From: Josh Hursey (jjhursey_at_[hidden])
Date: 2006-08-30 10:03:55
yet another point (sorry for the spam). This may not be an MTT issue
but a broken ORTE on the trunk :(
When I try to run in a allocation (srun -N 16 -A) things run fine.
But if I try to run in batch mode (srun -N 16 -b myscript.sh) then I
see the same hang as in MTT. seems that mpirun is not getting
properly notified of the completion of the job. :(
I'll try to investigate a bit further today. Any thoughts on what
might be causing this?
Cheers,
Josh
On Aug 30, 2006, at 9:54 AM, Josh Hursey wrote:
> forgot this bit in my mail. With the mpirun just hanging out there I
> attached GDB and got the following stack trace:
> (gdb) bt
> #0 0x0000003d1b9bd1af in poll () from /lib64/tls/libc.so.6
> #1 0x0000002a956e6389 in opal_poll_dispatch (base=0x5136d0,
> arg=0x513730, tv=0x7fbfffee70) at poll.c:191
> #2 0x0000002a956e28b6 in opal_event_base_loop (base=0x5136d0,
> flags=5) at event.c:584
> #3 0x0000002a956e26b7 in opal_event_loop (flags=5) at event.c:514
> #4 0x0000002a956db7c7 in opal_progress () at runtime/opal_progress.c:
> 259
> #5 0x000000000040334c in opal_condition_wait (c=0x509650,
> m=0x509600) at ../../../opal/threads/condition.h:81
> #6 0x0000000000402f52 in orterun (argc=9, argv=0x7fbffff0b8) at
> orterun.c:444
> #7 0x00000000004028a3 in main (argc=9, argv=0x7fbffff0b8) at
> main.c:13
>
> Seems that mpirun is waiting for things to complete :/
>
> On Aug 30, 2006, at 9:53 AM, Josh Hursey wrote:
>
>>
>> On Aug 30, 2006, at 7:19 AM, Jeff Squyres wrote:
>>
>>> On 8/29/06 8:57 PM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:
>>>
>>>>> Does this apply to *all* tests, or only some of the tests (like
>>>>> allgather)?
>>>>
>>>> All of the tests: Trivial and ibm. They all timeout :(
>>>
>>> Blah. The trivial tests are simply "hello world", so they should
>>> take just
>>> about no time at all.
>>>
>>> Is this running under SLURM? I put the code in there to know how
>>> many procs
>>> to use in SLURM but have not tested it in eons. I doubt that's the
>>> problem,
>>> but that's one thing to check.
>>>
>>
>> Yep it is in SLURM. and it seems that the 'number of procs' code is
>> working fine as it changes with different allocations.
>>
>>> Can you set a super-long timeout (e.g., a few minutes), and while
>>> one of the
>>> trivial tests is running, do some ps's on the relevant nodes and
>>> see what,
>>> if anything, is running? E.g., mpirun, the test executable on the
>>> nodes,
>>> etc.
>>
>> Without setting a long timeout. It seems that mpirun is running, but
>> nothing else and only on the launching node.
>>
>> When a test starts you see the mpirun launching properly:
>> $ ps aux | grep ...
