Hi.<br><br>I think while doing make mdrun & make install-mdrun, only drivers installed in bin folder of gramcas is mdrun_mpi.<br><br>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.<br>
<br>HIH.<br><br>BR<br><br><div class="gmail_quote">On Fri, Apr 18, 2008 at 3:30 PM, <<a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6) (Mukesh K Srivastava)<br>
2. Re: GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6) (Daniel Larsson)<br>
3. Re: GDB Debugging - GROMACS(v-3.3.3) Application with<br>
OpenMPI(v-1.2.5/v-1.2.6) (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 17 Apr 2008 23:06:50 +0530<br>
From: "Mukesh K Srivastava" <<a href="mailto:srimks11@gmail.com">srimks11@gmail.com</a>><br>
Subject: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3) Application<br>
with OpenMPI(v-1.2.5/v-1.2.6)<br>
To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>, <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Cc: <a href="mailto:gmx-announce@gromacs.org">gmx-announce@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:3efa6bfc0804171036y26bce920vdb332fed3837f675@mail.gmail.com">3efa6bfc0804171036y26bce920vdb332fed3837f675@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi.<br>
<br>
Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3) application<br>
with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had properly configured<br>
OpenMPI with debug option and also configured Gromacs alongwith FFTW<br>
succesfully. I can perform p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mpi<br>
compilation and finally mdrun_mpi without any error or warning messages. But<br>
while executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.<br>
<br>
I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &<br>
LD_LIBRARY_PATH in etc/bashrc file and also tried with providing softlink to<br>
libmpi.so.0, but everytime I get same error message of "libmpi.so.0" not<br>
found.<br>
<br>
I had check ldd and it's dependency of executable mdrun_mpi, checked it's<br>
symbol table content, and finally all lib's configured for 64 bit with ELF<br>
format but still getting same error of libmpi.so.0 not found while<br>
performing GDB serial debugging with single node.<br>
<br>
Note: I had performed GDB debugging for small MPI program(hello world) using<br>
OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association succesfully.<br>
<br>
Any clue plz?<br>
<br>
BR<br>
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<br>
Message: 2<br>
Date: Thu, 17 Apr 2008 22:08:35 +0200<br>
From: Daniel Larsson <<a href="mailto:larsson@xray.bmc.uu.se">larsson@xray.bmc.uu.se</a>><br>
Subject: Re: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3)<br>
Application with OpenMPI(v-1.2.5/v-1.2.6)<br>
To: Discussion list for GROMACS development<br>
<<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Message-ID: <<a href="mailto:5F74B961-9BF0-4678-80E7-0AC65E5219BC@xray.bmc.uu.se">5F74B961-9BF0-4678-80E7-0AC65E5219BC@xray.bmc.uu.se</a>><br>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed<br>
<br>
<br>
On Apr 17, 2008, at 19:36, Mukesh K Srivastava wrote:<br>
> Hi.<br>
><br>
> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)<br>
> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I<br>
> had properly configured OpenMPI with debug option and also<br>
> configured Gromacs alongwith FFTW succesfully. I can perform<br>
> p2bdbx_mpi, editconf_mpi, genbox_mpi, grompp_mpi compilation and<br>
> finally mdrun_mpi without any error or warning messages. But while<br>
> executing mdrun_mpi w.r.t mprun, I get libmpi.so.0 not found.<br>
<br>
This is probably not really any help but just to clarify, as far as I<br>
know, only mdrun can be run in parallel.<br>
<br>
> I had tried with LD_LIBRARY_PATH, forcefully mentioning PATH &<br>
> LD_LIBRARY_PATH in etc/bashrc file and also tried with providing<br>
> softlink to libmpi.so.0, but everytime I get same error message of<br>
> "libmpi.so.0" not found.<br>
><br>
> I had check ldd and it's dependency of executable mdrun_mpi,<br>
> checked it's symbol table content, and finally all lib's configured<br>
> for 64 bit with ELF format but still getting same error of<br>
> libmpi.so.0 not found while performing GDB serial debugging with<br>
> single node.<br>
><br>
> Note: I had performed GDB debugging for small MPI program(hello<br>
> world) using OpenMPI(v1.2.5/v1.2.6) wthout GROMACS association<br>
> succesfully.<br>
><br>
> Any clue plz?<br>
> BR<br>
><br>
> _______________________________________________<br>
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<br>
---<br>
<br>
Daniel Larsson<br>
Molecular Biophysics group<br>
Department of Cell and Molecular Biology<br>
Uppsala University<br>
<br>
+46-18-471 4006 (phone)<br>
+46-18-511 755 (fax)<br>
<a href="http://xray.bmc.uu.se/%7Elarsson" target="_blank">http://xray.bmc.uu.se/~larsson</a><br>
<a href="mailto:larsson@xray.bmc.uu.se">larsson@xray.bmc.uu.se</a><br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 18 Apr 2008 11:07:55 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-developers] GDB Debugging - GROMACS(v-3.3.3)<br>
Application with OpenMPI(v-1.2.5/v-1.2.6)<br>
To: Discussion list for GROMACS development<br>
<<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4807F46B.5090403@anu.edu.au">4807F46B.5090403@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Daniel Larsson wrote:<br>
><br>
> On Apr 17, 2008, at 19:36, Mukesh K Srivastava wrote:<br>
>> Hi.<br>
>><br>
>> Anyone had performed GDB debugging for Gromacs(v3.x - v3.3.3)<br>
>> application with FFTW(v3.1) using OpenMPI(v-1.2.5 or v-1.2.6). I had<br>
>> properly configured OpenMPI with debug option and also configured<br>
>> Gromacs alongwith FFTW succesfully. I can perform p2bdbx_mpi,<br>
>> editconf_mpi, genbox_mpi, grompp_mpi compilation and finally mdrun_mpi<br>
>> without any error or warning messages. But while executing mdrun_mpi<br>
>> w.r.t mprun, I get libmpi.so.0 not found.<br>
><br>
> This is probably not really any help but just to clarify, as far as I<br>
> know, only mdrun can be run in parallel.<br>
<br>
True. The online instructions for installation indicate that you need to<br>
do "make mdrun" and "make install-mdrun" only when compiling an MPI version.<br>
<br>
Mark<br>
<br>
<br>
------------------------------<br>
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End of gmx-developers Digest, Vol 48, Issue 14<br>
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</blockquote></div><br>