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