same vm on all machines that is virt-manager
On Sat, Apr 5, 2014 at 12:32 PM, Nisha Dhankher -M.Tech(CSE) < nishadhankher-coaese...@pau.edu> wrote: > opmpi version 1.4.3 > > > On Fri, Apr 4, 2014 at 8:13 PM, Ralph Castain <r...@open-mpi.org> wrote: > >> Okay, so if you run mpiBlast on all the non-name nodes, everything is >> okay? What do you mean by "names nodes"? >> >> >> On Apr 4, 2014, at 7:32 AM, Nisha Dhankher -M.Tech(CSE) < >> nishadhankher-coaese...@pau.edu> wrote: >> >> 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 >>> >> >> _______________________________________________ >> 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 >> > >
