From: Ross Walker <>
Date: Wed, 14 Dec 2011 21:37:54 -0800

Hi Neha,

> I have run few simulations using pmemd.MPI on CPU cluster. I latter
> copied
> these files to GPU cluster and tried running jobs using pmemd.cuda.MPI.
> But
> the jobs don't run ending with following error:
> At line 402 of file mdin_ctrl_dat.f90 (unit = 5, file = 'sander.in4')
> Fortran runtime error: End of file

This is a weird error that suggests your mdin file is truncated. Can you try
in the CUDA code in serial and see if that works. I suspect it is related to
the issue below though.

> Is it because AMBER was compiled using intel-compilers on CPU whereas
> the
> GPU uses the gcc compilers?

Probably. You MUST use the exact same mpirun as the mpif90 that was used to
compile AMBER. E.g. if your mpirun was part of an intel compiled MPI but you
use it to try to run an MPI installation built with a different compiler
then you'll get all sorts of weird errors.

So I'd start by rebuilding pmemd.cuda.MPI with the current version of MPI
that you are using.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Wed Dec 14 2011 - 22:00:03 PST
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