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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?<br>
<br>
Anybody?<br>
<br>
Thanx in advance, Jeroen.<br>
<br>
<br>
Jeroen Mesters wrote:
<blockquote cite="mid433BD8A4.3070501@biochem.uni-luebeck.de"
type="cite">
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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 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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<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)
--
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