<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Message: 2<br>
Date: Mon, 1 Feb 2010 12:31:32 +0530<br>
From: Chandan Choudhury <<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>><br>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with<br>
mpicc<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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<<a href="mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com">4e22679c1001312301x5ee854dbn401b1e11f8d4b6f3@mail.gmail.com</a>><br>
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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 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 able to<br>
guarantee that all other processes were killed!<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br></blockquote><div><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 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><br>-- <br>B. Sarath Kumar, B.tech.<br>