[torqueusers] pbs_mom dies on exit of interactive session

DuChene, StevenX A stevenx.a.duchene at intel.com
Mon Apr 30 10:20:51 MDT 2012


If you can tell me what additional information you need I can try to obtain it.
--
Steven DuChene

From: torqueusers-bounces at supercluster.org [mailto:torqueusers-bounces at supercluster.org] On Behalf Of David Beer
Sent: Monday, April 30, 2012 9:00 AM
To: Torque Users Mailing List
Subject: Re: [torqueusers] pbs_mom dies on exit of interactive session

Roy,

I'm sorry your message wasn't attended to - its the nature of a mailing list that sometimes messages are lost. Can you (or Steve) describe the TM connect issues in a bit more detail? We should get a bug report filed for this.

David
On Sun, Apr 29, 2012 at 11:03 AM, Roy Dragseth <roy.dragseth at cc.uit.no> wrote:
I can confirm this too (reported the same problem to the mailing list a month ago, but nobody seemed to care). Torque 3.0.4 works fine with exactly the same system config.
 
r.
 
 
On Saturday 28. April 2012 03.21.05 DuChene, StevenX A wrote:
I am running torque-4.0.1 that I pulled from the svn 4.0.1 branch just today.
Earlier today I was running the 4.0-fixes tree from 04/03 and I had the same results.
I was hoping the update to current sources would fix these problems but no such luck.
 
If I run the following:
 
qsub -I -l nodes=7 -l arch=atomN570
 
from my pbs job submission host I get:
 
qsub: waiting for job 4.login2.sep.here to start
qsub: job 4.login2.sep.here ready
 
and then I get a shell prompt on the node 0 of this job.
 
If I then do:
 
$ echo $PBS_NODEFILE
/var/spool/torque/aux//4.login2.sep.here
 
And then:
 
$ cat /var/spool/torque/aux//4.login2.sep.here
atom255
atom255
atom255
atom255
atom254
atom254
atom254
 
and then I try:
 
$ pbsdsh -h atom254 ls /tmp
pbsdsh: error from tm_poll() 17002
 
Alternatively if I use the -v option it says:
 
$ pbsdsh -v -h atom254 /bin/ls /tmp
pbsdsh: tm_init failed, rc = TM_ESYSTEM (17000)
 
Then when I exit the shell I get back to my job submission node but when I then check for the pbs_mom process on that node 0 for the job that I just had the shell prompt on, the pbs_mom process is no longer running and the status message from the init script says:
 
pbs_mom dead but subsys locked
 
Also if I run any mpi jobs through torque that are run on cpu cores on one system, they seem to run just fine but for mpi jobs where the job spans across separate nodes I get the following error out each time:
 
$ cat script_viking_7nodes.pbs.e12
[viking12.sep.here:12360] plm:tm: failed to poll for a spawned daemon, return status = 17002
--------------------------------------------------------------------------
A daemon (pid unknown) died unexpectedly on signal 1  while attempting to
launch so we are aborting.
 
There may be more information reported by the environment (see above).
 
This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons on the nodes shown
below. Additional manual cleanup may be required - please refer to
the "orte-clean" tool for assistance.
--------------------------------------------------------------------------
        viking11.sep.here - daemon did not report back when launched
 
The PBS job script for this MPI job is very simple:
 
#PBS -l nodes=7:Viking:ppn=1
#PBS -l arch=xeon
 
mpirun --machinefile $PBS_NODEFILE /home/sadX/mpi_test/mpi_hello_hostname > hello_out_viking7nodes
 
Also if I ssh to any node in my cluster and create a mpi nodes file by hand and then use that to run like this:
 
mpirun --machinefile ../nodefile ./mpi_hello_hostname
 
I get back all of the expected output from all of the nodes listed in the manually created nodes file.
--
Steven DuChene
  

-- 
 
The Computer Center, University of Tromsø, N-9037 TROMSØ Norway.
phone:+47 77 64 41 07, fax:+47 77 64 41 00
Roy Dragseth, Team Leader, High Performance Computing
Direct call: +47 77 64 62 56. email: roy.dragseth at uit.no
 

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-- 
David Beer | Software Engineer
Adaptive Computing



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