On Tue, Sep 17, 2013 at 2:04 AM, Kate Stafford <kastaff...@gmail.com> wrote: > 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. > --------------------------------------------------------------------------
Hmm. That warning is a known issue in some cases: http://www.open-mpi.org/faq/?category=openfabrics#ofa-fork but should not be an issue for the above mdrun command, since it should call none of popen/fork/system. You might like to try some of the diagnostics on that page. > ...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. I can think of no reason for or past experience of this behaviour. Is it possible for you to run mdrun_mpi in a debugger and get a call stack trace to help us diagnose? > 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. OK, thanks, good diagnosis. Some low-level stuff did get refactored after 4.6.1. I don't think that will be the issue here, but you could see if it produces the same symptoms / magically works. > 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? So far I'd say the problem is not of your making :-( Mark -- 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
