On Apr 3, 2014, at 8:03 PM, Nisha Dhankher -M.Tech(CSE) <nishadhankher-coaese...@pau.edu> wrote:
> thankyou Ralph. > Yes cluster is heterogenous... And did you configure OMPI --enable-heterogeneous? And are you running it with ---hetero-nodes? What version of OMPI are you using anyway? Note that we don't care if the host pc's are hetero - what we care about is the VM. If all the VMs are the same, then it shouldn't matter. However, most VM technologies don't handle hetero hardware very well - i.e., you can't emulate an x86 architecture on top of a Sparc or Power chip or vice versa. > And i haven't made compute nodes on direct physical nodes (pc's) becoz in > college it is not possible to take whole lab of 32 pc's for your work so i > ran on vm. Yes, but at least it would let you test the setup to run MPI across even a couple of pc's - this is simple debugging practice. > In Rocks cluster, frontend give the same kickstart to all the pc's so openmpi > version should be same i guess. Guess? or know? Makes a difference - might be worth testing. > Sir > mpiformatdb is a command to distribute database fragments to different > compute nodes after partitioning od database. > And sir have you done mpiblast ? Nope - but that isn't the issue, is it? The issue is with the MPI setup. > > > On Fri, Apr 4, 2014 at 4:48 AM, Ralph Castain <r...@open-mpi.org> wrote: > What is "mpiformatdb"? We don't have an MPI database in our system, and I > have no idea what that command means > > As for that error - it means that the identifier we exchange between > processes is failing to be recognized. This could mean a couple of things: > > 1. the OMPI version on the two ends is different - could be you aren't > getting the right paths set on the various machines > > 2. the cluster is heterogeneous > > You say you have "virtual nodes" running on various PC's? That would be an > unusual setup - VM's can be problematic given the way they handle TCP > connections, so that might be another source of the problem if my > understanding of your setup is correct. Have you tried running this across > the PCs directly - i.e., without any VMs? > > > On Apr 3, 2014, at 10:13 AM, 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 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 >>> >>> 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 >> >> >> >> _______________________________________________ >> 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
