sorry Ralph my mistake its not names...it is "it does not happen on same nodes."
On Sat, Apr 5, 2014 at 12:33 PM, Nisha Dhankher -M.Tech(CSE) < nishadhankher-coaese...@pau.edu> wrote: > 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 >>> >> >> >
