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From: Heywood, Todd (heywood_at_[hidden])
Date: 2007-02-06 09:44:07


Hi Ralph,

Thanks for the reply. This is a tough one. It is OpenLDAP. I had thought that I might be hitting a file descriptor limit for slapd (LDAP daemon), which ulimit -n does not effect (you have to rebuild LDAP with a different FD_SETSIZE variable). However, I simply turned on more expressive logging to /var/log/slapd, and that resulted in smaller jobs (which successfully ran before) hanging. Go figure. It appears that daemons are up and running (from ps), and everything hangs in MPI_Init. Ctl-C gives

[blade1:04524] ERROR: A daemon on node blade26 failed to start as expected.
[blade1:04524] ERROR: There may be more information available from
[blade1:04524] ERROR: the remote shell (see above).
[blade1:04524] ERROR: The daemon exited unexpectedly with status 255.

I'm interested in any suggestion, semi-fixes, etc. which might help get to the bottom of this. Right now: whether the daemons are indeed up and running, or if there are some that are not (causing MPI_Init to hang).

Thanks,

Todd

-----Original Message-----
From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf Of Ralph H Castain
Sent: Tuesday, February 06, 2007 8:52 AM
To: Open MPI Users <users_at_[hidden]>
Subject: Re: [OMPI users] large jobs hang on startup (deadlock?)

Well, I can't say for sure about LDAP. I did a quick search and found two
things:

1. there are limits imposed in LDAP that may apply to your situation, and

2. that statement varies tremendously depending upon the specific LDAP
implementation you are using

I would suggest you see which LDAP you are using and contact the respective
organization to ask if they do have such a limit, and if so, how to adjust
it.

It sounds like maybe we are hitting the LDAP server with too many requests
too rapidly. Usually, the issue is not starting fast enough, so this is a
new one! We don't currently check to see if everything started up okay, so
that is why the processes might hang - we hope to fix that soon. I'll have
to see if there is something we can do to help alleviate such problems -
might not be in time for the 1.2 release, but perhaps it will make a
subsequent "fix" or, if you are willing/interested, I could provide it to
you as a "patch" you could use until a later official release.

Meantime, you might try upgrading to 1.2b3 or even a nightly release from
the trunk. There are known problems with 1.2b2 (which is why there is a b3
and soon to be an rc1), though I don't think that will be the problem here.
At the least, the nightly trunk has a much better response to ctrl-c in it.

Ralph

On 2/5/07 9:50 AM, "Heywood, Todd" <heywood_at_[hidden]> wrote:

> Hi Ralph,
>
> Thanks for the reply. The OpenMPI version is 1.2b2 (because I would like to
> integrate it with SGE).
>
> Here is what is happening:
>
> (1) When I run with ­debug-daemons (but WITHOUT ­d), I get ³Daemon
> [0,0,27] checking in as pid 7620 on host blade28² (for example) messages for
> most but not all of the daemons that should be started up, and then it hangs.
> I also notice ³reconnecting to LDAP server² messages in various
> /var/log/secure files, and cannot login while things are hung (with ³su:
> pam_ldap: ldap_result Can't contact LDAP server² in /var/log/messages). So
> apparently LDAP hits some limit to opening ssh sessions, and I¹m not sure how
> to address this.
> (2) When I run with ­debug-daemons AND the debug option ­d, all daemons
> start start up and check-in, albeit slowly (debug must slow things down so
> LDAP can handle all the requests??). Then apparently, the cpi process is
> started for each task but it then hangs:
>
> [blade1:23816] spawn: in job_state_callback(jobid = 1, state = 0x4)
> [blade1:23816] Info: Setting up debugger process table for applications
> MPIR_being_debugged = 0
> MPIR_debug_gate = 0
> MPIR_debug_state = 1
> MPIR_acquired_pre_main = 0
> MPIR_i_am_starter = 0
> MPIR_proctable_size = 800
> MPIR_proctable:
> (i, host, exe, pid) = (0, blade1, /home4/itstaff/heywood/ompi/cpi, 24193)
> Ð
> Ð(i, host, exe, pid) = (799, blade213, /home4/itstaff/heywood/ompi/cpi, 4762)
>
> A ³ps² on the head node shows 200 open ssh sessions, and 4 cpi processes doing
> nothing. A ^C gives this:
>
> mpirun: killing job...
>
> --------------------------------------------------------------------------
> WARNING: A process refused to die!
>
> Host: blade1
> PID: 24193
>
> This process may still be running and/or consuming resources.
>
>
>
>
> Still got a ways to go, but any ideas/suggestions are welcome!
>
> Thanks,
>
> Todd
>
>
>
>
> From: users-bounces_at_[hidden] [mailto:users-bounces_at_[hidden]] On Behalf
> Of Ralph Castain
> Sent: Friday, February 02, 2007 5:20 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] large jobs hang on startup (deadlock?)
>
> Hi Todd
>
> To help us provide advice, could you tell us what version of OpenMPI you are
> using?
>
> Meantime, try adding ³-mca pls_rsh_num_concurrent 200² to your mpirun command
> line. You can up the number of concurrent daemons we launch to anything your
> system will support ­ basically, we limit the number only because some systems
> have limits on the number of ssh calls we can have active at any one time.
> Because we hold stdio open when running with ‹debug-daemons, the number of
> concurrent daemons must match or exceed the number of nodes you are trying to
> launch on.
>
> I have a ³fix² in the works that will help relieve some of that restriction,
> but that won¹t come out until a later release.
>
> Hopefully, that will allow you to obtain more debug info about why/where
> things are hanging.
>
> Ralph
>
>
> On 2/2/07 11:41 AM, "Heywood, Todd" <heywood_at_[hidden]> wrote:
> I have OpenMPI running fine for a small/medium number of tasks (simple hello
> or cpi program). But when I try 700 or 800 tasks, it hangs, apparently on
> startup. I think this might be related to LDAP, since if I try to log into my
> account while the job is hung, I get told my username doesn¹t exist. However,
> I tried adding ­debug to the mpirun, and got the same sequence of output as
> for successful smaller runs, until it hung again. So I added ­-debug-daemons
> and got this (with an exit, i.e. no hanging):
> Ð
> [blade1:31733] [0,0,0] wrote setup file
> --------------------------------------------------------------------------
> The rsh launcher has been given a number of 128 concurrent daemons to
> launch and is in a debug-daemons option. However, the total number of
> daemons to launch (200) is greater than this value. This is a scenario that
> will cause the system to deadlock.
>
> To avoid deadlock, either increase the number of concurrent daemons, or
> remove the debug-daemons flag.
> --------------------------------------------------------------------------
> [blade1:31733] [0,0,0] ORTE_ERROR_LOG: Fatal in file
> ../../../../../orte/mca/rmgr/urm/
> rmgr_urm.c at line 455
> [blade1:31733] mpirun: spawn failed with errno=-6
> [blade1:31733] sess_dir_finalize: proc session dir not empty - leaving
>
> Any ideas or suggestions appreciated.
>
> Todd Heywood
>
>
>
>
>
>
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