[OMPI users] openmpi query

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 . A

[OMPI users] simple way to build OpenMPI

All, for those interested in simplifying the OpenMPI build process, I've provided a Dockerfile that automatically includes all the dependencies, etc. It is geared towards Ubuntu, but I'm happy to accept pull requests. Hope it's useful for some here. https://github.com/opencore/openmpi-builder --J

Re: [OMPI users] openmpi query

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

Re: [OMPI users] simple way to build OpenMPI

thank you. On Thu, Apr 3, 2014 at 5:54 PM, James Horey wrote: > All, for those interested in simplifying the OpenMPI build process, > I've provided a Dockerfile that automatically includes all the > dependencies, etc. It is geared towards Ubuntu, but I'm happy to > accept pull requests. Hope it

[OMPI users] question

hoe btl_tcp_endpoint.c error 113 can be solved while executing mpiblast on rocks 6.0 which uses openmpi...on 8 nodes

Re: [OMPI users] question

You haven't provided enough information to even guess at the issue - please see my response to your last post on this question On Apr 3, 2014, at 9:53 AM, Nisha Dhankher -M.Tech(CSE) wrote: > hoe btl_tcp_endpoint.c error 113 can be solved while executing mpiblast on > rocks 6.0 which uses ope

Re: [OMPI users] openmpi query

my hostnodes to which this error came are are 10.1.255.254,10.1.255.236,10.1.255,241 On Thu, Apr 3, 2014 at 8:37 PM, Ralph Castain 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 fail

Re: [OMPI users] openmpi query

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.

Re: [OMPI users] openmpi query

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 runninggave no result uptill 3 hours...

Re: [OMPI users] openmpi query

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 rock

Re: [OMPI users] question

i hope you would have understood now On Thu, Apr 3, 2014 at 10:27 PM, Ralph Castain wrote: > You haven't provided enough information to even guess at the issue - > please see my response to your last post on this question > > On Apr 3, 2014, at 9:53 AM, Nisha Dhankher -M.Tech(CSE) < > nisha

[OMPI users] Contributing Examples for Java Binding

Hi, I've been working on some applications in our group where I've been using OpenMPI Java binding. Over the course of this work, I've accumulated several samples that I wrote primarily for me to get some experience. These include some tests for primitive communication operations plus kmeans clust

Re: [OMPI users] Contributing Examples for Java Binding

We'd be happy to add them both to our examples section, and to our regression test area, if okay with you. Feel free to send them to me offlist. Thanks! Ralph On Apr 3, 2014, at 1:44 PM, Saliya Ekanayake wrote: > Hi, > > I've been working on some applications in our group where I've been usin

Re: [OMPI users] Contributing Examples for Java Binding

Great. I will cleanup and send you a tarball. Thank you Saliya On Apr 3, 2014 5:51 PM, "Ralph Castain" wrote: > We'd be happy to add them both to our examples section, and to our > regression test area, if okay with you. Feel free to send them to me > offlist. > > Thanks! > Ralph > > On Apr 3, 2

Re: [OMPI users] openmpi query

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 d

Re: [OMPI users] openmpi query

thankyou Ralph. Yes cluster is heterogenous... 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. In Rocks cluster, frontend give the same kickstart to all the pc's so openmpi version shoul

Re: [OMPI users] openmpi query

On Apr 3, 2014, at 8:03 PM, Nisha Dhankher -M.Tech(CSE) 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'