For future reference, this is caused by the "-xHost" flag that is scattered
throughout the config.h. If you remove "-xHost" from config.h and
recompile, this problem should go away.
This problem is caused because -xHost applies all vectorization
optimizations that the 'current' processor supports. (That is, whatever
machine you are compiling on). This is a problem for heterogeneous
clusters that have nodes with different CPUs present. Whenever you run a
program on a node that has a CPU that does not support all of the
instructions that the machine you compiled Amber on supported, this error
will occur (that's why some programs may appear to work while others do
not).
Note that removing -xHost will hurt performance (by disabling
vectorization). If you absolutely *must* have that 10-15% performance
boost, you'll need to look into the Intel compiler documentation and
manually turn on each vectorization optimization supported by every
processor in your cluster.
HTH,
Jason
On Tue, Jul 3, 2012 at 7:54 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Jul 03, 2012, Yubo Fan wrote:
> >
> > I recently compiled Amber 11 and 12 on our new Opteron server.
> > Everything works fine except pmemd.MPI of Amber 11.
>
> "Obvious" workaround: don't use pmemd.MPI from Amber11. I don't think it
> has
> any functionality not present in the Amber12 version.
>
> If you are curious, edit the config.h file and look at the PMEMD_* flags,
> especially PMEMD_FOPTFLAGS and PMEMD_COPTFLAGS. See what is different
> between
> Amber11 and Amber12; consider copying the flags from Amber12 to the Amber11
> config.h file.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 03 2012 - 05:30:02 PDT
