Re: [AMBER] cpptraj.MPI query

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Mon, 4 Nov 2019 20:07:53 +0000

It works as I just executed it and it reads the input properly:

while read x ; do echo "$x" "being processed" ; $MPI_HOME/bin/mpiexec -n 6 cpptraj.MPI -i "$x" ; done<xac
distance_549.in being processed

CPPTRAJ: Trajectory Analysis. V18.01 MPI
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

| Running on 6 threads
| Date/time: 11/04/19 15:05:42
| Available memory: 2.024 GB














Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

From: Daniel Roe<mailto:daniel.r.roe.gmail.com>
Sent: Monday, November 4, 2019 2:54 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] cpptraj.MPI query

Hi,

Since executing cpptraj.MPI manually works, this makes me think the
problem is in the script that calls cpptraj.MPI:

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

Have you tried e.g. replacing the 'mpiexec' command with something
like echo "$x" to make sure your variable is actually picking up the
correct input file?

-Dan


On Mon, Nov 4, 2019 at 2:41
PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Yes it works for the manual input files: but why would not a simple for loop work?
> Cant cpptraj.MPI take $x as a input file argument.
>
>
>
> Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Monday, November 4, 2019 2:17:11 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] cpptraj.MPI query
>
> Hi,
>
> What version of cpptraj are you using? I'm using similar input and I
> see no reasons why the run shouldn't complete.
>
> Maybe there's something odd with your script loop? Can you try to run
> a test script where you specify the input files manually, e.g.
>
> mpirun -n 8 cpptraj.MPI -i distance_1.in
> mpirun -n 8 cpptraj.MPI -i distance_2.in
> mpirun -n 8 cpptraj.MPI -i distance_3.in
> mpirun -n 8 cpptraj.MPI -i distance_4.in
>
> -Dan
>
> On Mon, Nov 4, 2019 at 10:35 AM Debarati DasGupta
> <debarati_dasgupta.hotmail.com> wrote:
> >
> > Okay,this is the content of my distance_299.in file
> >
> >
> > parm ~/setup_solvbox/pdb_layer_IPA_H2O_5-95vv.prmtop
> > trajin New4A_production.1.crd 1 1250 1
> > trajin New4B_production.1.crd 1 1250 1
> > trajin New4C_production.1.crd 1 1250 1
> > trajin New4D_production.1.crd 1 1250 1
> > trajin New4E_production.1.crd 1 1250 1
> > trajin New4F_production.1.crd 1 1250 1
> > trajin New4G_production.1.crd 1 1250 1
> > trajin New4H_production.1.crd 1 1250 1
> > trajin New4I_production.1.crd 1 5000 1
> > trajin New4J_production.1.crd 1 5000 1
> > strip :WAT
> > strip :Na+
> >
> > solvent pdb_layer_IPA_H2O_5-95vv.prmtop none
> >
> > reference PDB_layer_IPA_H2O.pdb
> >
> > rms reference mass out IPA_299_RMSD.txt :1-274.CA
> >
> > distance IPA_site1_RUN1 :299.C2 point -3 -0.875 7.25 noimage out distance_299_site1_RUN1.out
> > distance IPA_site2_RUN1 :299.C2 point -15.25 -4.75 -24.375 noimage out distance_299_site2_RUN1.out
> > go
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Monday, November 4, 2019 10:20:00 AM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] cpptraj.MPI query
> >
> > Sorry, I mean what is in e.g. 'distance_1.in'?
> >
> > -Dan
> >
> > On Mon, Nov 4, 2019 at 9:02 AM Debarati DasGupta
> > <debarati_dasgupta.hotmail.com> wrote:
> > >
> > > 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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> > >
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> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
> > >
> > > ________________________________
> > > 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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Received on Mon Nov 04 2019 - 12:30:02 PST
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