no it does not happen on names nodes
On Fri, Apr 4, 2014 at 7:51 PM, Ralph Castain <r...@open-mpi.org> wrote: > Hi Nisha > > I'm sorry if my questions appear abrasive - I'm just a little frustrated > at the communication bottleneck as I can't seem to get a clear picture of > your situation. So you really don't need to keep calling me "sir" :-) > > The error you are hitting is very unusual - it means that the processes > are able to make a connection, but are failing to correctly complete a > simple handshake exchange of their process identifications. There are only > a few ways that can happen, and I'm trying to get you to test for them. > > So let's try and see if we can narrow this down. You mention that it works > on some machines, but not all. Is this consistent - i.e., is it always the > same machines that work, and the same ones that generate the error? If you > exclude the ones that show the error, does it work? If so, what is > different about those nodes? Are they a different architecture? > > > On Apr 3, 2014, at 11:09 PM, Nisha Dhankher -M.Tech(CSE) < > nishadhankher-coaese...@pau.edu> wrote: > > sir > smae virt-manager is bein used by all pc's.no i did n't enable > openmpi-hetro.Yes openmpi version is same in all through same kickstart > file. > ok...actually sir...rocks itself installed,configured openmpi and mpich on > it own through hpc roll. > > > On Fri, Apr 4, 2014 at 9:25 AM, Ralph Castain <r...@open-mpi.org> wrote: > >> >> 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<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 >>>>>> >>>>> >>>>> >>>> >>> _______________________________________________ >>> 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 >
