Hi Ralph, fs.file-max = 100000
is this ok or less? Best Regards, Ashwani On Fri, Oct 14, 2011 at 11:45 PM, Ralph Castain <r...@open-mpi.org> wrote: > Can't offer much about the qsub job. On the first one, what is your limit > on the number of file descriptors? Could be your sys admin has it too low. > > > On Oct 14, 2011, at 12:07 PM, Ashwani Kumar Mishra wrote: > > 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 > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users >
