Hi Josh,
The OpenMPI version is 1.3.3.
The command ompi-ps doesn't work.
[root@compute-3-18 ~]# ompi-ps -j 2726959 -p 16241
[root@compute-3-18 ~]# ompi-ps -v -j 2726959 -p 16241
[compute-3-18.local:16254] orte_ps: Acquiring list of HNPs and setting
contact info into RML...
[root@compute-3-18 ~]# ompi-ps -v -j 2726959
[compute-3-18.local:16255] orte_ps: Acquiring list of HNPs and setting
contact info into RML...
[root@compute-3-18 ~]# ps uaxf | grep sdiaz
root 16260 0.0 0.0 51084 680 pts/0 S+ 13:38 0:00
\_ grep sdiaz
sdiaz 16203 0.0 0.0 53164 1220 ? Ss 13:37 0:00 \_
-bash /opt/cesga/sge62/default/spool/compute-3-18/job_scripts/2726959
sdiaz 16241 0.0 0.0 41028 2480 ? S 13:37 0:00
\_ mpirun -np 2 -am ft-enable-cr ./pi3
sdiaz 16242 0.0 0.0 36484 1840 ? Sl 13:37
0:00 \_ /opt/cesga/sge62/bin/lx24-x86/qrsh -inherit
-nostdin -V compute-3-17.local orted -mca ess env -mca orte_ess_jobid
2769879040 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 2 --hnp-uri
"2769879040.0;tcp://192.168.4.143:57010" -mca mca_base_param_file_prefix
ft-enable-cr -mca mca_base_param_file_path
/opt/cesga/openmpi-1.3.3/share/openmpi/amca-param-sets:/home_no_usc/cesga/sdiaz/mpi_test
-mca mca_base_param_file_path_force /home_no_usc/cesga/sdiaz/mpi_test
sdiaz 16245 0.1 0.0 99464 4616 ? Sl 13:37
0:00 \_ ./pi3
[root@compute-3-18 ~]# ompi-ps -n c3-18
[root@compute-3-18 ~]# ompi-ps -n compute-3-18
[root@compute-3-18 ~]# ompi-ps -n
There is not directory on the /tmp of the node. However, if the
application is run without SGE, the directory is created but if I do
ompi-ps -j MPIRUN_PID, it seems hanged and I interrupt it. Does it take
long time?
what means the option -j of ompi-ps command? isn't it related to a batch
system(like sge, condor...), is it?
Thanks for the ticket. I will follow it.
Talking with Alan, I realized that there are few transport protocols
that are supported. And maybe it is the problem. Currently, SGE is using
qrsh to expand mpi process. I can change this protocol and use ssh. So,
I'm going to test it this afternoon and I will comment to you the results.
Regards,
Sergio
Josh Hursey escribió:
On Oct 28, 2009, at 7:41 AM, Sergio Díaz wrote:
Hello,
I have achieved the checkpoint of an easy program without SGE. Now,
I'm trying to do the integration openmpi+sge but I have some
problems... When I try to do checkpoint of the mpirun PID, I got an
error similar to the error gotten when the PID doesn't exit. The
example below.
I do not have any experience with the SGE environment, so I suspect
that there may something 'special' about the environment that is
tripping up the ompi-checkpoint tool.
First of all, what version of Open MPI are you using?
Somethings to check:
- Does 'ompi-ps' work when your application is running?
- Is there an /tmp/openmpi-sessions-* directory on the node where
mpirun is currently running? This directory contains information on
how to connect to the mpirun process from an external tool, if it's
missing then this could be the cause of the problem.
Any ideas?
Somebody have a script to do it automatic with SGE?. For example I
have one to do checkpoint each X seconds with BLCR and non-mpi jobs.
It is launched by SGE if you have configured the queue and the ckpt
environment.
I do not know of any integration of the Open MPI checkpointing work
with SGE at the moment.
As far as time triggered checkpointing, I have a feature ticket open
about this:
https://svn.open-mpi.org/trac/ompi/ticket/1961
It is not available yet, but in the works.
Is it possible choose the name of the ckpt folder when you do the
ompi-checkpoint? I can't find the option to do it.
