Re: [OMPI users] Running a hybrid MPI+openMP program

Hi, I think this is a broader issue in case an MPI library is used in conjunction with threads while running inside a queuing system. First: whether your actual installation of Open MPI is SGE-aware you can check with: $ ompi_info | grep grid MCA ras: gridengine (MCA v2.0, API

Re: [OMPI users] GCC 4.9 and MPI_F08?

On Aug 14, 2014, at 5:52 AM, Christoph Niethammer wrote: > I just gave gcc 4.9.0 a try and the mpi_f09 module Wow -- that must be 1 better than the mpi_f08 module! :-p > is there but it seems to miss some functions: > > mpifort test.f90 > /tmp/ccHCEbXC.o: In function

Re: [OMPI users] Running a hybrid MPI+openMP program

Guys I changed the line to run the program in the script with both options /usr/bin/time -f "%E" /opt/openmpi/bin/mpirun -v --bind-to-none -np $NSLOTS ./inverse.exe /usr/bin/time -f "%E" /opt/openmpi/bin/mpirun -v --bind-to-socket -np $NSLOTS ./inverse.exe but I got the same results. When I

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

One more, Maxime, can you please make sure you've covered everything here: http://www.open-mpi.org/community/help/ Josh On Thu, Aug 14, 2014 at 3:18 PM, Joshua Ladd wrote: > And maybe include your LD_LIBRARY_PATH > > Josh > > > On Thu, Aug 14, 2014 at 3:16 PM, Joshua

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

And maybe include your LD_LIBRARY_PATH Josh On Thu, Aug 14, 2014 at 3:16 PM, Joshua Ladd wrote: > Can you try to run the example code "ring_c" across nodes? > > Josh > > > On Thu, Aug 14, 2014 at 3:14 PM, Maxime Boissonneault < > maxime.boissonnea...@calculquebec.ca>

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Can you try to run the example code "ring_c" across nodes? Josh On Thu, Aug 14, 2014 at 3:14 PM, Maxime Boissonneault < maxime.boissonnea...@calculquebec.ca> wrote: > Yes, > Everything has been built with GCC 4.8.x, although x might have changed > between the OpenMPI 1.8.1 build and the

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Yes, Everything has been built with GCC 4.8.x, although x might have changed between the OpenMPI 1.8.1 build and the gromacs build. For OpenMPI 1.8.2rc4 however, it was the exact same compiler for everything. Maxime Le 2014-08-14 14:57, Joshua Ladd a écrit : Hmmm...weird. Seems like maybe a

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Hmmm...weird. Seems like maybe a mismatch between libraries. Did you build OMPI with the same compiler as you did GROMACS/Charm++? I'm stealing this suggestion from an old Gromacs forum with essentially the same symptom: "Did you compile Open MPI and Gromacs with the same compiler (i.e. both gcc

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

I just tried Gromacs with two nodes. It crashes, but with a different error. I get [gpu-k20-13:142156] *** Process received signal *** [gpu-k20-13:142156] Signal: Segmentation fault (11) [gpu-k20-13:142156] Signal code: Address not mapped (1) [gpu-k20-13:142156] Failing at address: 0x8

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

What about between nodes? Since this is coming from the OpenIB BTL, would be good to check this. Do you know what the MPI thread level is set to when used with the Charm++ runtime? Is it MPI_THREAD_MULTIPLE? The OpenIB BTL is not thread safe. Josh On Thu, Aug 14, 2014 at 2:17 PM, Maxime

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Hi, I ran gromacs successfully with OpenMPI 1.8.1 and Cuda 6.0.37 on a single node, with 8 ranks and multiple OpenMP threads. Maxime Le 2014-08-14 14:15, Joshua Ladd a écrit : Hi, Maxime Just curious, are you able to run a vanilla MPI program? Can you try one one of the example programs

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Hi, Maxime Just curious, are you able to run a vanilla MPI program? Can you try one one of the example programs in the "examples" subdirectory. Looks like a threading issue to me. Thanks, Josh

[OMPI users] Intermittent, somewhat architecture-dependent hang with Open MPI 1.8.1

Open MPI Users, I work on a large climate model called GEOS-5 and we've recently managed to get it to compile with gfortran 4.9.1 (our usual compilers are Intel and PGI for performance). In doing so, we asked our admins to install Open MPI 1.8.1 as the MPI stack instead of MVAPICH2 2.0 mainly

