Hi Ralph, No idea how much this program consumes the numbers of file descriptors :(
Best Regards, Ashwani On Sat, Oct 15, 2011 at 12:08 AM, Ralph Castain <r...@open-mpi.org> wrote: > Should be plenty for us - does your program consume a lot? > > > On Oct 14, 2011, at 12:25 PM, Ashwani Kumar Mishra wrote: > > 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 >> > > _______________________________________________ > 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 >
