Re: [AMBER] cpptraj.MPI query

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Mon, 4 Nov 2019 14:01:28 +0000

Hi.

These are the contents of the script:
#! /bin/bash
#SBATCH -J distance_on-off_IPA_xac
#SBATCH --partition=cluster1
#SBATCH --array=1-29%2
#SBATCH -n 8 # This means 8 core jobs will be running..

###############################################################
export submit_dir=/users/debarati/CHK_Kinase/ON_OFF/IPA/$1
cd $submit_dir
echo Working Directory = $submit_dir

echo Hostname = `hostname -s`

echo Date = `date`

export AMBERHOME=/usr/local/amber18
export MPI_HOME=/usr/local/mpich-3.2.1
export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH

name=$(awk -F "_" '{print $2}' "$2"| sed 's:.in::g')


for x in `cat xac`;
do $MPI_HOME/bin/mpiexec -n 8 cpptraj.MPI -i "$x"
done




























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________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Sunday, November 3, 2019 8:00:50 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj.MPI query

If you just run cpptraj.MPI with distance_1.in, does it complete normally?
What commands are in that script?

-Dan

On Sun, Nov 3, 2019 at 12:39 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:

> Can we execute cpptra.MPI using a simple for loop in bash:
>
> Like, I have done this with cpptraj it works; but I cant get it to work
> for cpptraj.MPI
>
> So when I type this:
> For x in `cat list` ; do cpptraj<$x ; echo done for $x ; done
>
> I get my distances calculated.. list is actually 100 input files by the
> name of distance_1.in distance_2.in distance_3.in .... so on till
> distance_100.in
>
>
> Now when I try doing the same thing for cpptraj.MPI
>
> While read x ;
> do $MPI_HOME/bin/mpiexec -n 12 cpptraj.MPI -i $x ;
> done<list
>
> It works for the first entry that is I get output for distance_1.in, but
> not the other 99 input files..
> Any reason what I am be doing wrong.
> Just to let you all know, I have exported AMBERHOME, MPI HOME, and
> LD_LIBRARY PATH properly in my slurm script...
> Thanks
>
>
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>
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Received on Mon Nov 04 2019 - 06:30:08 PST
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