Re: [AMBER] cpptraj.MPI query

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Sun, 3 Nov 2019 20:00:50 -0500

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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Received on Sun Nov 03 2019 - 17:30:02 PST
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