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Subject: [OMPI users] Job fails after hours of running on a specific node
From: Sangamesh B (forum.san_at_[hidden])
Date: 2009-09-20 11:30:11


Dear all,

     The CPMD application which is compiled with OpenMPI-1.3 (Intel 10.1
compilers) on CentOS-4.5, fails only, when a specific node i.e. node-0-2 is
involved. But runs well on other nodes.

      Initially job failed after 5-10 mins (on node-0-2 + some other
nodes). After googling error, I added options "-mca
btl_openib_ib_min_rnr_timer 25 -mca btl_openib_ib_timeout 20" to mpirun
command in the SGE script:

$ cat cpmdrun.sh
#!/bin/bash
#$ -N cpmd-acw
#$ -S /bin/bash
#$ -cwd
#$ -e err.$JOB_ID.$JOB_NAME
#$ -o out.$JOB_ID.$JOB_NAME
#$ -pe ib 32
unset SGE_ROOT
PP_LIBRARY=/home/user1/cpmdrun/wac/prod/PP
CPMD=/opt/apps/cpmd/3.11/ompi/SOURCE/cpmd311-ompi-mkl.x
MPIRUN=/opt/mpi/openmpi/1.3/intel/bin/mpirun
$MPIRUN -np $NSLOTS -hostfile $TMPDIR/machines -mca
btl_openib_ib_min_rnr_timer 25 -mca btl_openib_ib_timeout 20 $CPMD
wac_md26.in $PP_LIBRARY > wac_md26.out
After adding these options, job executed for 24+ hours then failed with the
same error as earlier. The error is:

$ cat err.6186.cpmd-acw
--------------------------------------------------------------------------
The OpenFabrics stack has reported a network error event. Open MPI
will try to continue, but your job may end up failing.
  Local host: node-0-2.local
  MPI process PID: 11840
  Error number: 10 (IBV_EVENT_PORT_ERR)
This error may indicate connectivity problems within the fabric;
please contact your system administrator.
--------------------------------------------------------------------------
[node-0-2.local:11836] 7 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] Set MCA parameter "orte_base_help_aggregate" to 0 to
see all help / error messages
[node-0-2.local:11836] 1 more process has sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 7 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 1 more process has sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 7 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 1 more process has sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 7 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 1 more process has sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 7 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 1 more process has sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 15 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 16 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[node-0-2.local:11836] 16 more processes have sent help message
help-mpi-btl-openib.txt / of error event
[[718,1],20][btl_openib_component.c:2902:handle_wc] from node-0-22.local to:
node-0-2
--------------------------------------------------------------------------
The InfiniBand retry count between two MPI processes has been
exceeded. "Retry count" is defined in the InfiniBand spec 1.2
(section 12.7.38):
    The total number of times that the sender wishes the receiver to
    retry timeout, packet sequence, etc. errors before posting a
    completion error.
This error typically means that there is something awry within the
InfiniBand fabric itself. You should note the hosts on which this
error has occurred; it has been observed that rebooting or removing a
particular host from the job can sometimes resolve this issue.
Two MCA parameters can be used to control Open MPI's behavior with
respect to the retry count:
* btl_openib_ib_retry_count - The number of times the sender will
  attempt to retry (defaulted to 7, the maximum value).
* btl_openib_ib_timeout - The local ACK timeout parameter (defaulted
  to 10). The actual timeout value used is calculated as:
     4.096 microseconds * (2^btl_openib_ib_timeout)
  See the InfiniBand spec 1.2 (section 12.7.34) for more details.
Below is some information about the host that raised the error and the
peer to which it was connected:
  Local host: node-0-22.local
  Local device: mthca0
  Peer host: node-0-2
You may need to consult with your system administrator to get this
problem fixed.
--------------------------------------------------------------------------
error polling LP CQ with status RETRY EXCEEDED ERROR status number 12 for
wr_id 66384128 opcode 128 qp_idx 3
--------------------------------------------------------------------------
mpirun has exited due to process rank 20 with PID 10425 on
node ibc22 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
rm: cannot remove `/tmp/6186.1.iblong.q/rsh': No such file or directory

The openibd service is running fine:

$ service openibd status
  HCA driver loaded
Configured devices:
ib0
Currently active devices:
ib0
The following OFED modules are loaded:
  rdma_ucm
  ib_sdp
  rdma_cm
  ib_addr
  ib_ipoib
  mlx4_core
  mlx4_ib
  ib_mthca
  ib_uverbs
  ib_umad
  ib_ucm
  ib_sa
  ib_cm
  ib_mad
  ib_core
But still the job is failing after hours of running, that to for a
particular node. What's the wrong with node-0-2? How can it be resolved?

Thanks,
Sangamesh