[gmx-users] Re:mpi_run issue
Mark Abraham
mark.abraham at anu.edu.au
Fri Jan 29 02:34:57 CET 2010
----- Original Message -----
From: #ZHAO LINA# <ZHAO0139 at ntu.edu.sg>
Date: Friday, January 29, 2010 12:24
Subject: [gmx-users] Re:mpi_run issue
To: gmx-users at gromacs.org
> Hi everyone,
>
> I still do not know how to modify it.
Sure, but it isn't the job of anyone here to teach you how to do it. This is a GROMACS mailing list, and you have a problem crafting a PBS submission script. We can't know which version of PBS you are using, and don't have access to your machine for trial-and-error, even if we were motivated to do your work for you, and if we did it for you then you'd learn very little and have to come running back for every little problem. Please find and read the PBS (and/or MPI) documentation and learn how to solve the problem for yourself. It (or your system admins) will explain what PBS_NODEFILE is doing. I hinted last time about useful ways to approach solving the problem.
Mark
>
> -----------------------------------------------------------------
> -----
>
> Hi,
>
> Here is the example file I based on to modify,
> mpi.sh
>
> #!/bin/bash
> #
> ## Specify the job name
> #PBS -N jobname
>
> ## Join the standard error and the standard output into 1 file output
> #PBS -j oe
> #PBS -V
>
> ## To run on 16 cpus
> #PBS -l nodes=2:ppn=8
>
> ## pre-processing script
> cd $PBS_O_WORKDIR
> NCPUS=`cat $PBS_NODEFILE | wc -l`
> echo $NCPUS
>
> ## program to run
> /usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile
> $PBS_NODEFILE ./myprog
>
>
> My working directory is ${HOME}/Jobs/1A7W/tryScript. By the way,
> I do not know the NODEFILE mean.
>
> Thanks and best regards,
>
> Elsa
>
> -----------------------------------------------------------------
> -----
>
>
> > Hi,
> >
> > I tried to run the command
> > mdrun -deffnm em
> > on cluster,
> > blow is the script, but I worried that it might be some place
> > wrong, seems no files came out after several hours running
> > Is anyone please help me to modify it, and how can know the
> > process of its running in the cluster.
>
> We can't know the best procedure for your cluster because we
> haven't read its documentation or talked to its admins... (hint, hint)
>
> > Thanks and best regards,
> >
> > Elsa
> >
> > #!/bin/bash
> > #
> > ## Specify the job name
> > #PBS -N emMDrunSecondOne
> >
> > ## Join the standard error and the standard output into 1 file
> output> #PBS -j oe
> > #PBS -V
> >
> > ## To run on 16 cpus
> > #PBS -l nodes=2:ppn=8
> >
> > PBS_O_WORKDIR=${HOME}/Jobs/1A7W/tryScript
> > [ -d ${PBS_O_WORKDIR}] || exit 1
>
> This looks wrong. PBS usually has flags that let you specify
> running the job in directory from which submission occured - use them.
>
> > cd $PBS_O_WORKDIR
> > NCPUS=`cat $PBS_NODEFILE | wc -l`
> > echo $NCPUS
>
> If PBS is defining $PBS_NODEFILE to point to some file it
> creates, then that file won't be local to the directory you've
> arbitrarily changed to, so NCPUS won't get defined suitably, so
> mpirun won't work.
>
> I'd suggest you start again from some example script that is
> known to work on your cluster and modify only the mpirun line.
>
> Mark
>
> > ## program to run
> > /usr/local/openmpi/bin/mpirun -np $NCPUS mdrun_mpi -deffnm em
> > exit 0
> > > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > before posting!
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>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 28 Jan 2010 16:03:50 +0100
> From: Erik Marklund <erikm at xray.bmc.uu.se>
> Subject: Re: [gmx-users] hblife
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4B61A756.7060505 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> afsaneh maleki skrev:
> > thanks dear justin'
> >
> > it is right that the output of the analysis tools generally
> writes
> > axis labels and data set legends. in hblife.xyg file is
> written that
> > x axis label "Time (ps)" and the last time is written
> 14300.001
> > whereas my simulated time is 40000 ps not 143000.00
> ps
> > i send you this file
> I don't remember the details about the calculation of lifetimes,
> but I
> believe it's an estimate of how the half lifes of hydrogen
> bonds. You
> can also get this quantity, along with the kinetic constants and
> energies for hb breaking and frormation, using -ac. If I
> remember
> correctly, -ac uses a more reliable method.
