As Justin said give the command line options for mdrun and also check that your mpi environment is running. Better to run a parallel job and check its output.<div><br></div><div>Chadnan <br clear="all"><br>--<br>Chandan kumar Choudhury<br>
NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Mon, Feb 8, 2010 at 8:02 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="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Jennifer Williams wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear All,<br>
<br>
I am having problems compiling gromacs 4.0.7 in parallel. I am following the<br>
Quick and Dirty Installation instructions on the gromacs webpage.<br>
I downloaded the the versions of fftw, OpenMPI and gromacs-4.0.7 following these instructions.<br>
<br>
Everything seems to compile OK and I get all the serial executables including mdrun written to my bin directory and they seem to run fine. However when I try to run mdrun_mpi on 6 nodes I get the following:<br>
<br>
[vlxbig16:08666] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>
[vlxbig16:08667] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>
[vlxbig16:08700] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>
[vlxbig16:08670] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>
[vlxbig16:08681] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182<br>
[vlxbig16:08659] [NO-NAME] ORTE_ERROR_LOG: Not found in file 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>
Does anyone have any idea what is causing this? Computer support at my University is not sure.<br>
<br>
</blockquote>
<br>
How are you launching mdrun_mpi (command line)?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Thanks<br>
<br>
<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<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>
<br>
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