Hello Gromacs users. In the CVS version, I experience that mdrun crashes instantly when run in parallel across nodes (for any simulation system). The cluster consists of 8 nodes with Intel 6600 Quad-Core processors. As long as a job is run on a single node (using 1,2 or 4 CPU:s) everything works fine but when trying to run on several nodes mdrun crashes directly with the following error message (no output or log files are written to disk):
> Getting Loaded... > Reading file topol.tpr, VERSION 3.3.99_development_20071104 (single precision) > Loaded with Money > > [warhol8:29695] *** An error occurred in MPI_Allreduce > [warhol8:29695] *** on communicator MPI_COMM_WORLD > [warhol8:29695] *** MPI_ERR_COMM: invalid communicator > [warhol8:29695] *** MPI_ERRORS_ARE_FATAL (goodbye) For the 1024 DPPC benchmark system the following two commands were used to start the simulation (default names on input files): > /opt/gromacs/cvs/bin/grompp > /opt/openmp/1.2.4/bin/mpirun --hostfile hostfile /opt/gromacs/cvs/bin/mdrun_mpi -v -dd 2 2 2 where hostfile contains two specific nodes with 4 slots each. The OS is Ubuntu 7.10 x86_64 on all nodes. mdrun_mpi is compiled with OpenMPI 1.2.4 but I have also tried with LAM/MPI 7.1.2 and it crashes in the same manner with an identical error message. Furthermore I have tried a static compilation on another cluster (Intel Xeon EM64T Processors) and copied the files to our cluster with the same result. I have searched the web for this error and there are some suggestions that this may be related to 64 bit architecture, see e.g. http://www.open-mpi.org/community/lists/users/2006/04/0978.php The MPI installation on the cluster works for the 3.3.2 version of Gromacs and also for some simple test programs for MPI such as nodes writing out their name and rank. Does anyone have any ideas on the origins of these crashes and/or suggestions on how to resolve them? Regards Erik Brandt Ph.D. Student Theoretical Physics, KTH, Stockholm, Sweden -- Erik Brandt <[EMAIL PROTECTED]> KTH
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