[molpro-user] Killing Molpro Jobs using SGE

Javier Díaz Montes javier.diaz at uclm.es
Tue Dec 4 12:41:00 GMT 2007

I can not kill the jobs using kill command, because I run the jobs from  
the Frontend of the cluster. Therefore, I would have to login in each node  
to run the kill command.
I have a cluster built using Rocks. I have openmpi-1.1-1.
I want an instance of molpro for each node, because I have AMD64 machines.
I run molpro using the next command:

	molprop -n $NSLOTS --mpirun-machinefile $TMPDIR/machines < infile >  

How can I specify that I only want a instance per node? Because I think  
that it consider an instance per node, but I do not know why this create  
two processes. This is the tree:

27481 ?        R    654:36  \_  
27483 ?        S      0:04      \_  

These are the first lines of the Molpro output:

ARMCI configured for 6 cluster nodes. Network protocol is 'TCP/IP Sockets'.

  MPP nodes  nproc
  compute-0-19.loc    1
  compute-0-5.loca    1
  compute-0-22.loc    1
  compute-0-12.loc    1


En Tue, 04 Dec 2007 12:03:23 +0100, Miguel Guilherme Fernandes de Souza  
<guilhermefsmiguel at gmail.com> escribió:

> Mr. Javier,
> I have molpro runing on a 6 64bits computers, using mpich as mpi  
> interfacer.
> I think that this that is happening is normal.
> did you try to kill the job using kill -9 <number of the processes> ?
> as example kill -9 9988
> i always use this command to kill my jobs, and when i do it, all the
> instances, on all the nodes have been killed.
> molpro can create 2 instances of the same processes on each node just if  
> you
> want.
> The question, do you build this cluster ? if yes, what mpi did you use ?
> how are you calling your jobs?
> all of these affects on your execution...
> for example, i will try to explain you what i usually do here:
> first of all, i insert all of my machine cluster names to my mpdboot  
> file.
> node1
> node2
> ...
> node6
> then, i call all of them to be a part of cluster, using the command  
> mpbtrace
> if everything gets ok, the command list me the name of the machines that  
> are
> on the cluster:
> node1
> node2
> ...
> node6
> then i can run molpro using:
> molpro -n 6 -o CAS.out CAS.in
> in my case, this call 6 instances of molpro to mpi.
> you need to think that you use multithread computers ( if they are  
> pentium 4
> HT ), so, you will need to call 2 instances on the same machine. Doing  
> this,
> your computer gets fully used, otherwise, it will use only 50% of your
> processor, and your calculus will spend a lot more time ...
> to mpi call 2 instances on the same machine, you need to specify it on  
> the
> mpdboot file.
> i realy don´t have it running on my cluster, because we use Athlon 64
> processor, and, as you know, they don´t have Hyper Threading support, so,
> only one instance per node it is ok.
> So, i hope all of these have been helping to you.
> you can ask me if you have any other doubts .
> best regards
> On Dec 4, 2007 8:16 AM, Javier Díaz Montes <javier.diaz at uclm.es> wrote:
>> Hi,
>> I have a problem when I run Molpro in several nodes of a cluster. The
>> problem is when I try to kill a job.
>> If I kill the job, using the qdel command of sge, some processes of  
>> Molpro
>> remain running. I have seen that molpro create 2 processes, in each  
>> node,
>> of molprop_2006_1_i4_p4_mpi.exe, one running and another one sleep.  
>> Then,
>> when I kill the job, the processes running are killed and the process
>> which was sleeping starts to run.
>> Molpro create 2 processes of molprop_2006_1_i4_p4_mpi.exe in each node,  
>> is
>> this normal?
>> How could I kill a Molpro job?, because Now I have to kill these  
>> processes
>> using pkill command in each node.
>> Regards,
>> Javi
>> --
>> +---------------------------------------------------------------+
>> Javier Diaz Montes
>> PhD Candidate
>> Grupo de Quimica Computacional y Computacion de Alto Rendimiento.
>> Departamento de Tecnologias y Sistemas de Informacion.
>> Escuela Superior de Informatica.
>> Universidad de Castilla-La Mancha.
>> Paseo de la Universidad, 4; 13071 Ciudad Real; SPAIN
>> Tel.: 34-926295300; Ext: 3724
>> e-mail: javier.diaz at uclm.es
>> +---------------------------------------------------------------+

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