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 <http://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
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