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 >>>>> >>>>> 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
