In addition specifically in your case try this
exe=/export/home/embele/amber/amber12/bin/pmemd.MPI
exeg=/export/home/embele/amber/amber12/bin/pmemd.cuda.MPI
source /etc/profile.d/modules.sh
module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
nproc=`cat $PBS_NODEFILE|wc -l`
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
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 $exeg -O -i md.in -o
md.out -p com_solvated.top -c equil.rst -r md.rst -x md.mdcrd
Understand the concept here is exe is denoting pmemd.MPI for CPU running
and exeg is using pmemd.cuda.MPI for GPU running.
On Tue, Jul 15, 2014 at 10:51 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> HELLO;
>
> Try these scripts. Your MD input is wrong and how come you started running
> MD directly without Partial_Mini, Fulll_mIni, Heating and equilibration
> steps.
> Though the bash script seems ok.
>
> When running minimisation use the CPU version not with CUDA one. In that
> case use #$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
>
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue Jul 15 2014 - 02:30:03 PDT
