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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