From: Josh Hursey (jjhursey_at_[hidden])
Date: 2006-08-30 12:10:23
On Aug 30, 2006, at 11:36 AM, Jeff Squyres wrote:
> (sorry -- been afk much of this morning)
>
> MTT directly sets environment variables in its own environment (via
> $ENV{whatever} = "foo") before using fork/exec to launch compiles
> and runs.
> Hence, the forked children inherit the environment variables that
> we set
> (E.g., PATH and LD_LIBRARY_PATH).
>
> So if you source the env vars files that MTT drops, that should be
> sufficient.
Does it drop them to a file, or is it printed in the debugging output
anywhere? I'm having a bit of trouble finding these strings in the
output.
>
> As for setting the values on *remote* nodes, we do it solely via the
> --prefix option. I wonder if --prefix is broken under SLURM...?
> That might
> be something to check -- youmight be inadvertantly mixing
> installations of
> OMPI...?
Yep I'll check it out.
Cheers,
Josh
>
>
> On 8/30/06 10:36 AM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:
>
>> I'm trying to replicate the MTT environment as much as possible, and
>> have a couple of questions.
>>
>> Assume there is no mpirun in my PATH/LD_LIBRARY_PATH when I start
>> MTT. After MTT builds Open MPI, how does it export these variables so
>> that it can build the tests? How does it export these when it runs
>> those tests (solely via --prefix)?
>>
>> Cheers,
>> josh
>>
>> On Aug 30, 2006, at 10:25 AM, Josh Hursey wrote:
>>
>>> I already tried that. However I'm trying it in a couple different
>>> ways and getting some mixed results. Let me formulate the error
>>> cases
>>> and get back to you.
>>>
>>> Cheers,
>>> Josh
>>>
>>> On Aug 30, 2006, at 10:17 AM, Ralph H Castain wrote:
>>>
>>>> Well, why don't you try first separating this from MTT? Just run
>>>> the command
>>>> manually in batch mode and see if it works. If that works, then the
>>>> problem
>>>> is with MTT. Otherwise, we have a problem with notification.
>>>>
>>>> Or are you saying that you have already done this?
>>>> Ralph
>>>>
>>>>
>>>> On 8/30/06 8:03 AM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:
>>>>
>>>>> 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
>>>>>>> ,o
>>>>>>> d
>>>>>>> in
>>>>>>> 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
>>>>>>> ,o
>>>>>>> d
>>>>>>> in
>>>>>>> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> mtt-users mailing list
>>>>>>> mtt-users_at_[hidden]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/mtt-users
>>>>>>
>>>>>> _______________________________________________
>>>>>> mtt-users mailing list
>>>>>> mtt-users_at_[hidden]
>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/mtt-users
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> mtt-users mailing list
>>> mtt-users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/mtt-users
>>
>> _______________________________________________
>> mtt-users mailing list
>> mtt-users_at_[hidden]
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>
>
> --
> Jeff Squyres
> Server Virtualization Business Unit
> Cisco Systems