[molpro-user] Killing Molpro Jobs using SGE

[Javier Díaz Montes]

Hi,
I have 2 processes tree in the MPICH master:

  2679 ?        S      4:45 /opt/gridengine/bin/lx26-amd64/sge_execd
27260 ?        S      0:00  \_ sge_shepherd-230612 -bg
27315 ?        Ss     0:00      \_ -sh  
/opt/gridengine/default/spool/compute-0-19/job_scripts/230612
27423 ?        S      0:00          \_ /bin/bash -xv .gw_mluisa_1/.wrapper
27442 ?        S      0:00              \_ /bin/bash  
/home/programs/molpro/bin/gwmolprop MgO3is2dbl1.com
27472 ?        S      0:00                  \_  
/home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molpro -n6  
--mpirun-machinefile /home/dartakan/.230612/machines
27473 ?        S      0:00                      \_ mpirun -np 6  
-machinefile /home/dartakan/.230612/machines  
/home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molprop_2006_1_i8_p4_mpi.exe

27480 ?        Ss     0:00 orted --bootproxy 1 --name 0.0.6 --num_procs 7  
--vpid_start 0 --nodename compute-0-19 --universe  
dartakan at compute-0-19.local:default-universe --nsreplica  
"0.0.0;tcp://192.168.1.235:33312" --gprreplica  
"0.0.0;tcp://192.168.1.235:33312" --mpi-call-yield 0
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


And this other one on each MPICH slave:

  4471 ?        Ss     0:00 orted --bootproxy 1 --name 0.0.5 --num_procs 7  
--vpid_start 0 --nodename compute-0-5 --universe dar
  4472 ?        R    624:03  \_  
/home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molprop_2006_1_i8_p4_mpi.exe
  4474 ?        S      0:00      \_  
/home/programs/molpro/molpro-Linux-x86_64-i8-2006.1/molprop_2006_1_i8_p4_mpi.exe

Then, if I kill a job from SGE, The second molprop_2006_1_i8_p4_mpi.exe  
process will start to run

Regards,
Javi

En Tue, 04 Dec 2007 12:31:22 +0100, Reuti <reuti at staff.uni-marburg.de>  
escribió:

> 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.
>
> this is unusual. For MPICH it's normal to have two processes for each  
> started task.
>
> What does the process tree look like on one of these nodes with a  
> running job:
>
> ps -e f -o pid,ppid,pgrp,command
>
> (f w/o -) -- Reuti
>
>> 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
>> +---------------------------------------------------------------+
>
>
>