TY - GEN
T1 - Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated openPOWER platforms
AU - Stone, John E.
AU - Hynninen, Antti Pekka
AU - Phillips, James C.
AU - Schulten, Klaus J
N1 - Funding Information:
The authors acknowledge support from NIH grants 9P41GM10 4601 and 5R01GM098243-02, the CUDA Center of Excellence at the University of Illinois, the Blue Waters sustained-petascale computing project supported by NSF awards OCI-0725070 and ACI-1238993, the state of Illinois, ?The Computational Microscope? NSF PRAC awards OCI-0832673 and ACI-1440026, and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory supported by the Department of Energy under Contract DE-AC05-00OR22725.
Publisher Copyright:
© Springer International Publishing AG 2016.
PY - 2016
Y1 - 2016
N2 - All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.
AB - All-atom molecular dynamics simulations of biomolecules provide a powerful tool for exploring the structure and dynamics of large protein complexes within realistic cellular environments. Unfortunately, such simulations are extremely demanding in terms of their computational requirements, and they present many challenges in terms of preparation, simulation methodology, and analysis and visualization of results. We describe our early experiences porting the popular molecular dynamics simulation program NAMD and the simulation preparation, analysis, and visualization tool VMD to GPU-accelerated OpenPOWER hardware platforms. We report our experiences with compiler-provided autovectorization and compare with hand-coded vector intrinsics for the POWER8 CPU. We explore the performance benefits obtained from unique POWER8 architectural features such as 8-way SMT and its value for particular molecular modeling tasks. Finally, we evaluate the performance of several GPU-accelerated molecular modeling kernels and relate them to other hardware platforms.
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U2 - 10.1007/978-3-319-46079-6_14
DO - 10.1007/978-3-319-46079-6_14
M3 - Conference contribution
C2 - 29202130
AN - SCOPUS:84992554684
SN - 9783319460789
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 188
EP - 206
BT - High Performance Computing - ISC High Performance 2016 International Workshops ExaComm, E-MuCoCoS, HPC-IODC, IXPUG, IWOPH, P^3MA, VHPC, WOPSSS, Revised Selected
A2 - Mohr, Bernd
A2 - Kunkel, Julian M.
A2 - Taufer, Michela
PB - Springer-Verlag Berlin Heidelberg
T2 - International Workshops on High Performance Computing, ISC High Performance 2016 and Workshop on 2nd International Workshop on Communication Architectures at Extreme Scale, ExaComm 2016, Workshop on Exascale Multi/Many Core Computing Systems, E-MuCoCoS 2016, HPC I/O in the Data Center, HPC-IODC 2016, Application Performance on Intel Xeon Phi – Being Prepared for KNL and Beyond, IXPUG 2016, International Workshop on OpenPOWER for HPC, IWOPH 2016, International Workshop on Performance Portable Programming Models for Accelerators, P^3MA 2016, Workshop on Virtualization in High-Performance Cloud Computing, VHPC 2016, Workshop on Performance and Scalability of Storage Systems, WOPSSS 2016
Y2 - 19 June 2016 through 23 June 2016
ER -