Matlab may have its own MPI installed. It definitely does if you have the parallel computing toolbox. If you have that, it could be causing problems. If you can, you might consider compiling your Matlab application into a standalone executable, then call that from your own program. That bypasses the Matlab user interface and may prove more tractable See the documentation for mcc if you have that.
http://www.mathworks.com/help/compiler/mcc.html If you have that toolbox. -- bennet On Wed, Oct 5, 2016 at 8:03 PM, Gilles Gouaillardet <gil...@rist.or.jp> wrote: > Juraj, > > > if i understand correctly, the "master" task calls MPI_Init(), and then > fork&exec matlab. > > In some cases (lack of hardware support), fork cannot even work. but let's > assume it is fine for now. > > Then, if i read between the lines, matlab calls mexFunction that MPI_Init(). > > As far as i am concerned, that cannot work. > > The blocker is that a child cannot call MPI_Init() if its parent already > called MPI_Init() > > > Fortunatly, you have some options :-) > 1) start matlab from mpirun. > for example, if you want one master, two slaves and matlab, you can do > something like > mpirun -np 1 master : -np 1 matlab : -np 2 slave > > 2) MPI_Comm_spawn matlab > master can MPI_Comm_spawn() matlab, and then matlab can merge the parent > communicator, > and communicate to master and slaves > > 3) use the approach suggested by Dmitry > /* this is specific to matlab, and i have no experience with it */ > > One last point, MPI_Init() can be invoked only once per task > (e.g. if your mexFunction does > MPI_Init(); work(); MPI_Finalize(); > then it can be invoked only once per mpirun > > Cheers, > > Gilles > > On 10/5/2016 6:41 PM, Dmitry N. Mikushin wrote: > > Hi Juraj, > > Although MPI infrastructure may technically support forking, it's known that > not all system resources can correctly replicate themselves to forked > process. For example, forking inside MPI program with active CUDA driver > will result into crash. > > Why not to compile down the MATLAB into a native library and link it with > the MPI application directly? E.g. like here: > https://www.mathworks.com/matlabcentral/answers/98867-how-do-i-create-a-c-shared-library-from-mex-files-using-the-matlab-compiler?requestedDomain=www.mathworks.com > > Kind regards, > - Dmitry Mikushin. > > > 2016-10-05 11:32 GMT+03:00 juraj2...@gmail.com <juraj2...@gmail.com>: >> >> Hello, >> >> I have an application in C++(main.cpp) that is launched with multiple >> processes via mpirun. Master process calls matlab via system('matlab >> -nosplash -nodisplay -nojvm -nodesktop -r "interface"'), which executes >> simple script interface.m that calls mexFunction (mexsolve.cpp) from which I >> try to set up communication with the rest of the processes launched at the >> beginning together with the master process. When I run the application as >> listed below on two different machines I experience: >> >> 1) crash at MPI_Init() in the mexFunction() on cluster machine with Linux >> 4.4.0-22-generic >> >> 2) error in MPI_Send() shown below on local machine with Linux >> 3.10.0-229.el7.x86_64 >> [archimedes:31962] shmem: mmap: an error occurred while determining >> whether or not >> /tmp/openmpi-sessions-1007@archimedes_0/58444/1/shared_mem_pool.archimedes >> could be created. >> [archimedes:31962] create_and_attach: unable to create shared memory BTL >> coordinating structure :: size 134217728 >> [archimedes:31962] shmem: mmap: an error occurred while determining >> whether or not >> /tmp/openmpi-sessions-1007@archimedes_0/58444/1/0/vader_segment.archimedes.0 >> could be created. >> >> [archimedes][[58444,1],0][../../../../../opal/mca/btl/tcp/btl_tcp_endpoint.c:800:mca_btl_tcp_endpoint_complete_connect] >> connect() to <MY_IP> failed: Connection refused (111) >> >> I launch application as following: >> mpirun --mca mpi_warn_on_fork 0 --mca btl_openib_want_fork_support 1 -np >> 2 -npernode 1 ./main >> >> I have openmpi-2.0.1 configured with --prefix=${INSTALLDIR} >> --enable-mpi-fortran=all --with-pmi --disable-dlopen >> >> For more details, the code is here: https://github.com/goghino/matlabMpiC >> >> Thanks for any suggestions! >> >> Juraj >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > > > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users _______________________________________________ users mailing list users@lists.open-mpi.org https://rfd.newmexicoconsortium.org/mailman/listinfo/users
