Hello,
When i try to run the following command i receive the following error when i try to submit this job on the cluster having 40 nodes with each node having 8 processor & 8 GB RAM:

Both the command work well, as long as i use only upto 88 processors in the cluster, but the moment i allocate more than 88 processors it gives me the below 2 errors:

I tried to set the ulimit to unlimited & setting mca parameter opal_set_max_sys_limits to 1 but still the problem wont go.


$ mpirun=/opt/psc/ompi/bin/mpirun abyss-pe np=100 name=cattle k=50 n=10  in=s_1_1_sequence.txt

/opt/mpi/openmpi/1.3.3/intel/

bin/mpirun -np 100 ABYSS-P -k50 -q3  --coverage-hist=coverage.hist -s cattle-bubbles.fa  -o cattle-1.fa s_1_1_sequence.txt
[coe:19807] [[62863,0],0] ORTE_ERROR_LOG: The system limit on number of pipes a process can open was reached in file base/iof_base_setup.c at line 107
[coe.:19807] [[62863,0],0] ORTE_ERROR_LOG: The system limit on number of pipes a process can open was reached in file odls_default_module.c at line 203
[coe.:19807] [[62863,0],0] ORTE_ERROR_LOG: The system limit on number of network connections a process can open was reached in file oob_tcp.c at line 447
--------------------------------------------------------------------------
Error: system limit exceeded on number of network connections that can be open

This can be resolved by setting the mca parameter opal_set_max_sys_limits to 1,
increasing your limit descriptor setting (using limit or ulimit commands),
or asking the system administrator to increase the system limit.
--------------------------------------------------------------------------
make: *** [cattle-1.fa] Error 1

When i submit the same job through qsub, i receive the following error:
$ qsub  -cwd -pe  orte 100 -o qsub.out -e qsub.err -b y -N  abyss `which mpirun` /home/genome/abyss/bin/ABYSS-P -k 50 s_1_1_sequence.txt -o av


[compute-0-19.local][[28273,1]

,125][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 173.16.255.231 failed: Connection refused (111)
[compute-0-19.local][[28273,1],127][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 173.16.255.231 failed: Connection refused (111)
[compute-0-23.local][[28273,1],135][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 173.16.255.228 failed: Connection refused (111)
[compute-0-23.local][[28273,1],133][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 173.16.255.228 failed: Connection refused (111)
[compute-0-4.local][[28273,1],113][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 173.16.255.231 failed: Connection refused (111)

Best Regards,
Ashwani



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