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 >
