Dear all,
The PBS input file :
----------------------------------------
/bin/csh
#BSUB -J 192.sh
#BSUB -e 192.sh.err
#BSUB -o 192.sh.stderr
#BSUB -R 'span[ptile=48]'
#BSUB -q 192cpu
#BSUB -n 192
source /pkg/chem/amber11/setamber
cat $LSB_DJOB_HOSTFILE > ./hostlist.29669
echo "Your AMBER job starts at `date`"
./192.sh.tmp
wait
echo "Your AMBER job completed at `date` "
192.sh.tmp:
------------------------------------------------------
mpirun_rsh -np 192 -hostfile ./hostlist.29669 IPATH_UNIT=0 /pkg/chem/amber11.intel/bin/sander.MPI -ng 192 -groupfile groupfile
I have submitted my simulation in NCHC ALPS Cluster and there is nothing outputting in my work dictionary. Could you tell me how to fix the problem?
Thank you
Yeng-Tseng Wang
-----Original message-----
From:Carlos Simmerling <carlos.simmerling.gmail.com>
To:AMBER Mailing List <amber.ambermd.org>
Date:Thu, 27 Oct 2011 13:01:36 -0400
Subject:Re: [AMBER] Nudged Elastic Band (NEB) with torque PBS system
Also we need to know if the test cases pass for you.
On Oct 27, 2011 12:55 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Thu, Oct 27, 2011 at 12:47 PM, <c00jsw00.nchc.narl.org.tw> wrote:
>
> > Dear all,
> > When I used the NEB method with torque PBS system (Linux cluster), the
> > Amber didn't work, such as the comand "mpirun -np 32
> > $AMBERHOME/exe/sander.MPI -ng 32 -groupfile groupfile" Could you tell me
> > how to fix the problem?
> >
>
> No. Without more details it's impossible to tell why it didn't work. We
> need exact commands and exact error messages to help. (We don't even know
> if it's an Amber problem)
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 31 2011 - 00:30:02 PDT
