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Hi David,<br>
<br>
1) during the make step it used <b>mpicc</b> instead of normal cc. The
latter compiler was used when I left out the --enable-mpi. So, I think
it is really compiled for mpi??!? See also my comments further below.<br>
2) I used either <b>mpirun -np 2 mdrun_mpi -s new.trp</b> or <b>mpirun
-np 2 mdrun_mpi -s new.trp -np 2</b> and both produce the same first
line in the md.log file.<br>
3) Installing from the gromacs home page lamxxx.rpm and fftwxxx.rpms
does not work properly on SuSE linux 9.2. Complains about<br>
<br>
So my question is again, where does mdrun_mpi get the nnodes=1
information from?<br>
And, does anybody have an example of a machines file for dual
processor!?<br>
<br>
De groeten uit Luebeck! (Dutch for greetings from Luebeck!), Jeroen<br>
<br>
David wrote:
<blockquote
cite="mid1128006835.6493.1.camel@217-208-143-88-o1123.tbon.telia.com"
type="cite">
<pre wrap="">On Thu, 2005-09-29 at 17:06 +0200, Jeroen Mesters wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Looking at the md.log file, the first line states the following: Log
file opened: nodeid 0, nnodes = 1, host = orange, process = 7356
Where does mdrun_mpi get the nnodes=1 information from?
Does anyone have an mpich/share/machines file that shows me how a
dual-processor 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?
</pre>
</blockquote>
<pre wrap=""><!---->
you sure that mdrun was compiled for mpi?
try
ldd `which mdrun_mpi` and see whether anyhing mpi shows up. If so then
check other commands to start mpi jobs like mpiexec or mpirun
in general try to avoid mpich.
</pre>
<blockquote type="cite">
<pre wrap="">Anybody?
Thanx in advance, Jeroen.
Jeroen Mesters wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Machine: dual processor dell precision 650 with SuSE linux 9.2
Software: 1) mpich installed, machines file constructed, mpd started
2) 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).
Step 1: grompp -np 2 -f full.mdp -c after_pr_CA.gro -p ph5.top -n
index.ndx -o 2cpu.tpr
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.
Question 1. Are my commands correct i.e. is this the proper why to
start?
Question 2. Can this work at all or do I really need 2 computers (2
nodes)?
Thanx for any hints, Jeroen.
--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:mesters@biochem.uni-luebeck.de">mesters@biochem.uni-luebeck.de</a>
<a class="moz-txt-link-freetext" href="Http://www.biochem.uni-luebeck.de">Http://www.biochem.uni-luebeck.de</a>
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
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</pre>
</blockquote>
<pre wrap="">
--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:mesters@biochem.uni-luebeck.de">mesters@biochem.uni-luebeck.de</a>
<a class="moz-txt-link-freetext" href="Http://www.biochem.uni-luebeck.de">Http://www.biochem.uni-luebeck.de</a>
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
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</pre>
</blockquote>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Ratzeburger Allee 160, D-23538 Luebeck
Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: <a class="moz-txt-link-abbreviated" href="mailto:mesters@biochem.uni-luebeck.de">mesters@biochem.uni-luebeck.de</a>
<a class="moz-txt-link-freetext" href="Http://www.biochem.uni-luebeck.de">Http://www.biochem.uni-luebeck.de</a>
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me (Macbeth)
--
</pre>
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