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Dear Omololu,<br>
Dear Peter,<br>
Dear David,<br>
<br>
thanks a lot guys for not giving up on me! <br>
<br>
Expecially the comment by Omololu and Peter "not needing to start mpd
deamon" made me think again........<br>
Oooops, somehow I am running /opt/mpich/<b>ch-p4mpd</b>/bin/mpirun
instead of /opt/mpich/<b>ch-p4</b>/bin/mpirun!!! sorry....<br>
<br>
Aha, now it works! Super, excellent, I am happy! Yippeeeeee<br>
<br>
Cheers, thanx a lot, Jeroen.<br>
<br>
Peter C. Lai wrote:
<blockquote cite="mid20050929195440.GI405@cowbert.2y.net" type="cite">
<pre wrap="">On Thu, Sep 29, 2005 at 05:06:18PM +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=""><!---->
[plai@pulau]:~/speptide % more /usr/local/mpich/share/machines.freebsd
# Change this file to contain the machines that you want to use
# to run MPI jobs on. The format is one host name per line, with either
# hostname
# or
# hostname:n
# where n is the number of processors in an SMP. The hostname should
# be the same as the result from the command "hostname"
pulau:2
I invoke both grompp and mpirun using the -np 2 flag. grompp is also invoked
using the -sort flag.
See <a class="moz-txt-link-freetext" href="http://www.gromacs.org/documentation/howtos/mpich_howto.html">http://www.gromacs.org/documentation/howtos/mpich_howto.html</a>
In my linked libs, I noticed that both grompp and mdrun were linked to:
/usr/local/bin/grompp:
libmd_mpi.so.3 => /usr/local/lib/libmd_mpi.so.3 (0x280c7000)
libgmx_mpi.so.3 => /usr/local/lib/libgmx_mpi.so.3 (0x2810b000)
libsrfftw_mpi.so.2 => /usr/local/lib/libsrfftw_mpi.so.2 (0x28225000)
libsfftw_mpi.so.2 => /usr/local/lib/libsfftw_mpi.so.2 (0x28228000)
libsrfftw.so.2 => /usr/local/lib/libsrfftw.so.2 (0x2822f000)
libsfftw.so.2 => /usr/local/lib/libsfftw.so.2 (0x28254000)
libm.so.3 => /lib/libm.so.3 (0x28843000)
libpthread.so.1 => /usr/lib/libpthread.so.1 (0x2885e000)
libc.so.5 => /lib/libc.so.5 (0x28884000)
(X11 libs not shown)
You do not need mpd if you aren't in a clustered env. (it's for cluster
job control).
</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)
--
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
<blockquote type="cite">
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</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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