On Nov 12, 2009, at 10:54 AM, Sergio Díaz wrote:

Hi Josh,

You were right. The main problem was the /tmp. SGE uses a scratch directory in which the jobs have temporary files. Setting TMPDIR to /tmp, checkpoint works!
However, when I try to restart it... I got the following error (see ERROR1). Option -v agrees these lines (see ERRO2).

It is concerning that ompi-restart is segfault'ing when it errors out. The error message is being generated between the launch of the opal-restart starter command and when we try to exec(cr_restart). Usually the failure is related to a corruption of the metadata stored in the checkpoint.

Can you send me the file below:
 ompi_global_snapshot_28454.ckpt/0/opal_snapshot_0.ckpt/snapshot_meta.data

I was able to reproduce the segv (at least I think it is the same one). We failed to check the validity of a string when we parse the metadata. I committed a fix to the trunk in r22290, and requested that the fix be moved to the v1.4 and v1.5 branches. If you are interested in seeing when they get applied you can follow the following tickets:
  https://svn.open-mpi.org/trac/ompi/ticket/2140
  https://svn.open-mpi.org/trac/ompi/ticket/2141

Can you try the trunk to see if the problem goes away? The development trunk and v1.5 series have a bunch of improvements to the C/R functionality that were never brought over the v1.3/v1.4 series.

I was trying to use ssh instead of rsh but I was impossible. By default it should use ssh and if it finds a problem, it will use rsh. It seems that ssh doesn't work because always use rsh.
If I change this MCA parameter, It still uses rsh.
If I set OMPI_MCA_plm_rsh_disable_qrsh variable to 1, It try to use ssh and doesn't works. I got --> "bash: orted: command not found" and the mpi process dies.
The command which try to execute is the following and I haven't found yet the reason why this command doesn't found orted because I set the /etc/bashrc in order to get always the right path and I have the right path into my application. (see ERROR4).

This seems like an SGE specific issue, so a bit out of my domain. Maybe others have suggestions here.

-- Josh

Many thanks!,
Sergio

P.S. Sorry about these long emails. I just try to show you useful information to identify my problems.


ERROR 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> [sdiaz@compute-3-18 ~]$ ompi-restart ompi_global_snapshot_28454.ckpt
> --------------------------------------------------------------------------
> Error: Unable to obtain the proper restart command to restart from the
>        checkpoint file (opal_snapshot_0.ckpt). Returned -1.
>
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> Error: Unable to obtain the proper restart command to restart from the
>        checkpoint file (opal_snapshot_1.ckpt). Returned -1.
>
> --------------------------------------------------------------------------
> [compute-3-18:28792] *** Process received signal ***
> [compute-3-18:28792] Signal: Segmentation fault (11)
> [compute-3-18:28792] Signal code:  (128)
> [compute-3-18:28792] Failing at address: (nil)
> [compute-3-18:28792] [ 0] /lib64/tls/libpthread.so.0 [0x33bbf0c430]
> [compute-3-18:28792] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x33bb669135]
> [compute-3-18:28792] [ 2] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_argv_free+0x2e) [0x2a95586658]
> [compute-3-18:28792] [ 3] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_event_fini+0x1e) [0x2a9557906e]
> [compute-3-18:28792] [ 4] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_finalize+0x36) [0x2a9556bcfa]
> [compute-3-18:28792] [ 5] opal-restart [0x40312a]
> [compute-3-18:28792] [ 6] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x33bb61c3fb]
> [compute-3-18:28792] [ 7] opal-restart [0x40272a]
> [compute-3-18:28792] *** End of error message ***
> [compute-3-18:28793] *** Process received signal ***
> [compute-3-18:28793] Signal: Segmentation fault (11)
> [compute-3-18:28793] Signal code:  (128)
> [compute-3-18:28793] Failing at address: (nil)
> [compute-3-18:28793] [ 0] /lib64/tls/libpthread.so.0 [0x33bbf0c430]
> [compute-3-18:28793] [ 1] /lib64/tls/libc.so.6(__libc_free+0x25) [0x33bb669135]
> [compute-3-18:28793] [ 2] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_argv_free+0x2e) [0x2a95586658]
> [compute-3-18:28793] [ 3] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_event_fini+0x1e) [0x2a9557906e]
> [compute-3-18:28793] [ 4] /opt/cesga/openmpi-1.3.3/lib/libopen-pal.so.0(opal_finalize+0x36) [0x2a9556bcfa]
> [compute-3-18:28793] [ 5] opal-restart [0x40312a]
> [compute-3-18:28793] [ 6] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x33bb61c3fb]
> [compute-3-18:28793] [ 7] opal-restart [0x40272a]
> [compute-3-18:28793] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 28792 on node compute-3-18.local exited on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


ERROR 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> [sdiaz@compute-3-18 ~]$ ompi-restart -v ompi_global_snapshot_28454.ckpt
>[compute-3-18.local:28941] Checking for the existence of (/home/cesga/sdiaz/ompi_global_snapshot_28454.ckpt)
> [compute-3-18.local:28941] Restarting from file (ompi_global_snapshot_28454.ckpt)
> [compute-3-18.local:28941]       Exec in self
> .......
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


ERROR3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>[sdiaz@compute-3-18 ~]$ ompi_info  --all|grep "plm_rsh_agent"
>         How many plm_rsh_agent instances to invoke concurrently (must be > 0)
>         MCA plm: parameter "plm_rsh_agent" (current value: "ssh : rsh", data source: default value, synonyms: pls_rsh_agent)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

ERROR4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>/usr/bin/ssh -x compute-3-17.local  orted --debug-daemons -mca ess env -mca orte_ess_jobid 2152464384 -mca orte_ess_vpid 1 -mca orte_ess_num_procs 2 --hnp-uri >"2152464384.0;tcp://192.168.4.143:59176" -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
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>










Josh Hursey escribió:

On Nov 9, 2009, at 5:33 AM, Sergio Díaz wrote:

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

This may be the core of the problem. ompi-ps and other command line tools (e.g., ompi-checkpoint) look for the Open MPI session directory in /tmp in order to find the connection information to connect to the mpirun process (internally called the HNP or Head Node Process).

Can you change the location of the temporary directory in SGE? The temporary directory is usually set via an environment variable (e.g., TMPDIR, or TMP). So removing the environment variable or setting it to /tmp might help.

but if I do ompi-ps -j MPIRUN_PID, it seems hanged and I interrupt it. Does it take long time?

It should not take a long time. It is just querying the mpirun process for state information.

what means the option -j of ompi-ps command? isn't it related to a batch system(like sge, condor...), is it?

The '-j' option allows the user to specify the Open MPI jobid. This is completely different than the jobid provided by the batch system. In general, users should not need to specify the -j option. It is useful when you have multiple Open MPI jobs, and want a summary of just one of them.

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.

Try 'ssh' and see if that helps. I suspect the problem is with the session directory location though.

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: sdiaz@cesga.es ; http://www.cesga.es/
<image002.jpg>
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users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
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: sdiaz@cesga.es ; http://www.cesga.es/
<image002.jpg>
------------------------------------------------
_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
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: sdiaz@cesga.es ; http://www.cesga.es/
<image002.jpg>
------------------------------------------------
_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

_______________________________________________
users mailing list
users@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users

--
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: sdiaz@cesga.es ; http://www.cesga.es/

------------------------------------------------