SAN DIEGO SUPERCOMPUTER CENTER

Advanced User SupportProject Outline

October 9th 2008

Ross C. Walker

SAN DIEGO SUPERCOMPUTER CENTER

Project Listing

• 1) Adrian Roitberg (UFL)• Ross Walker (SDSC) [25 %]• Sudhakar Pamidighantam (NCSA) [10 %]• Christian Halloy (NICS) [5 %]

• 2) Markus Buehler (MIT)• Ross Walker (SDSC) [15 %]• Dodi Heryadi (NCSA) [10 %]

SAN DIEGO SUPERCOMPUTER CENTER

Adrian RoitbergImprovements to the AMBER MD Code

• Does NOT just cover simple MD simulations but also more complex approaches such as QM/MM etc.• Amber QM/MM performance in parallel / serial

• Focused on improving existing codes.• Looking at new / novel approaches for QM/MM in parallel.

– predictive scf.

– parallel Fock matrix prediction.

– Faster distance algorithms for variable QM solvent models.

• PMEMD Performance on multicore machines.• Improvements to Replica Exchange Simulations.• Parallelization of Ptraj Analysis Tools.

SAN DIEGO SUPERCOMPUTER CENTER

PMEMD 10 Performance• Currently performs exceptionally well in parallel.

• E.g. As fast or faster than NAMD for equivalent simulations.• Currently suffers on multi-core machines. It can be cheaper

to leave cores idle due to the improved performance.• Performance on Kraken and Ranger is equivalent at lower

processor counts. At higher counts Kraken seems to perform better on these benchmarks.

• Can we improve on this?

– Multiple compilers / MPI Libraries - which combination works best.– Can we improve TACC_AFFINITY etc?

• Ultimately publish the benchmarks and instructions for compiling etc on the AMBER website.

SAN DIEGO SUPERCOMPUTER CENTER

SAN DIEGO SUPERCOMPUTER CENTER

SAN DIEGO SUPERCOMPUTER CENTER

Markus Buehler

• Works on nano-material simulations.• Spider silk• Carbon nano tubes• ...

• Use modified versions of Lammps and NAMD• Have their own code internally.• Do not have experience in coding within Lammps / NAMD

for parallel.• Transmitting arrays around etc...• Hopefully we can educate his students / postdocs to be self

suffcient.