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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>I would suggest that you test OpenMPI first using a simple hello
world on 32 processors to see if it can run successfully:<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>$ mkdir -p ~/jobs/helloworld &amp;&amp; cd ~/jobs/helloworld<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>$ vi ./helloworld-mpi.c<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>/*-------------------------code------------------------*/<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>#include &lt;stdio.h&gt;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>#include &lt;mpi.h&gt;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>int<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>main(argc, argv)<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>int &nbsp;&nbsp;argc;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>char&nbsp; *argv[];<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>{<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; int&nbsp; rank, size, len;<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; char name[MPI_MAX_PROCESSOR_NAME];<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; MPI_Init(&amp;argc, &amp;argv);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; MPI_Comm_rank(MPI_COMM_WORLD, &amp;rank);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; MPI_Comm_size(MPI_COMM_WORLD, &amp;size);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; MPI_Get_processor_name(name, &amp;len);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; printf (&quot;Hellow world! I'm %d of %d on %s\n&quot;,
rank, size, name);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; MPI_Finalize();<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>&nbsp; exit(0);<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>}<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>/*---------------------end code------------------------*/<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>$ rm helloworld*.o &amp;&amp; /path/to/openmpi/bin/mpicc -o
helloworld-openmpi helloworld-mpi.c<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>$ mpirun -np 32 -hostfile mpd.hosts helloworld-openmpi<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>See if that works properly first.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'>Mike<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Courier New";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>hui sun<br>
<b>Sent:</b> Thursday, November 06, 2008 8:04 AM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] problem with openmpi and gromacs4.0 <o:p></o:p></span></p>

</div>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

<div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>Dear
all,<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>&nbsp;<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>Recently,
we&nbsp;installed the gromacs4.0 with openmpi&nbsp;parallel program. When we
started a simulation with np=1, the simulation was finished normally. But when
the same tpr file was run with np=n (n&gt;1), I obtained the following error
message:<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'><o:p>&nbsp;</o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>MPI_ABORT
invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><o:p>&nbsp;</o:p></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>My
used command is &amp; mpirun -np 32 -hostfile mpd.hosts mdrun_mpi -s large.tpr
-o large.trr -c large.gro -g large.log<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt'><o:p>&nbsp;</o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>The
content of the mpd.hosts file is following,<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
node1&nbsp; slots=8<o:p></o:p></span></p>

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<div>

<p class=MsoNormal style='text-indent:65.0pt'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>. <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal style='text-indent:65.0pt'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal style='text-indent:65.0pt'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>.</span><o:p></o:p></p>

</div>

<div>

<p class=MsoNormal style='text-indent:65.0pt'><span style='font-size:10.0pt;
font-family:"Times New Roman","serif"'>nodex&nbsp; slots=8 <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif"'>It
must be noted that my tpr file is produced via the gromacs 3.3.3. Is this
related to the error?<o:p></o:p></span></p>

</div>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif";
color:#333333'>I don't know what to do now and how can I overcome this. Could
you help me?</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#333333'><o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif";
color:#333333'>&nbsp;</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#333333'><o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif";
color:#333333'>Thanks in advance!<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;color:#333333'><o:p>&nbsp;</o:p></span></p>

<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Times New Roman","serif";
color:#333333'>Hui Sun</span><span style='font-size:10.0pt;font-family:"Arial","sans-serif";
color:#333333'><o:p></o:p></span></p>

</div>

<p>&nbsp; <o:p></o:p></p>

<div class=MsoNormal align=center style='text-align:center'>

<hr size=1 width="100%" align=center>

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<p class=MsoNormal><a href="http://cn.mail.yahoo.com/"><span lang=ZH-CN>ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡</span></a><o:p></o:p></p>

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