>> USER PID %CPU %MEM VSZ RSS TTY STAT START TIME
>> COMMAND
>> mpiteam 15117 0.5 0.8 113024 33680 ? S 09:32 0:06
>> perl ./
>> client/mtt --debug --scratch /u/mpiteam/tmp/mtt-scratch --file /u/
>> mpiteam/local/etc/ompi-iu-odin-core.ini --verbose --print-time
>> mpiteam 15294 0.0 0.0 0 0 ? Z 09:32 0:00 [sh]
>> <defunct>
>> mpiteam 28453 0.2 0.0 38072 3536 ? S 09:50 0:00 mpirun
>> -mca btl tcp,self -np 32 --prefix /san/homedirs/mpiteam/tmp/mtt-
>> scratch/installs/ompi-nightly-trunk/odin_gcc_warnings/1.3a1r11497/
>> install collective/allgather_in_place
>> mpiteam 28454 0.0 0.0 41716 2040 ? Sl 09:50 0:00
>> srun --
>> nodes=16 --ntasks=16 --
>> nodelist=odin022,odin021,odin020,odin019,odin018,odin017,odin016,odin
>> 0
>> 15
>> ,odin014,odin013,odin012,odin011,odin010,odin009,odin008,odin007
>> orted --no-daemonize --bootproxy 1 --ns-nds slurm --name 0.0.1 --
>> num_procs 16 --vpid_start 0 --universe
>> mpiteam_at_[hidden]:default-universe-28453 --nsreplica
>> "0.0.0;tcp://129.79.240.107:40904" --gprreplica "0.0.0;tcp://
>> 129.79.240.107:40904"
>> mpiteam 28455 0.0 0.0 23212 1804 ? Ssl 09:50 0:00
>> srun --
>> nodes=16 --ntasks=16 --
>> nodelist=odin022,odin021,odin020,odin019,odin018,odin017,odin016,odin
>> 0
>> 15
>> ,odin014,odin013,odin012,odin011,odin010,odin009,odin008,odin007
>> orted --no-daemonize --bootproxy 1 --ns-nds slurm --name 0.0.1 --
>> num_procs 16 --vpid_start 0 --universe
>> mpiteam_at_[hidden]:default-universe-28453 --nsreplica
>> "0.0.0;tcp://129.79.240.107:40904" --gprreplica "0.0.0;tcp://
>> 129.79.240.107:40904"
>> mpiteam 28472 0.0 0.0 36956 2256 ? S 09:50 0:00 /san/
>> homedirs/mpiteam/tmp/mtt-scratch/installs/ompi-nightly-trunk/
>> odin_gcc_warnings/1.3a1r11497/install/bin/orted --no-daemonize --
>> bootproxy 1 --ns-nds slurm --name 0.0.1 --num_procs 16 --vpid_start 0
>> --universe mpiteam_at_[hidden]:default-universe-28453 --
>> nsreplica "0.0.0;tcp://129.79.240.107:40904" --gprreplica
>> "0.0.0;tcp://129.79.240.107:40904"
>> mpiteam 28482 0.1 0.0 64296 3564 ? S 09:50 0:00
>> collective/allgather_in_place
>> mpiteam 28483 0.1 0.0 64296 3564 ? S 09:50 0:00
>> collective/allgather_in_place
>>
>> But once the test finishes, mpirun seems to just be hanging out.
>> $ ps aux | grep ...
>> USER PID %CPU %MEM VSZ RSS TTY STAT START TIME
>> COMMAND
>> mpiteam 15083 0.0 0.0 52760 1040 ? S 09:31 0:00 /bin/
>> bash /var/tmp/slurmd/job148126/script
>> root 15086 0.0 0.0 42884 3172 ? Ss 09:31 0:00 sshd:
>> mpiteam [priv]
>> mpiteam 15088 0.0 0.0 43012 3252 ? S 09:31 0:00 sshd:
>> mpiteam_at_pts/1
>> mpiteam 15089 0.0 0.0 56680 1912 pts/1 Ss 09:31 0:00 -tcsh
>> mpiteam 15117 0.5 0.8 113024 33680 ? S 09:32 0:06
>> perl ./
>> client/mtt --debug --scratch /u/mpiteam/tmp/mtt-scratch --file /u/
>> mpiteam/local/etc/ompi-iu-odin-core.ini --verbose --print-time
>> mpiteam 15294 0.0 0.0 0 0 ? Z 09:32 0:00 [sh]
>> <defunct>
>> mpiteam 28453 0.0 0.0 38204 3568 ? S 09:50 0:00 mpirun
>> -mca btl tcp,self -np 32 --prefix /san/homedirs/mpiteam/tmp/mtt-
>> scratch/installs/ompi-nightly-trunk/odin_gcc_warnings/1.3a1r11497/
>> install collective/allgather_in_place
>>
>> Thoughts?
>>
>>>
>>> --
>>> Jeff Squyres
>>> Server Virtualization Business Unit
>>> Cisco Systems
>>
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