HELLO;
Try these scripts. Your MD input is wrong and how come you started running
MD directly without Partial_Mini, Fulll_mIni, Heating and equilibration
steps.
Though the bash script seems ok.
When running minimisation use the CPU version not with CUDA one. In that
case use #$AMBERHOME/bin/pmemd for minimization means for partial_Mini and
Full_Mini.
In your script put something like
exe=pmemd
exeg=pmemd.cuda
this signifies you are running minimization in CPU and from heating to MD
in GPU.
Now it should look like
#Run the minimization with just CPU AMBER.
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i
Partial_Mini.in -o Partial_Mini.out -p com_solvated.top -c com_solvated.crd
-ref com_solvated.crd -r Partial_Mini.rst
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i Full_Mini.in
-o Full_Mini.out -p com_solvated.top -c Partial_Mini.rst -r Full_Mini.rst
#Run MD using GPU AMBER.
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exeg -O -i Heating.in -o
Heating.out -p com_solvated.top -c Full_Mini.rst -r Heating.rst -ref
Full_Mini.rst -x Heating.mdcrd
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exeg -O -i equil.in -o
equil.out -p com_solvated.top -c Heating.rst -r equil.rst -x equil.mdcrd
time mpirun -np $nproc -machinefile $PBS_NODEFILE $exeg -O -i md.in -o
md2.out -p com_solvated.top -c equil.rst -r md2.rst -x md2.mdcrd
Enjoy computation.
On Tue, Jul 15, 2014 at 10:17 AM, Faez Iqbal khan <khanfaeziqbal.gmail.com>
wrote:
> *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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue Jul 15 2014 - 02:00:02 PDT
