[gmx-users] problem with mpi
Mark.Abraham at anu.edu.au
Thu May 7 02:01:17 CEST 2009
jagannath mondal wrote:
> 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 ***.
Unless you actually need 3.3.3 for some scientific reason, go and
install 4.0.4. Otherwise, you seem to have some kind of broken/ancient
MPI installation that also might need an update.
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