanced
uses of PBS that help make more efficient use of available resources:
http://jswails.wikidot.com/using-pbs
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 22 2013 - 06:30:03 PST
