[molpro-user] Killing Molpro Jobs using SGE

Reuti reuti at staff.uni-marburg.de
Tue Dec 4 15:05:37 GMT 2007

Zitat von Javier Díaz Montes <javier.diaz at uclm.es>:

> Hi,
> 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.

Hi again,

I'm getting confused: are you now using MPICH or Open MPI? The mpirun  
command must be the one used for compilation, they are not  

All my hints up to now were for using MPICH with SGE. If you use Open  
MPI with SGE it's different.

Also in you other post I saw "orted" processes. So: you are using Open  
MPI, and not MPICH - right?

-- Reuti

> 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 > outfile
> 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  \_
> /home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molprop_2006_1_i8_p4_mpi.exe
> 27483 ?        S      0:04      \_
> /home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molprop_2006_1_i8_p4_mpi.exe
> 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
> .......
> Regards,
> Javi
> 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
>>> +---------------------------------------------------------------+

More information about the Molpro-user mailing list