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From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2006-08-30 14:45:40


?

How could that fix your hanging? The code I'm talking about in MTT is the
part that drops those files. We don't actually *use* those files in MTT
anywhere -- they're solely for humans to use after the fact...

If you're suddenly running properly, I'm suspicious. :-(

On 8/30/06 2:38 PM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:

> This fixes the hanging and gets me running (and passing) some/most of
> the tests [Trivial and ibm]. Yay!
>
> I have a 16 processor job running on Odin at the moment that seems to
> be going well so far.
>
> Thanks for your help.
>
> Want me to file a bug about the tcsh problem below?
>
> -- Josh
>
> On Aug 30, 2006, at 2:30 PM, Jeff Squyres wrote:
>
>> Bah!
>>
>> This is the result of perl expanding $? To 0 -- it seems that I
>> need to
>> escape $? So that it's not output as 0.
>>
>> Sorry about that!
>>
>> So is this just for the sourcing files, or for your overall (hanging)
>> problems?
>>
>>
>> On 8/30/06 2:28 PM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:
>>
>>> So here are the results of my exploration. I have things running now.
>>> The problem was that the user that I am running under does not set
>>> the LD_LIBRARY_PATH variable at any point. So when MTT tries to
>>> export the variable it does:
>>> if (0LD_LIBRARY_PATH == 0) then
>>> setenv LD_LIBRARY_PATH /san/<rest_of_path>/install/lib
>>> else
>>> setenv LD_LIBRARY_PATH /san/<rest_of_path>/install/lib:
>>> $LD_LIBRARY_PATH
>>> endif
>>>
>>> So this causes tcsh to emit the error the LD_LIBRARY_PATH is not
>>> defined. So it is not set due to the error.
>>>
>>> I fixed this by always declaring it in the .cshrc file to "". However
>>> MTT could do a sanity check before trying to check the value to see
>>> if it is defined. Something like:
>>>
>>> <code>
>>> if ($?LD_LIBRARY_PATH) then
>>> else
>>> setenv LD_LIBRARY_PATH ""
>>> endif
>>>
>>> if (0LD_LIBRARY_PATH == 0) then
>>> setenv LD_LIBRARY_PATH /san/<rest_of_path>/install/lib
>>> else
>>> setenv LD_LIBRARY_PATH /san/<rest_of_path>/install/lib:
>>> $LD_LIBRARY_PATH
>>> endif
>>> </code>
>>>
>>> or something of the sort.
>>>
>>> As another note, could we start a "How to debug MTT" Wiki page with
>>> some of the information that Jeff sent in this message regarding the
>>> dumping of env vars? I think that would be helpful when getting
>>> things started.
>>>
>>> Thanks for all your help, I'm sure I'll have more questions in the
>>> near future.
>>>
>>> Cheers,
>>> Josh
>>>
>>>
>>> On Aug 30, 2006, at 12:31 PM, Jeff Squyres wrote:
>>>
>>>> On 8/30/06 12:10 PM, "Josh Hursey" <jjhursey_at_[hidden]> wrote:
>>>>
>>>>>> 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.
>>>>
>>>> It does not put these in the -debug output.
>>>>
>>>> The files that it drops are in the scratch dir. You'll need to go
>>>> into
>>>> scratch/installs, and then it depends on what your INI file section
>>>> names
>>>> are. You'll go to:
>>>>
>>>> <scratch>/installs/<mpi get>/<mpi install>/<mpi_version>/
>>>>
>>>> And there should be files named "mpi_installed_vars.[csh|sh]" that
>>>> you can
>>>> source, depending on your shell. IT should set PATH and
>>>> LD_LIBRARY_PATH.
>>>>
>>>> The intent of these files is for exactly this purpose -- for a
>>>> human to test
>>>> borked MPI installs inside the MTT scratch tree.
>>>>
>>>>>>
>>>>>> 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,odi
>>>>>>>>>>>> n0
>>>>>>>>>>>> 16
>>>>>>>>>>>> ,o
>>>>>>>>>>>> d
>>>>>>>>>>>> in
>>>>>>>>>>>> 0
>>>>>>>>>>>> 15
>>>>>>>>>>>> ,odin014,odin013,odin012,odin011,odin010,odin009,odin008,odi
>>>>>>>>>>>> n0
>>>>>>>>>>>> 07
>>>>>>>>>>>> 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,odi
>>>>>>>>>>>> n0
>>>>>>>>>>>> 16
>>>>>>>>>>>> ,o
>>>>>>>>>>>> d
>>>>>>>>>>>> in
>>>>>>>>>>>> 0
>>>>>>>>>>>> 15
>>>>>>>>>>>> ,odin014,odin013,odin012,odin011,odin010,odin009,odin008,odi
>>>>>>>>>>>> n0
>>>>>>>>>>>> 07
>>>>>>>>>>>> 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]
>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/mtt-users
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>
>>>>
>>>> --
>>>> 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
>>
>>
>> --
>> 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

-- 
Jeff Squyres
Server Virtualization Business Unit
Cisco Systems