<br clear="all">Thanks You all. <br>Mark you were right. Some how mpi was screwed up. Now I am able to run the job parallely. <br>Actually there were two different versions of openmpi and I suppose they were conflicting. Uninstalling both of them and instally the recent openmpi solved the problem<br>
<br>Chandan<br><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Mon, Feb 1, 2010 at 5:02 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</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>On 01/02/10 20:19, Sarath Kumar wrote:<br>
</div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
<br>
<br>
Message: 2<br>
Date: Mon, 1 Feb 2010 12:31:32 +0530<br></div>
From: Chandan Choudhury <<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a> <mailto:<a href="mailto:iitdckc@gmail.com" target="_blank">iitdckc@gmail.com</a>>><div><br>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with<br>
mpicc<br>
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<br>
Thanks.<br>
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc<br>
file, and could compile the mpi version of gromacs.<br>
The next thing is I got the error on executing mdrun_mpi -h<br>
Following is the output. Kindly help.<br>
<br>
corsica:/usr/local/gromacs/bin # mdrun_mpi -h<br>
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file<br>
runtime/orte_init_stage1.c at line 182<br>
--------------------------------------------------------------------------<br>
It looks like orte_init failed for some reason; your parallel process is<br>
likely to abort. There are many reasons that a parallel process can<br>
fail during orte_init; some of which are due to configuration or<br>
environment problems. This failure appears to be an internal failure;<br>
here's some additional information (which may only be relevant to an<br>
Open MPI developer):<br>
<br>
orte_rml_base_select failed<br>
--> Returned value -13 instead of ORTE_SUCCESS<br>
<br>
--------------------------------------------------------------------------<br>
--------------------------------------------------------------------------<br>
It looks like MPI_INIT failed for some reason; your parallel process is<br>
likely to abort. There are many reasons that a parallel process can<br>
fail during MPI_INIT; some of which are due to configuration or<br>
environment<br>
problems. This failure appears to be an internal failure; here's some<br>
additional information (which may only be relevant to an Open MPI<br>
developer):<br>
<br>
ompi_mpi_init: orte_init_stage1 failed<br>
--> Returned "Not found" (-13) instead of "Success" (0)<br>
--------------------------------------------------------------------------<br>
*** An error occurred in MPI_Init<br>
*** before MPI was initialized<br>
*** MPI_ERRORS_ARE_FATAL (goodbye)<br>
[corsica:17130] Abort before MPI_INIT completed successfully; not<br>
able to<br>
guarantee that all other processes were killed!<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
<br>
<br>
U will be getting error s like this<br>
as the MPI failed.<br>
When u run mdrun with MPI.<br>
If u use this CPPFLAGS, and i also had a problem.<br>
When i used this option, after that i was unable to revert back it to<br>
the original state also.<br>
<br>
So the better option update the gcc, c++ compilers,<br>
If u have doubt in this, remove gromacs, All MPi.<br>
<br>
then do yum install -y *openmpi*<br>
<br>
--It will automatically install the missing libraries in dependencies.<br>
<br>
and then download fftw ---latest<br>
<br>
the install fftw with<br>
./configure --enable-threads --enable-mpi<br>
the gromacs<br>
./configure --enable-threads --enable-mpi<br>
<br>
<br>
this will surely work, because in order gromacs work with MPI.<br>
U should compile fftw with MPI as above.<br>
</div></div></blockquote>
<br>
None of this will help if the MPI environment is not configured, e.g. a hostfile set up. Chandan needs to get a test MPI program to run before there is evidence any of this discussion belongs on the GROMACS mailing last.<br>
<font color="#888888">
<br>
Mark</font><div><div></div><div><br>
-- <br>
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