>
> Erik
> >
> > Best wishes,
> > Afsaneh
> >
> > On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul
> <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > afsaneh maleki wrote:
> >
> > Hi,
> >
> > would you
> please elaborate the first column in the hblife.xvg
> > file?
> > hblife.xyg is
> the output of the following command:
> > g_hbond -life
> hblife.xvg> this
> column don't show the real time in simulated system.what
> > are these times?
> >
> >
> > Check the headers in the .xvg file;
> the output of the analysis
> > tools generally writes axis labels and
> data set legends. If it
> > still doesn't make sense, post a
> snippet of your file.
> >
> > -Justin
> >
> > thanks in advance,
> > Afsaneh
> >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu>
> | (540) 231-9080
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > ========================================
> > --
> > gmx-users mailing
> list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> >
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe
> requests to the list. Use the www
> > interface or send it to gmx-users-
> request at gromacs.org> <mailto:gmx-
> users-request at gromacs.org>.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> >
> > --
> >
> >
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Laboratory of Molecular Biophysics,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471
> 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se
> http://xray.bmc.uu.se/molbiophys
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Jan 2010 10:07:07 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] hblife
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4B61A81B.8060207 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> afsaneh maleki wrote:
> > thanks dear justin'
> >
> > it is right that the output of the analysis tools generally
> writes axis
> > labels and data set legends. in hblife.xyg file is
> written that x
> > axis label "Time (ps)" and the last time is written
> 14300.001 whereas
> > my simulated time is 40000 ps not 143000.00 ps
> > i send you this file
>
> It is better to not send attachments, rather cut and paste from
> your file.
> Sorry, some of us are paranoid about accepting files unless
> they're specifically
> requested :)
>
> If I recall, the hblife.xvg file should be some sort of
> probability function,
> p(t) for hydrogen bond half-life. If it trails off to
> zero, the file probably
> truncates instead of writing lots of zeroes.
>
> And certainly 14300.001 ps is within the 40000 ps timeframe of
> your simulation,
> it may just indicate that whatever your analyzing doesn't last
> terribly long.
>
> You can also use the -ac flag to generate lots of useful
> information about
> hydrogen bonds, although there are some reproducibility
> questions that have been
> raised before (see the archives).
>
> -Justin
>
> >
> > Best wishes,
> > Afsaneh
> >
> > On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul
> <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > afsaneh maleki wrote:
> >
> > Hi,
> >
> > would you
> please elaborate the first column in the hblife.xvg file?
> > hblife.xyg is
> the output of the following command:
> > g_hbond -life
> hblife.xvg> this
> column don't show the real time in simulated system.what
> > are these times?
> >
> >
> > Check the headers in the .xvg file;
> the output of the analysis tools
> > generally writes axis labels and data
> set legends. If it still
> > doesn't make sense, post a snippet of
> your file.
> >
> > -Justin
> >
> > thanks in advance,
> > Afsaneh
> >
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu>
> | (540) 231-9080
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > ========================================
> > --
> > gmx-users mailing
> list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> >
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe
> requests to the list. Use the www
> > interface or send it to gmx-users-
> request at gromacs.org> <mailto:gmx-
> users-request at gromacs.org>.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php>
> >
> >
> >
> > --
> >
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 29 Jan 2010 02:14:19 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] hblife
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbd7d90076af.4b62447b at anu.edu.au>
> Content-Type: text/plain; CHARSET=US-ASCII
>
>
>
> ----- Original Message -----
> From: afsaneh maleki <maleki.afsaneh at gmail.com>
> Date: Friday, January 29, 2010 1:56
> Subject: Re: [gmx-users] hblife
> To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-
> users at gromacs.org>
> > thanks dear justin'
> >
> > it is right that the output of the analysis tools generally
> writes axis labels and data set legends. in hblife.xyg
> file is written that x axis label "Time (ps)" and
> the last time is written 14300.001 whereas my simulated time is
> 40000 ps not 143000.00 ps
>
> Axis labels are different from legend labels.
>
> Please cite the full command line, not an abbreviated one. The
> .xvg shows the full line. Other options can have effects on the
> output, though it is not clear if/why that might be true here.
> Try a simple g_hbond -life calculation and see if it differs.
>
> Mark
>
> i send you this file
> >
> > Best wishes,
> > Afsaneh
> >
> > On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul
> <jalemkul at vt.edu> wrote:
>
> >
>
> >
> >
> afsaneh maleki wrote:
>
> >
> Hi,
>
> >
> >
> would you please elaborate the first column in the
> hblife.xvg file?
