From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2006-08-30 14:49:58
More specifically -- I have now fixed this on the trunk (that the csh file
that gets dropped emits
if (\$?LD_LIBRARY_PATH == 0) then
setenv LD_LIBRARY_PATH $ret->{libdir}
else
setenv LD_LIBRARY_PATH $ret->{libdir}:\$LD_LIBRARY_PATH
endif\n";
(I didn't have the $? Escaped before, so it emitted "0LD_LIBRARY_PATH)
I have not yet moved this over to the release branch; I will do so shortly
(needs to be reviewed first).
But we don't use this file in MTT; it's purely for human convenience. MTT
sets its own environment variables via Perl's $ENV, and the fork/exec's of
tests pick up the parent environment.
Make sense?
So if you're suddenly working properly, something else changed... :-(
On 8/30/06 2:45 PM, "Jeff Squyres" <jsquyres_at_[hidden]> wrote:
> ?
>
> 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