Re: [OMPI users] 3D domain decomposition with MPI

On Thu, 11 Mar 2010 12:44:01 -0500, "Cole, Derek E" wrote: > I am replying to this via the daily-digest message I got. Sorry it > wasn't sooner... I didn't realize I was getting replies until I got > the digest. Does anyone know how to change it so I get the emails as > you all send them? Log in

[OMPI users] psm plm failure when infinipathlibs installed but no psm device present

We rely heavily on OpenMPI's ability to 'fall though' to the next best option on our cluster. Example we have some IB (verbs nodes) and most have TCP. Recently we added some qlogic IB that uses PSM to get good performance. We built OpenMPI to include PSM in addition to verbs, and TCP. W

Re: [OMPI users] 3D domain decomposition with MPI

I am replying to this via the daily-digest message I got. Sorry it wasn't sooner... I didn't realize I was getting replies until I got the digest. Does anyone know how to change it so I get the emails as you all send them? >>Unless your computation is so "embarrassingly parallel" that each proc

Re: [OMPI users] mpi error?

perfect.. that is exactly what I wanted to know.. that is was an issue with the program- rather than an issue with openmpi.. Thanks, Jeff. Matt _ Matthew MacManes PhD Candidate University of California- Berkeley Museum of Vertebrate Zoology Phone: 510-495-5833 Lab W

Re: [OMPI users] mpi error?

Debugging this is probably not going to be within the scope of Open MPI -- it looks like your app is seg faulting inside some routine called DoCharset. If you're getting corefiles, you might try loading them up in the debugger and see what is going wrong, etc. I.e., standard debugging rules ap

Re: [OMPI users] mpi error?

I "unlimited" my stack space- got a different error, which maybe is a clue.. Im not sure how to vary the rank, like you suggested, so if you have a tip that would be great. Here is the new error: [macmanes:05298] *** Process received signal *** [macmanes:05298] Signal: Segmentation fault (11) [mac

Re: [OMPI users] OPenMpi: How to specify login name in machinefile passed to mpirun

2010/3/11 Ralph Castain > Yeah, it was a bug in the parser - fix scheduled for 1.4.2 release. > > Thanks! > Ralph > OK, thanks Ralph for the test and the quick analyse. Regards, Olivier > > On Mar 11, 2010, at 4:32 AM, Olivier Riff wrote: > > Hello Ralph, > > Thanks for you quick reply. >

Re: [OMPI users] mpi error?

On Thursday 11 March 2010, Matthew MacManes wrote: > Can anybody tell me if this is an error associated with openmpi, versus an > issue with the program I am running (MRBAYES, > https://sourceforge.net/projects/mrbayes/) > > We are trying to run a large simulated dataset using 1,000,000 bases > div

Re: [OMPI users] OPenMpi: How to specify login name in machinefile passed to mpirun

Yeah, it was a bug in the parser - fix scheduled for 1.4.2 release. Thanks! Ralph On Mar 11, 2010, at 4:32 AM, Olivier Riff wrote: > Hello Ralph, > > Thanks for you quick reply. > Sorry I did not mention the version : it is the v1.4 (which indeed is not the > very last one). > I will appreciat

[OMPI users] mpi error?

Can anybody tell me if this is an error associated with openmpi, versus an issue with the program I am running (MRBAYES, https://sourceforge.net/projects/mrbayes/) We are trying to run a large simulated dataset using 1,000,000 bases divided up into 1000 genes, 5 taxa.. An error is occurring, but w

Re: [OMPI users] running externalprogram on same processor (Fortran)

On Mar 10, 2010, at 9:25 PM, abc def wrote: > -- > Fatal error in MPI_Comm_spawn: Other MPI error, error stack: > MPI_Comm_spawn(130).: MPI_Comm_spawn(cmd="./mpitest-2.ex", > argv=0x75e920, maxprocs=1, info=0x9c00, root=0, MPI_COMM_SELF, > intercomm=0x7fff

Re: [OMPI users] MPI and DRMAA

Hi, Am 11.03.2010 um 03:03 schrieb Brian Smith: This may seem like an odd query (or not; perhaps it has been brought up before). My work recently involves HPC usability i.e. making things easier for new users by abstracting away the scheduler. I've been working with DRMAA for interfacing wi

Re: [OMPI users] OPenMpi: How to specify login name in machinefile passed to mpirun

Hello Ralph, Thanks for you quick reply. Sorry I did not mention the version : it is the v1.4 (which indeed is not the very last one). I will appreciate if you could make a short test. Thanks and Regards, Olivier 2010/3/10 Ralph Castain > Probably a bug - I don't recall if/when anyone actuall

Re: [OMPI users] 3D domain decomposition with MPI

On Wed, 10 Mar 2010 22:25:43 -0500, Gus Correa wrote: > Ocean dynamics equations, at least in the codes I've seen, > normally use "pencil" decomposition, and are probably harder to > handle using 3D "chunk" decomposition (due to the asymmetry imposed by > gravity). There is also a lot to be said

Re: [OMPI users] 3D domain decomposition with MPI

Gus Correa wrote: I am not an MPI expert, just a user/programmer, so I may be dead wrong in what I wrote. Please, correct me if I am wrong. It all sounds not only right to me but also well put.

Re: [OMPI users] running externalprogram on same processor (Fortran)

Thank you very much for the examples. I tried the following program, based on the guidance here and additional information I found through google: --- PROGRAM mpitest1 IMPLICIT none CHARACTER*6 :: dir CHARACTER*1 :: crank ! MPI parameters INCLUDE 'mpif.h' INTEGER :