> >
> hblife.xyg is the output of the following command:
> >
> g_hbond -life hblife.xvg
> >
> this column don't show the real time in simulated system.what
> are these times?
>
> >
>
>
> >
> >
> Check the headers in the .xvg file; the output of the analysis
> tools generally writes axis labels and data set legends.
> If it still doesn't make sense, post a snippet of your file.
>
> >
> >
> -Justin
>
> >
>
> >
> thanks in advance,
> >
> Afsaneh
>
> >
>
>
> >
> >
> --
> >
> ========================================
>
> >
> >
> Justin A. Lemkul
> >
> Ph.D. Candidate
> >
> ICTAS Doctoral Scholar
> >
> MILES-IGERT Trainee
> >
> Department of Biochemistry
> >
> Virginia Tech
> >
> Blacksburg, VA
> >
> jalemkul[at]vt.edu | (540) 231-9080
>
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> >
> >
> ========================================
> >
> --
> >
> gmx-users mailing list gmx-users at gromacs.org
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >
> Please search the archive at http://www.gromacs.org/search
> before posting!
> >
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> >
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> >
> > >
> > --
> >
> >
>
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 29 Jan 2010 02:20:15 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] hblife
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbdbce0553bf.4b6245df at anu.edu.au>
> Content-Type: text/plain; CHARSET=US-ASCII
>
>
>
> ----- Original Message -----
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Date: Friday, January 29, 2010 2:16
> Subject: Re: [gmx-users] hblife
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> >
> >
> > ----- Original Message -----
> > From: afsaneh maleki <maleki.afsaneh at gmail.com>
> > Date: Friday, January 29, 2010 1:56
> > Subject: Re: [gmx-users] hblife
> > To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-
> > users at gromacs.org>
> > > thanks dear justin'
> > >
> > > it is right that the output of the analysis tools generally
> > writes axis labels and data set legends. in hblife.xyg
> > file is written that x axis label "Time (ps)" and
> > the last time is written 14300.001 whereas my simulated time
> is
> > 40000 ps not 143000.00 ps
> >
> > Axis labels are different from legend labels.
> >
> > Please cite the full command line, not an abbreviated one. The
> > .xvg shows the full line. Other options can have effects on
> the
> > output, though it is not clear if/why that might be true here.
> > Try a simple g_hbond -life calculation and see if it differs.
>
> It won't. Now that my brain is turned on, you're just getting
> what you asked for, which is a frequency plot of H-bond
> lifetimes. Evidently you have none which persist longer than 14.3ns.
>
> Mark
>
> > Mark
> >
> > i send you this file
> > >
> > > Best wishes,
> > > Afsaneh
> > >
> > > On Thu, Jan 28, 2010 at 6:04 PM, Justin A. Lemkul
> > <jalemkul at vt.edu> wrote:
> >
> > >
> >
> > >
> > >
> > afsaneh maleki wrote:
> >
> > >
> > Hi,
> >
> > >
> > >
> > would you please elaborate the first column in the
> > hblife.xvg file?
> > >
> > hblife.xyg is the output of the following command:
> > >
> > g_hbond -life hblife.xvg
> > >
> > this column don't show the real time in simulated system.what
> > are these times?
> >
> > >
> >
> >
> > >
> > >
> > Check the headers in the .xvg file; the output of the analysis
> > tools generally writes axis labels and data set legends.
> > If it still doesn't make sense, post a snippet of your file.
> >
> > >
> > >
> > -Justin
> >
> > >
> >
> > >
> > thanks in advance,
> > >
> > Afsaneh
> >
> > >
> >
> >
> > >
> > >
> > --
> > >
> > ========================================
> >
> > >
> > >
> > Justin A. Lemkul
> > >
> > Ph.D. Candidate
> > >
> > ICTAS Doctoral Scholar
> > >
> > MILES-IGERT Trainee
> > >
> > Department of Biochemistry
> > >
> > Virginia Tech
> > >
> > Blacksburg, VA
> > >
> > jalemkul[at]vt.edu | (540) 231-9080
> >
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > >
> > >
> > ========================================
> > >
> > --
> > >
> > gmx-users mailing list gmx-users at gromacs.org
> >
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > >
> > Please search the archive at http://www.gromacs.org/search
> > before posting!
> > >
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > >
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> > >
> > > >
> > > --
> > >
> > >
> >
> > > --
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search
> > > before posting!
> > > Please don't post (un)subscribe requests to the list. Use
> the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search
> > before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
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