[gmx-users] about the error on using rerun

[Erik Lindahl]

xu yechun wrote:

> Dear all,
> I used -rerun to calculate the energy file of one trr file. The trr is
> produced at cluster machine, but I use -resun to calculate the energy
> at SGI(iris3800). The size of the trr file is about 8G and the trr
> file include about 21ns time. But when I use rerun, the error comes:
> step 4090, will finish at Fri Nov 22 09:07:53 2002
> step 4100, will finish at Fri Nov 22 09:21:34 2002
> step 4110, will finish at Fri Nov 22 09:35:11 2002
> step 4120, will finish at Fri Nov 22 08:58:11 2002
> MPI: STDOUT or STDERR Buffer exhausted.
> MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192 characters
> MPI: between newlines.
> Any information is appreciated. Thanks in advance.

This looks like a problem with your MPI implementation and not a Gromacs
problem.

Try setting the environment variable MPI_UNBUFFERED_STDIO as they
suggest before starting the job.

Still, there's something strange going on since we definitely don't
write more than 8192 characters to STDOUT/STDERR without a newline....

Cheers,

Erik