Hi all, I'm trying to install and test gromacs 4.6.3 on our new cluster, and am having difficulty with MPI. Gromacs has been compiled against openMPI 1.6.5. The symptom is, running a very simple MPI process for any of the DHFR test systems:
orterun -np 2 mdrun_mpi -s topol.tpr produces this openMPI warning: -------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: hb0c1n1.hpc (PID 58374) MPI_COMM_WORLD rank: 1 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -------------------------------------------------------------------------- ...which is immediately followed by program termination by the cluster queue due to exceeding the allotted memory for the job. This behavior persists no matter how much memory I use, up to 16GB per thread, which is surely excessive for any of the DHFR benchmarks. Turning the warning off, of course, simply suppresses the output, but doesn't affect the memory usage. The openMPI install works fine with other MPI-enabled programs, including gromacs 4.5.5, so the problem is specific to 4.6.3. The thread-MPI version of 4.6.3 is also fine. The 4.6.3 MPI executable was compiled with: cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/nfs/apps/cuda/5.5.22 -DGMX_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON But the presence of the GPU or static libs related flags seems not to affect the behavior. The gcc version (4.4 or 4.8) doesn't matter either. Any insight as to what I'm doing wrong here? Thanks! -Kate -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists