i first formatted my database with mpiformatdb command then i ran command : mpirun -np 64 -machinefile mf mpiblast -d all.fas -p blastn -i query.fas -o output.txt but then it gave this error 113 from some hosts and continue to run for other but with no results even after 2 hours lapsed.....on rocks 6.0 cluster with 12 virtual nodes on pc's ...2 on each using virt-manger , 1 gb ram to each
On Thu, Apr 3, 2014 at 10:41 PM, Nisha Dhankher -M.Tech(CSE) < nishadhankher-coaese...@pau.edu> wrote: > i also made machine file which contain ip adresses of all compute nodes + > .ncbirc file for path to mpiblast and shared ,local storage path.... > Sir > I ran the same command of mpirun on my college supercomputer 8 nodes each > having 24 processors but it just running....gave no result uptill 3 hours... > > > On Thu, Apr 3, 2014 at 10:39 PM, Nisha Dhankher -M.Tech(CSE) < > nishadhankher-coaese...@pau.edu> wrote: > >> i first formatted my database with mpiformatdb command then i ran command >> : >> mpirun -np 64 -machinefile mf mpiblast -d all.fas -p blastn -i query.fas >> -o output.txt >> but then it gave this error 113 from some hosts and continue to run for >> other but with results even after 2 hours lapsed.....on rocks 6.0 cluster >> with 12 virtual nodes on pc's ...2 on each using virt-manger , 1 gb ram to >> each >> >> >> >> On Thu, Apr 3, 2014 at 8:37 PM, Ralph Castain <r...@open-mpi.org> wrote: >> >>> I'm having trouble understanding your note, so perhaps I am getting this >>> wrong. Let's see if I can figure out what you said: >>> >>> * your perl command fails with "no route to host" - but I don't see any >>> host in your cmd. Maybe I'm just missing something. >>> >>> * you tried running a couple of "mpirun", but the mpirun command wasn't >>> recognized? Is that correct? >>> >>> * you then ran mpiblast and it sounds like it successfully started the >>> processes, but then one aborted? Was there an error message beyond just the >>> -1 return status? >>> >>> >>> On Apr 2, 2014, at 11:17 PM, Nisha Dhankher -M.Tech(CSE) < >>> nishadhankher-coaese...@pau.edu> wrote: >>> >>> error btl_tcp_endpint.c: 638 connection failed due to error >>> 113<http://biosupport.se/questions/696/error-btl_tcp_endpintc-638-connection-failed-due-to-error-113> >>> >>> In openmpi: this error came when i run my mpiblast program on rocks >>> cluster.Connect to hosts failed on ip 10.1.255.236,10.1.255.244 . And when >>> i run following command linux_shell$ perl -e 'die$!=113' this msg comes: >>> "No route to host at -e line 1." shell$ mpirun --mca btl ^tcp shell$ mpirun >>> --mca btl_tcp_if_include eth1,eth2 shell$ mpirun --mca btl_tcp_if_include >>> 10.1.255.244 was also executed but it did nt recognized these >>> commands....nd aborted.... what should i do...? When i run my mpiblast >>> program for the frst time then it give mpi_abort error...bailing out of >>> signal -1 on rank 2 processor...then i removed my public ethernet >>> cable....and then give btl_tcp endpint error 113.... >>> _______________________________________________ >>> 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 >>> >> >> >