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Hi, I just did with 1.8.2rc4 and it does the same : [mboisson@helios-login1 simplearrayhello]$ ./hello [helios-login1:11739] *** Process received signal *** [helios-login1:11739] Signal: Segmentation fault (11) [helios-login1:11739] Signal code: Address not mapped (1) [helios-login1:11739]

Re: [OMPI users] Running a hybrid MPI+openMP program

Hi, You DEFINITELY need to disable OpenMPI's new default binding. Otherwise, your N threads will run on a single core. --bind-to socket would be my recommendation for hybrid jobs. Maxime Le 2014-08-14 10:04, Jeff Squyres (jsquyres) a écrit : I don't know much about OpenMP, but do you need

Re: [OMPI users] Running a hybrid MPI+openMP program

Hi, Am 14.08.2014 um 15:50 schrieb Oscar Mojica: > I am trying to run a hybrid mpi + openmp program in a cluster. I created a > queue with 14 machines, each one with 16 cores. The program divides the work > among the 14 processors with MPI and within each processor a loop is also > divided

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Can you try the latest 1.8.2 rc tarball? (just released yesterday) http://www.open-mpi.org/software/ompi/v1.8/ On Aug 14, 2014, at 8:39 AM, Maxime Boissonneault wrote: > Hi, > I compiled Charm++ 6.6.0rc3 using > ./build charm++ mpi-linux-x86_64 smp

Re: [OMPI users] Running a hybrid MPI+openMP program

I don't know much about OpenMP, but do you need to disable Open MPI's default bind-to-core functionality (I'm assuming you're using Open MPI 1.8.x)? You can try "mpirun --bind-to none ...", which will have Open MPI not bind MPI processes to cores, which might allow OpenMP to think that it can

[OMPI users] Running a hybrid MPI+openMP program

Hello everybody I am trying to run a hybrid mpi + openmp program in a cluster. I created a queue with 14 machines, each one with 16 cores. The program divides the work among the 14 processors with MPI and within each processor a loop is also divided into 8 threads for example, using openmp.

Re: [OMPI users] Segmentation fault in OpenMPI 1.8.1

Note that if I do the same build with OpenMPI 1.6.5, it works flawlessly. Maxime Le 2014-08-14 08:39, Maxime Boissonneault a écrit : Hi, I compiled Charm++ 6.6.0rc3 using ./build charm++ mpi-linux-x86_64 smp --with-production When compiling the simple example

[OMPI users] Segmentation fault in OpenMPI 1.8.1

Hi, I compiled Charm++ 6.6.0rc3 using ./build charm++ mpi-linux-x86_64 smp --with-production When compiling the simple example mpi-linux-x86_64-smp/tests/charm++/simplearrayhello/ I get a segmentation fault that traces back to OpenMPI : [mboisson@helios-login1 simplearrayhello]$ ./hello

Re: [OMPI users] GCC 4.9 and MPI_F08?

Hello, I just gave gcc 4.9.0 a try and the mpi_f09 module is there but it seems to miss some functions: mpifort test.f90 /tmp/ccHCEbXC.o: In function `MAIN__': test.f90:(.text+0x35a): undefined reference to `mpi_win_lock_all_' test.f90:(.text+0x373): undefined reference to `mpi_win_lock_all_'

[OMPI users] how MPI_Get can work with multiple memory regions attached to a window via MPI_Win_attach

Hi, In http://www.mpich.org/static/docs/v3.1/www3/MPI_Win_attach.html, for MPI 3, The API MPI_Win_attach is supported : int MPI_Win_attach(MPI_Win win, void *base, MPI_Aint size) It allows multiple (but non-overlapping) memory regions to be attached to the same window, after the window

Re: [OMPI users] mpi+openshmem hybrid

You can use hybrid mode. following code works for me with ompi 1.8.2 #include #include #include "shmem.h" #include "mpi.h" int main(int argc, char *argv[]) { MPI_Init(, ); start_pes(0); { int version = 0; int subversion = 0; int num_proc = 0; int

[OMPI users] mpi+openshmem hybrid

Hello! I use Open MPI v1.9a132520. Can I use hybrid mpi+openshmem?
Where can i read about? I have some problems in simple programm: #include #include "shmem.h" #include "mpi.h" int main(int argc, char* argv[]) { int proc, nproc; int rank, size, len; char

Re: [OMPI users] GCC 4.9 and MPI_F08?

Hi Jeff, Works for me! (With mpi_f08, GCC 4.9.1 absolutely insists on getting the finer details right on things like MPI_User_function types for MPI_Op_create. So I'll assume the rest of the type checking is just as good, and be glad I took that minor detour..) Thanks, Marcus