[gmx-developers] Re: gmx-developers Digest, Vol 48, Issue 14

Mukesh K Srivastava srimks11 at gmail.com
Mon Apr 21 11:12:41 CEST 2008 

Hi.

I think while doing make mdrun & make install-mdrun, only drivers installed
in bin folder of gramcas is mdrun_mpi.

But w.r.t my previous E-mail as send earlier I need in bin folder of gromacs
following drivers too - p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mp
w.r.t given gromacs application so that mdrun_mpi can be finall;y executed.

HIH.

BR

On Fri, Apr 18, 2008 at 3:30 PM, <gmx-developers-request at gromacs.org> wrote:

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> Today's Topics:
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>   1. GDB Debugging - GROMACS(v-3.3.3) Application with
>      OpenMPI(v-1.2.5/v-1.2.6) (Mukesh K Srivastava)
>   2. Re: GDB Debugging - GROMACS(v-3.3.3) Application  with
>      OpenMPI(v-1.2.5/v-1.2.6) (Daniel Larsson)
>   3. Re: GDB Debugging - GROMACS(v-3.3.3) Application  with
>      OpenMPI(v-1.2.5/v-1.2.6) (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 17 Apr 2008 23:06:50 +0530
> From: "Mukesh K Srivastava" <srimks11 at gmail.com>
> Subject: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3) Application
>        with    OpenMPI(v-1.2.5/v-1.2.6)
> To: gmx-developers at gromacs.org, gmx-users at gromacs.org
> Cc: gmx-announce at gromacs.org
> Message-ID:
>        <3efa6bfc0804171036y26bce920vdb332fed3837f675 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi.
>
> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application
> with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly
> configured
> OpenMPI with debug option and also configured Gromacs alongwith FFTW
> succesfully. I can perform p2bdbx_mpi, editconf_mpi, genbox_mpi,
> grompp_mpi
> compilation and finally mdrun_mpi without any error or warning messages.
> But
> while executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.
>
> I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &
> LD_LIBRARY_PATH in etc/bashrc file and also tried with providing softlink
> to
> libmpi.so.0, but everytime I get same error message of "libmpi.so.0" not
> found.
>
> I had check ldd and it's dependency of executable mdrun_mpi, checked it's
> symbol table content, and finally all lib's configured for 64 bit with ELF
> format but still getting same error of libmpi.so.0 not found while
> performing GDB serial debugging with single node.
>
> Note: I had performed GDB debugging for small MPI program(hello world)
> using
> OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.
>
> Any clue plz?
>
> BR
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> ------------------------------
>
> Message: 2
> Date: Thu, 17 Apr 2008 22:08:35 +0200
> From: Daniel Larsson <larsson at xray.bmc.uu.se>
> Subject: Re: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3)
>        Application     with OpenMPI(v-1.2.5/v-1.2.6)
> To: Discussion list for GROMACS development
>        <gmx-developers at gromacs.org>
> Message-ID: <5F74B961-9BF0-4678-80E7-0AC65E5219BC at xray.bmc.uu.se>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Apr 17, 2008, at 19:36, Mukesh K Srivastava wrote:
> > Hi.
> >
> > Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)
> > application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I
> > had properly configured OpenMPI with debug option and also
> > configured Gromacs alongwith FFTW succesfully. I can perform
> > p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mpi compilation and
> > finally mdrun_mpi without any error or warning messages. But while
> > executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.
>
> This is probably not really any help but just to clarify, as far as I
> know, only mdrun can be run in parallel.
>
> >  I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &
> > LD_LIBRARY_PATH in etc/bashrc file and also tried with providing
> > softlink to libmpi.so.0, but everytime I get same error message of
> > "libmpi.so.0" not found.
> >
> > I had check ldd and it's dependency of executable mdrun_mpi,
> > checked it's symbol table content, and finally all lib's configured
> > for 64 bit with ELF format but still getting same error of
> > libmpi.so.0 not found while performing GDB serial debugging with
> > single node.
> >
> > Note: I had performed GDB debugging for small MPI program(hello
> > world) using OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association
> > succesfully.
> >
> > Any clue plz?
> > BR
> >
> > _______________________________________________
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> > gmx-developers at gromacs.org
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> ---
>
> Daniel Larsson
> Molecular Biophysics group
> Department of Cell and Molecular Biology
> Uppsala University
>
> +46-18-471 4006 (phone)
> +46-18-511 755  (fax)
> http://xray.bmc.uu.se/~larsson <http://xray.bmc.uu.se/%7Elarsson>
> larsson at xray.bmc.uu.se
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 18 Apr 2008 11:07:55 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3)
>        Application     with OpenMPI(v-1.2.5/v-1.2.6)
> To: Discussion list for GROMACS development
>        <gmx-developers at gromacs.org>
> Message-ID: <4807F46B.5090403 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Daniel Larsson wrote:
> >
> > On Apr 17, 2008, at 19:36, Mukesh K Srivastava wrote:
> >> Hi.
> >>
> >> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)
> >> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had
> >> properly configured OpenMPI with debug option and also configured
> >> Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,
> >> editconf_mpi, genbox_mpi, grompp_mpi compilation and finally mdrun_mpi
> >> without any error or warning messages. But while executing mdrun_mpi
> >> w.r.t mprun, I get libmpi.so.0 not found.
> >
> > This is probably not really any help but just to clarify, as far as I
> > know, only mdrun can be run in parallel.
>
> True. The online instructions for installation indicate that you need to
> do "make mdrun" and "make install-mdrun" only when compiling an MPI
> version.
>
> Mark
>
>
> ------------------------------
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> End of gmx-developers Digest, Vol 48, Issue 14
> **********************************************
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