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 <http://coe.iitd.ac.in: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 <http://coe.iitd.ac.in: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 <http://coe.iitd.ac.in: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
