*I am using this script running MD simulation on AMBER.*
#!/bin/bash
#PBS -N eric.job
#PBS -l select=1:ncpus=12:mpiprocs=12
#PBS -l walltime=1:00:00
#PBS -q kepla_k20
#PBS -m be
#PBS -o /export/home/kbisetty/scratch5/amber/faez/test/tion.out
#PBS -e /export/home/kbisetty/scratch5/amber/faez/test/tion.err
#PBS -M khanfaeziqbal.gmail.com
cd $PBS_O_WORKDIR
pwd
echo "My job starts here"
date
source /etc/profile.d/modules.sh
module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
module add amber/k20
exe=pmemd.cuda.MPI
nproc=`cat $PBS_NODEFILE|wc -l`
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i md.in -o
md.out -p prmtop -c inpcrd
echo "My job ends here"
date
*and md.in <
http://md.in> file:*
Initial minimization of solvent and solute, 10.0 cut
&cntrl
imin = 1,
ntb = 1, ntc = 2, ntf =2,
cut = 10.0,
maxcyc = 500,
ncyc = 500,
/
*PLease let ,me know any error here. I am generationg an error output files
as:*
PMEMD implementation of SANDER, Release 12
| Run on 07/15/2014 at 04:00:21
[-O]verwriting output
File Assignments:
| MDIN: md.in
| MDOUT: md.out
| INPCRD: inpcrd
| PARM: prmtop
| RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Initial minimization of solvent and solute, 10.0 cut
&cntrl
imin = 1,
ntb = 1, ntc = 2, ntf =2,
cut = 10.0,
maxcyc = 500,
ncyc = 500,
/
CUDA (GPU): Minimization is NOT supported in parallel on GPUs. Please use
the single GPU code for minimizations.
Input errors occurred. Terminating execution.
"md.out" 42L, 2132C
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Received on Tue Jul 15 2014 - 01:30:02 PDT
