Re: [AMBER] cpptraj.MPI query

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Mon, 4 Nov 2019 19:41:05 +0000

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.



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________________________________
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
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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: 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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> > 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 - 12:00:01 PST
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