[gmx-users] Gromacs in Parallel

[Mark Abraham]

Andrew Paluch wrote:
> To whom this may concern,
> 
> I am receiving the following errors when attempting to run Gromacs in
> parallel:
> 
> Making 1D domain decomposition 4 x 1 x 1
> p2_21562:  p4_error: Timeout in establishing connection to remote process: 0
> p2_21562: (302.964844) net_send: could not write to fd=5, errno = 32
> 
> 
> where I am using mpich 1.2.7 for 64 bit processors.  From what I can find,
> it seems as if this is a mpich issue and not an issue of Gromacs.  Has
> anyone else encountered such a problem?  Also, does anyone have any
> suggestions for a solution?

Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of 
problems with particular MPI libraries, but you might try compiling 
GROMACS with another such library. Whoever configured this machine 
should probably look into the problem.

Mark