Thanks Justin. ;)<br><br>Well, I'm using a simple script to run the tests. The script follows:<br><br>**********************<br>#!/bin/tcsh<br>source ../../tcshrc<br>source /opt/chemistry/gmx404.ompi/bin/GMXRC.csh<br>set path=( $path /opt/mpi/ompi131/bin )<br>
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/opt/mpi/ompi131/lib<br><br>set NCPUS = 2<br><br>set i = 1<br>while ($i <= $NCPUS)<br> if ($i == 1) then<br>echo Single Precision Tests:<br> ./gmxtest.pl simple #all<br> ./gmxtest.pl clean >& /dev/null<br>
echo Double Precision Tests:<br> ./gmxtest.pl -double simple #all<br> ./gmxtest.pl clean >& /dev/null<br> else<br>echo Single Precision Tests - Parallel in $i<br> ./gmxtest.pl -np $i simple #all<br> ./gmxtest.pl clean >& /dev/null<br>
echo Double Precision Tests - Parallel in $i<br> ./gmxtest.pl -np $i -double simple #all<br># ./gmxtest.pl clean >& /dev/null<br> endif<br> @ i++<br>end<br>**********************<br><br>Using just the "simple" tests now to try to find out where is the error. Since the error goes everywhere, it just simplify things.<br>
It outputs everything ok with the serial part, but it all gets really messy in the mpi section.<br><br>In version 4.0.4, it's complaining that the grompp is not understanding the "-np" flag (Invalid command line argument). Then, it doesn't even create a mdrun.out file. I tried to google this error, but basically nothing was found. It also can't be a mixing of compilations, since everything is done in completelly different and independent directories.<br>
<br>Version 3.3.3 on the other hand already failed in so many different places that I'm really thinking IF I'll make it available in the new cluster. :P<br><br>This has to be any sort of pretty stupid mistake so. But I'm clueless this time. :( Any ideas?<br>
<br>Thanks a lot in advance! :)<br><br>Jones<br><br><div class="gmail_quote">On Mon, May 11, 2009 at 7:53 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Jones de Andrade wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi everyone.<br>
<br>
Well, lets go straight to the point: last time I've installed gromacs, it was still 3.3.x and there was no testbed available yet. I've done some tests of my own and everything gone fine.<br>
<br>
I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem to work pretty well in serial, but absolutelly not with mpi. A whole "plethora" of different errors appear.<br>
<br>
Before bothering the list with error messages, my question is: someone has successfully used it with OpenMPI or MPIch? Before questions arise, I have different test users for each, and absolutelly independent compilations.<br>
<br>
</blockquote>
<br></div></div>
Every installation (serial and MPI) that I have installed worked flawlessly. Our cluster uses mpich, and our local machines (dual-core) use OpenMPI.<br>
<br>
Can you provide some of the error messages? Are the reported from Gromacs, or from the MPI implementations?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Thanks a lot for any answer in advance.<br>
<br>
Sincerally yours,<br>
<br>
Jones<br>
<br>
<br></div>
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-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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