Not at this time. Though I could see it as a useful feature, and
shouldn't be too hard to implement. I filed a ticket if you want to
follow the progress:
https://svn.open-mpi.org/trac/ompi/ticket/2098
-- Josh
Regards,
Sergio
--------------------------------
[sdiaz@compute-3-17 ~]$ ps auxf
....
root 20044 0.0 0.0 4468 1224 ? S 13:28 0:00 \_
sge_shepherd-2645150 -bg
sdiaz 20072 0.0 0.0 53172 1212 ? Ss 13:28 0:00
\_ -bash /opt/cesga/sge62/default/spool/compute-3-17/job_scripts/2645150
sdiaz 20112 0.2 0.0 41028 2480 ? S 13:28
0:00 \_ mpirun -np 2 -am ft-enable-cr pi3
sdiaz 20113 0.0 0.0 36484 1824 ? Sl 13:28
0:00 \_ /opt/cesga/sge62/bin/lx24-x86/qrsh -inherit
-nostdin -V compute-3-18..........
sdiaz 20116 1.2 0.0 99464 4616 ? Sl 13:28
0:00 \_ pi3
[sdiaz@compute-3-17 ~]$ ompi-checkpoint 20112
[compute-3-17.local:20124] HNP with PID 20112 Not found!
[sdiaz@compute-3-17 ~]$ ompi-checkpoint -s 20112
[compute-3-17.local:20135] HNP with PID 20112 Not found!
[sdiaz@compute-3-17 ~]$ ompi-checkpoint -s --term 20112
[compute-3-17.local:20136] HNP with PID 20112 Not found!
[sdiaz@compute-3-17 ~]$ ompi-checkpoint --hnp-pid 20112
--------------------------------------------------------------------------
ompi-checkpoint PID_OF_MPIRUN
Open MPI Checkpoint Tool
-am <arg0> Aggregate MCA parameter set file list
-gmca|--gmca <arg0> <arg1>
Pass global MCA parameters that are
applicable to
all contexts (arg0 is the parameter name;
arg1 is
the parameter value)
-h|--help This help message
--hnp-jobid <arg0> This should be the jobid of the HNP whose
applications you wish to checkpoint.
--hnp-pid <arg0> This should be the pid of the mpirun whose
applications you wish to checkpoint.
-mca|--mca <arg0> <arg1>
Pass context-specific MCA parameters; they are
considered global if --gmca is not used and
only
one context is specified (arg0 is the parameter
name; arg1 is the parameter value)
-s|--status Display status messages describing the
progression
of the checkpoint
--term Terminate the application after checkpoint
-v|--verbose Be Verbose
-w|--nowait Do not wait for the application to finish
checkpointing before returning
--------------------------------------------------------------------------
[sdiaz@compute-3-17 ~]$ exit
logout
Connection to c3-17 closed.
[sdiaz@svgd mpi_test]$ ssh c3-18
Last login: Wed Oct 28 13:24:12 2009 from svgd.local
-bash-3.00$ ps auxf |grep sdiaz
sdiaz 14412 0.0 0.0 1888 560 ? Ss 13:28 0:00
\_ /opt/cesga/sge62/utilbin/lx24-x86/qrsh_starter
/opt/cesga/sge62/default/spool/compute-3-18/active_jobs/2645150.1/1.compute-3-18
sdiaz 14419 0.0 0.0 35728 2260 ? S 13:28
0:00 \_ orted -mca ess env -mca orte_ess_jobid 2295267328
-mca orte_ess_vpid 1 -mca orte_ess_num_procs 2 --hnp-uri
2295267328.0;tcp://192.168.4.144:36596 -mca
mca_base_param_file_prefix ft-enable-cr -mca mca_base_param_file_path
/opt/cesga/openmpi-1.3.3/share/openmpi/amca-param-sets:/home_no_usc/cesga/sdiaz/mpi_test
-mca mca_base_param_file_path_force /home_no_usc/cesga/sdiaz/mpi_test
sdiaz 14420 0.0 0.0 99452 4596 ? Sl 13:28
0:00 \_ pi3
--
Sergio Díaz Montes
Centro de Supercomputacion de Galicia
Avda. de Vigo. s/n (Campus Sur) 15706 Santiago de Compostela (Spain)
Tel: +34 981 56 98 10 ; Fax: +34 981 59 46 16
email: sd...@cesga.es ; http://www.cesga.es/
<image002.jpg>
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--
Sergio Díaz Montes
Centro de Supercomputacion de Galicia
Avda. de Vigo. s/n (Campus Sur) 15706 Santiago de Compostela (Spain)
Tel: +34 981 56 98 10 ; Fax: +34 981 59 46 16
email: sd...@cesga.es ; http://www.cesga.es/
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