Hi Emanuele,
You need to change
system("qsub run.pbs.$dihed"); to
system("./run.$dihed.sh");
Good luck!
On Thu, Sep 27, 2018, 10:15 emanuele falbo <falbo.emanuele.gmail.com> wrote:
> Hi Marcos,
>
> I tried as you said, unfortunately it doesn't work. I got these two error
> messages when submitting the script:
>
> "
> Name "main::wd" used only once: possible typo at
> ./prepare_runs_0-90-modified.perl line 3.
> Preparing input files
> Processing dihedral: 0
> Can't exec "qsub": No such file or directory at
> ./prepare_runs_0-90-modified.perl line 27.
> Processing dihedral: 3
> "
>
> The "Can't exec .." is repeated for all runs till dihe=90. ( here is the
> files modified)
>
> Do you think I should change the qsub command when preparing the input
> files, if so how ?
>
> Note I simply renamed ala_tri.rst file with 03_prod_60. Your help is
> really appreacited.
>
> Emanuele
>
>
>
>
> Il giorno gio 27 set 2018 alle ore 14:56 emanuele falbo <
> falbo.emanuele.gmail.com> ha scritto:
>
> > thanks for promptly replying Marcos.
> > I will give it a try and then let you know. Thanks again.
> >
> > Cheers,
> > Emanuele
> >
> > Il giorno gio 27 set 2018 alle ore 14:52 Marcos Serrou do Amaral <
> > marcossamaral.gmail.com> ha scritto:
> >
> >> Dear Emanuele,
> >>
> >> You could try to change the write_batchfile function and try something
> >> like
> >> this:
> >>
> >> sub write_batchfile {
> >> open BATCHFILE, '>', "run.$dihed.sh";
> >> print BATCHFILE <<EOF;
> >>
> >> #!/bin/bash
> >>
> >> mpirun -np 2 pmemd.MPI -O \\
> >> -i mdin_min.$dihed -p ${name}.prmtop -c ala_tri_prod_60.rst -r
> >> ${name}_min_${dihed}.rst -o ${name}_min_${dihed}.out
> >> mpirun -np 2 pmemd.MPI -O \\
> >> -i mdin_equi.$dihed -p ${name}.prmtop -c ${name}_min_${dihed}.rst -r
> >> ${name}_equil_${dihed}.rst -o ${name}_equil_${dihed}.out
> >> mpirun -np 2 pmemd.MPI -O \\
> >> -i mdin_prod.$dihed -p ${name}.prmtop -c ${name}_equil_${dihed}.rst -r
> >> ${name}_prod_${dihed}.rst -o ${name}_prod_${dihed}.out -x
> >> ${name}_prod_${dihed}.mdcrd
> >> EOF
> >>
> >> print BATCHFILE "\necho \"Execution finished\"\n";
> >> close BATCHFILE;
> >> }
> >>
> >> Good luck!
> >> ---
> >> Marcos S.A.
> >>
> >>
> >>
> >> On Thu, Sep 27, 2018 at 9:34 AM emanuele falbo <
> falbo.emanuele.gmail.com>
> >> wrote:
> >>
> >> > Dear users,
> >> >
> >> > I am following the umbrella sampling tutorial on the web site
> >> > http://ambermd.org/tutorials/advanced/tutorial17/section2.htm .
> >> > I got a bit stuck when using the perl scripts for running all the
> >> > calculations., because I would like to use these scripts (here is
> >> attached
> >> > one type.) for running the calculations in parallel on my workstation
> >> ( it
> >> > is not a cluster).
> >> >
> >> > So , I am wondering if anybody knows the way to modify them and get
> the
> >> > calculations done successfully.
> >> >
> >> > Best Regards
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> > *Emanuele Falbo*
> >> > PhD student
> >> > Penfold group
> >> > School of Natural and Environmental Sciences
> >> > Bedson Building, Newcastle University
> >> > Newcastle upon Tyne, NE1 7RU
> >> > w: http://tompenfoldresearch.weebly.com/
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> > --
> >
> > *Emanuele Falbo*
> > PhD student
> > Penfold group
> > School of Natural and Environmental Sciences
> > Bedson Building, Newcastle University
> > Newcastle upon Tyne, NE1 7RU
> > w: http://tompenfoldresearch.weebly.com/
> >
> >
>
> --
>
> *Emanuele Falbo*
> PhD student
> Penfold group
> School of Natural and Environmental Sciences
> Bedson Building, Newcastle University
> Newcastle upon Tyne, NE1 7RU
> w: http://tompenfoldresearch.weebly.com/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 27 2018 - 08:00:02 PDT
