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