Re: [OMPI users] openmpi query

On 04/08/2014 06:37 AM, Jeff Squyres (jsquyres) wrote: You should ping the Rocks maintainers and ask them to upgrade. Open MPI 1.4.3 was released in September of 2010. On Rocks, you can install OpenMPI from source (and any other software application by the way) on their standard NFS shared d

Re: [OMPI users] openmpi query

You should ping the Rocks maintainers and ask them to upgrade. Open MPI 1.4.3 was released in September of 2010. On Apr 8, 2014, at 5:37 AM, Nisha Dhankher -M.Tech(CSE) wrote: > latest rocks 6.2 carry this version only > > > On Tue, Apr 8, 2014 at 3:49 AM, Jeff Squyres (jsquyres) > wrot

Re: [OMPI users] openmpi query

and thank you very much On Tue, Apr 8, 2014 at 3:07 PM, Nisha Dhankher -M.Tech(CSE) < nishadhankher-coaese...@pau.edu> wrote: > latest rocks 6.2 carry this version only > > > On Tue, Apr 8, 2014 at 3:49 AM, Jeff Squyres (jsquyres) < > jsquy...@cisco.com> wrote: > >> Open MPI 1.4.3 is *ancient*.

Re: [OMPI users] openmpi query

latest rocks 6.2 carry this version only On Tue, Apr 8, 2014 at 3:49 AM, Jeff Squyres (jsquyres) wrote: > Open MPI 1.4.3 is *ancient*. Please upgrade -- we just released Open MPI > 1.8 last week. > > Also, please look at this FAQ entry -- it steps you through a lot of basic > troubleshooting s

Re: [OMPI users] openmpi query

Open MPI 1.4.3 is *ancient*. Please upgrade -- we just released Open MPI 1.8 last week. Also, please look at this FAQ entry -- it steps you through a lot of basic troubleshooting steps about getting basic MPI programs working. http://www.open-mpi.org/faq/?category=running#diagnose-multi-host

Re: [OMPI users] openmpi query

Mpirun *--mca btl ^openib --mca btl_tcp_if_include eth0* -np 16 -machinefile mf mpiblast -d all.fas -p blastn -i query.fas -o out.txt was the command i executed on cluster... On Sat, Apr 5, 2014 at 12:34 PM, Nisha Dhankher -M.Tech(CSE) < nishadhankher-coaese...@pau.edu> wrote: > sorry Ralph m

Re: [OMPI users] openmpi query

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

Re: [OMPI users] openmpi query

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 wrote: > >> Okay, so if you run mpiBlast on all the non-name nodes, every

Re: [OMPI users] openmpi query

opmpi version 1.4.3 On Fri, Apr 4, 2014 at 8:13 PM, Ralph Castain 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: >

Re: [OMPI users] openmpi query

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) wrote: > no it does not happen on names nodes > > > On Fri, Apr 4, 2014 at 7:51 PM, Ralph Castain wrote: > Hi Nisha > > I

Re: [OMPI users] openmpi query

On Apr 4, 2014, at 7:39 AM, Reuti wrote: > Am 04.04.2014 um 05:55 schrieb Ralph Castain: > >> 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 runn

Re: [OMPI users] openmpi query

Am 04.04.2014 um 05:55 schrieb Ralph Castain: > 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 ar

Re: [OMPI users] openmpi query

no it does not happen on names nodes On Fri, Apr 4, 2014 at 7:51 PM, Ralph Castain 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 nee

Re: [OMPI users] openmpi query

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 process

Re: [OMPI users] openmpi query

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 wrote

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'

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

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

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] 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 results even after 2 hours lapsed.on rocks 6.

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'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

[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