Re: [ESPResSo-users] Compilation ESPResSo cluster

[Olaf Lenz]

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Hi!

On 03/08/2013 10:05 PM, Salvador H-V wrote:
> i) I tried to compile ESPResSo as a root in the folder: /opt/.

There is absolutely no reason to compile ESPResSo as root!
Maybe you want to *install* ESPResSo as root into /opt/ESPResSo, but we
do not even recommend that, as other people that want to use ESPResSo
will most probably need another configuration.
Just compile ESPResSo in some folder in the home directory of a user.

> But when I try run ESPResSo as a normal user,  I got the following 
> message
[clip]
> Executable: ./Espresso" ====
[clip]
> /opt/openmpi/bin/mpirun -n 2 ./Espresso < Mixt_Colloids.tcl

I do not know how a Rocks cluster looks like, but apparently the nodes
can not find the ESPResSo binary. There may be several reasons for this.
For example, you are giving the location of the executable as "./",
which is a relative path. This will only work if the working directory
on the node is the directory where you execute "qsub". One possible
solution could therefore be to give the path to ESPResSo as an absolute,
i.e. /opt/ESPResSo/bin/ESPResSo (or whatever). Another possible reason
could be that the nodes of the cluster do not use the same file system.
In that case you will first have to copy ESPResSo to the file system
that is visible on the nodes.

I would recommend to contact somebody who knows about your cluster.

> ii) My second problem is related with the number of processors that
>  ESPResSo recognizes during compilation. Because of the problem
> stated above, I decided to compile ESPResSo as a normal user in my
> home. I successfully compile it, and I able to run serial and
> parallel jobs that uses a number of processors EQUAL to the number
> of cores in each node.

The number of processors that ESPResSo recognizes is used only to
determine how many processes are used when running the testsuite. It has
absolutely no effect on how many processors you can use when doing your
own simulation!

> If I try to run a single job with say 8 processors, thus  ESPResSo 
> runs in parallel in one single node!

How do you try to run it with 8 processors? The only way to run it in
parallel is to use mpirun or mpiexec.

Olaf
- -- 
Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607
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