[gmx-users] problem with mpi

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 7 02:01:17 CEST 2009

jagannath mondal wrote:
> 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 ***.

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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