[gmx-users] problem with mpi

jagannath mondal jmondal2004 at yahoo.co.in
Wed May 6 07:27:49 CEST 2009

Hi,I am trying to use parallel gromacs3.3.3  mdrun programme  .I have installed mpich2 in our quadcore machine. But I am having 3 problems:   1. The scaling is very poor among 4 cores: varies between 30-70 %.    2. If I run the mdrun_mpi in background, the output log file cites following error:   "mpiexec_yethiraj22 (handle_stdin_input 1089): stdin problem; if pgm is run in background, redirect from /dev/null"3. The simulation also crashed citing error in the output log file: *** glibc detected *** mdrun_mpi: malloc(): memory corruption (fast): 0x000000000c37ea90 ***.
Any help and suggestion in this regard will be highly appreciated.ThanksJagannath Mondal

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