Am 04.04.2014 um 05:55 schrieb Ralph Castain: > 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.
Well - you have to emulate the CPU. There were products running a virtual x86 PC on a Mac with PowerPC chip. And IBM has a product called PowerVM Lx86 to run software compiled for Linux x86 directly on a PowerLinux machine. -- Reuti >> 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 > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
