[CPMD-list] script for PGI-LAMMPI

[Carme Rovira]

Dear Axel,

You are absolutely right. Here are some details
of how we proceed:

> this is usually not that easy to solve.
> since most of the ways how to start a lam job
> depends on the local installation.

> can you run any of the lam example programs?

Yes 

(We also did hello world with a simple mpi  code on the nodes). 
> 
> is lam installed on _all_ the machines you want to use?

Yes
> 
> do you have any kind of error message?
> 
> have you followed the instructions from the lam
> documentation on how to start a parallel job?

Yes.
> 
> especially that part, where it states that you
> need to be able to log into _all_ machines that
> you want to use without a password (either by
> rsh and .rhosts or /etc/hosts.equiv, or by
> ssh and creating a public/private key pair and
> adding/copying your public key to the authorized_keys
> file).

Yes, the remote login works with /etc/hosts.equiv 

> 
> if this works, you usually just have to create a file
> (e.g. hostlist) with all the machines you want to use
> in the lam-parallel-machine (name hosts where you want to use
> 2 cpus twice) and then initialize lam with

This is done using PBS batch system as  (lines ripped from the
batch script):

#create nodelist
set nodelist = `cat $PBS_NODEFILE`

# calc number of nodes
set N = `wc $PBS_NODEFILE | awk '{print $1}'`

# create lamhost file

cat $PBS_NODEFILE > lamhosts

> lamboot -v hostlist

Works on the nodes (i.e. lamboot -v lamhosts)

> 
> then you can start parallel cpmd by
> 
> mpirun C cpmd.x inputfile > outputfile

What is "C" doing (is it equivalent to "c")
> 

We tried  this as well as

mpirun -O -s n0 N cpmd-mpi-lam-large.x test.inp > test.out

and

mpirun N cpmd-mpi-lam-large.x test.inp > test.out

but no sucess...


Should we copy cpmd.x and input to the remote nodes, 
i.e., tried adding the following to the pbs script:

#
shift nodelist
foreach node ($nodelist)
  rcp /scratch/{test.inp,cpmd-mpi-lam-large.x} ${node}:/scratch
end


Note that the calculation is perfomed on /scratch
First everything (cpmd.x, input) is copied to here (/scratch)
one cd's to /scratch and then possibly remote copies
cpmd.x, input to the nodes

> or however you would run a serial cpmd job.
> after your job is finished you can stop the
> lam infrastructure with
> 
> lamhalt -v
> 
> or
> 
> wipe -v hostlist
> 
Also works fine

> if you have to submit your script to a batch system,
> then you have to determine how you get the list of
> allocated hosts from the batch system. with e.g.
> openpbs you have to use $PBS_NODEFILE instead of the
> file 'hostlist'.

Hope this is clear from the lines above


> 
> i hope this helps.
> 
> cheers,
>         axel.
> 
> >
> > Saludos,
> >
> >    Carme
> >
> > -------------------------------------------------------------
> > Carme Rovira i Virgili                  Tel: +34 93 4037112
> > Centre de Recerca en Química Teòrica    Fax: +34 93 4037225
> > Parc Científic de Barcelona             (http://www.pcb.ub.es)
> > Josep Samitier 1-5 Annex A              E-mail: crovira at pcb.ub.es
> > 08028 Barcelona, Spain   URL:http://www.qf.ub.es/personal/crovira
> > --------------------------------------------------------------
> > _______________________________________________
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> > CPMD-list at cpmd.org
> > http://www.cpmd.org/mailman/listinfo/cpmd-list
> >
> 
> --
> 
> =======================================================================
> Axel Kohlmeyer      e-mail:  axel.kohlmeyer at theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
> D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.

-- 
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Carme Rovira i Virgili                  Tel: +34 93 4037112
Centre de Recerca en Química Teòrica    Fax: +34 93 4037225
Parc Científic de Barcelona             (http://www.pcb.ub.es)
Josep Samitier 1-5 Annex A              E-mail: crovira at pcb.ub.es
08028 Barcelona, Spain   URL:http://www.qf.ub.es/personal/crovira
--------------------------------------------------------------