AMBER Archive (2006)

Subject: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband

From: Fabian Boes (
Date: Thu Jun 29 2006 - 10:58:26 CDT

Hash: SHA1

Dear Amber community,

i experience a strange problem with PMEMD (from the AMBER9 package) on a
  Xeon cluster with Infiniband. I used the Intel Fortran compiler 9.0
(as 9.1 will break the compilation of PMEMD with an internal compiler
error) together with Infiniband MPICH. Compilation went fine without
any errors.

Jobs (on different number of nodes) just start fine. Output and
trajectory files are written out. But suddenly, mostly after
50.000-150.000 steps, the writing of the output files stops. The PMEMD
executable is still running on all nodes with 99% cpu consumption. This
seems to go on for ever, until one manually kills the mpirun command
with CTRL-C or the PBS job reaches its walltime limit.

I tried the following things:

Compiled with/without Intel Math Kernel Lib
Compiled with/without netcdf support

Simulations with/without binary trajectory

Used 3 different file systems (GPFS, local node scratch, global cluster
scratch) to make sure it isn't an I/O problem.

The molecular system under investigation runs fine on an 8-way dual core
Opteron with PMEMD (compiled with Pathscale and LAM-MPI).

Has someone experienced the same? Or has some tips how to debug this? I
heard from various sources that the Intel Fortran compiler had problems
with PMEMD in the past. Unfortunately there are no other compilers
installed on this particular cluster.



- --

Fabian Bös

Institute of Technical Biochemistry
University of Stuttgart / Germany

Phone: +49-711-685-65156
Fax: +49-711-685-63196

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