<br><br><div><span class="gmail_quote">On 9/29/05, <b class="gmail_sendername">Jeroen Mesters</b> <<a href="mailto:mesters@biochem.uni-luebeck.de">mesters@biochem.uni-luebeck.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Looking at the md.log file, the first line states the following: <b>Log
file opened: nodeid 0, nnodes = 1, host = orange, process = 7356</b><br>
<br>
Where does mdrun_mpi get the <b>nnodes=1</b> information from?<br>
<br>
Does anyone have an <b>mpich/share/machines</b> file that shows me how
a <b>dual-processor</b> machine is configured i.e. how do I tell
mpich/gromacs there are two processors in one box and it should use
both to run the job?</blockquote><div><br>
I think that you should tell mdrun_mpi which nodes to run on, I mean you should use the flags <br>
-nolocal -machinefile machinefile<br>
in the machinefile you should write something like<br>
name of the node:number of processors for that node<br>
in your case you have node1:2, have I understood right?<br>
<br>
I hope this helps,<br>
MGiò<br>
<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Anybody?<br>
<br>
Thanx in advance, Jeroen.<br>
<br>
<br>
Jeroen Mesters wrote:
<blockquote cite="http://mid433BD8A4.3070501@biochem.uni-luebeck.de" type="cite">
Machine: <b>dual</b> processor dell precision 650 with SuSE linux 9.2<br>
Software: <b>1)</b> mpich installed, machines file constructed, mpd
started <b>2)</b>
compiled gromacs twice, once with and once without --enable-mpi (using
mpich). So, I ended up with two programmes, mdrun_mpi and mdrun. The
program versions are different in size which I would expect... Indeed,
one program was compiled with cc and the other with mpicc (no errors
during compilation).<br>
<br>
Step 1: grompp -np 2 -f full.mdp -c after_pr_CA.gro -p ph5.top -n
index.ndx -o 2cpu.tpr<br>
Step 2: mdrun_mpi -np 2 -s 2cpu.tpr >>>> Fatal error: run
input file 2cpu.tpr was made for 2 nodes, while mdrun_mpi expected it
to be for 1 nodes.<br>
<br>
Question 1. Are my commands correct i.e. is this the proper why to
start?<br>
Question 2. Can this work at all or do I really need <b>2</b>
computers (2 nodes)? <br>
<br>
<br>
Thanx for any hints, Jeroen.<br>
-- <br>
<pre cols="72">Jeroen Raymundus Mesters, Ph.D.<br>Institut fuer Biochemie, Universitaet zu Luebeck<br>Ratzeburger Allee 160, D-23538 Luebeck<br>Tel: +49-451-5004070, Fax: +49-451-5004068<br>E-mail: <a href="mailto:mesters@biochem.uni-luebeck.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
mesters@biochem.uni-luebeck.de</a><br><a href="Http://www.biochem.uni-luebeck.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">Http://www.biochem.uni-luebeck.de</a><br>--<br>If you can look into the seeds of time and say
<br>which grain will grow and which will not - speak then to me (Macbeth)<br>--<br> </pre>
<pre><hr size="4" width="90%"><br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the
<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.</pre>
</blockquote>
<br>
<br>
<pre cols="72">-- <br>Jeroen Raymundus Mesters, Ph.D.<br>Institut fuer Biochemie, Universitaet zu Luebeck<br>Ratzeburger Allee 160, D-23538 Luebeck<br>Tel: +49-451-5004070, Fax: +49-451-5004068<br>E-mail: <a href="mailto:mesters@biochem.uni-luebeck.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
mesters@biochem.uni-luebeck.de</a><br><a href="Http://www.biochem.uni-luebeck.de" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">Http://www.biochem.uni-luebeck.de</a><br>--<br>If you can look into the seeds of time and say
<br>which grain will grow and which will not - speak then to me (Macbeth)<br>--<br></pre>
<br>_______________________________________________<br>gmx-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br>