Dear Amber experts,
in our present procurement, we are asking the vendors to give
commitments for the Amber performance in their answers to our RFP.
The selected benchmark case is the standard "NPT cellulose"
testcase and they are expected to run the benchmark on 32+ nodes,
thus, with a considerably high number of MPI processes.
One vendor is now asking what pre-processor flags they are allowed
to use for compiling pmemd10 (the patch level is up to the vendors
as they have to get the sources and a benchmark license
themselves):
| I assume that it is allowed to set -DDIRFRC_NOVEC and
| -DSLOWINDIRECT_VEC, hence these invoke only different
| implementations of the same physics.
|
| But what about parameters that effect the physics itself like
| -DDIRFRC_EFS, -DDIRFRC_COMTRANS, -DNEED_ENE, -DNEED_VIR, and
| -DBUILD_PAIRS_CALC_xxx?
Coming from the compute center, I'm not an expert for the internals
of Amber and only some the defines mentioned above are listed in
the PMEMD README (DIRFRC_NOVEC, SLOWINDIRECT_VEC, DIRFRC_COMTRANS
while the remaining ones seem to be used internally all the time).
Thus, I'd appreciate any comments on what we should allow the
vendors (and what the impact of allowing/disallowing a certain flag
has on the "general usability for a wide range of input files").
Tuning for a certain hardware is fine but the tuning should not
influence the results from the chemical point of view.
Thanks,
--
Dr.-Ing. Thomas Zeiser, HPC Services
Friedrich-Alexander-Universitaet Erlangen-Nuernberg
Regionales Rechenzentrum Erlangen (RRZE)
Martensstrasse 1, 91058 Erlangen, Germany
http://www.rrze.uni-erlangen.de/hpc/
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Received on Wed Apr 21 2010 - 13:30:06 PDT
