COMPUTING for SCIENCE

A variety of performance and benchmarking data in computational chemistry is given below, with a focus on the GAMESS-UK code. This includes:

• The Performance of Various Computers in Computational Chemistry is a report comparing the performance of a number of different computer systems using a variety of software from the discipline of computational chemistry. The software includes matrix operations, a variety of chemistry kernels from quantum chemistry and molecular dynamics, twelve quantum chemistry calculations using GAMESS-UK and six molecular dynamics simulations using the DL_POLY code. The comparison involves approximately two hundred computers, ranging from a NEC SX-6i, to scientific workstations from IBM, Sun, Hewlett Packard, Digital and Silicon Graphics, plus IA32 Pentium and AMD Athlon-based CPUs, x86-64 AMD Opteron and Intel EM64T, plus IA64 Itanium1 and Itanium2-based systems. Copies of the associated MS powerpoint presentation are available in both HTML and PDF format (February 2005).
• Application Performance on High-End and Commodity-class Computers contrasts the performance of Beowulf clusters built from commodity "off the shelf" components in the support of major research and production codes, with current high-end hardware such as the IBM p690+, SGI Altix 3700, and the older Compaq AlphaServer SC and SGI Origin 3800. The results concentrate on the application areas of computational chemistry, computational materials and computational engineering. Using simple metrics, we consider the performance of a variety of computational chenmistry codes, including the electronic structure codes, GAMESS-UK and NWChem, and the molecular simulation codes, DLPOLY, DLMULTI and CHARMM. Computational materials and engineering codes include the Car Parrinello code, CPMD, and the computational fluid dynamics codes, ANGUS and SBLI. We overview performance data from some twenty commodity-based systems (CS1-CS20), featuring Intel IA32 and IA64 plus AMD Athlon and Opteron architectures, coupled to traditional Beowulf interconnects, such as Myrinet and Gbit Ethernet, plus the SCALI/SCI, Infiniband and Quadrics QSNet interconnect technologies. This presentation is a more detailed comparison compared to that above, and extends the comparisons below through the inclusion of seven new clusters (CS14-CS20). This presentation is also available in PDF format. (November 2004). .
• Communication Benchmarks are available for the commonly used MPI operations in computational chemistry codes. Written by Pallas , we provide data for MPI functions that describe point-to-point message-passing and global data movement. Also included are the Bandwidth benchmarks (B_EFF) from Pallas and a set of benchmarks showing the performance of the Global Array (GA) tools from PNNL. This presentation is also available in PDF format (October 2004). .
• GAMESS-UK Serial Benchmarks (2005), extracted from the full report above, including Twelve typical applications are included, featuring both conventional Hartree Fock self-consistent field (SCF) and direct SCF, complete active Space SCF (CASSCF) and multiconfiguration SCF (MCSCF), configuration interaction calculations, both direct-CI and conventional table-driven MRD-CI, Moller Plesset perturbation theory (MP2), and both SCF and MP2 analytic 2nd derivatives. .
• Application Performance on High-End and Commodity-class Computers contrasts the performance of Beowulf clusters built from commodity "off the shelf" components in the support of major research and production codes, with current high-end hardware such as the IBM SP/p690, Compaq AlphaServer SC and SGI Origin 3800. The results concentrate on the application area of computational chemistry. In addition to GAMESS-UK and NWChem, applications considered include those from computational chemistry (DLPOLY, DLMULTI and CHARMM), computational materials (CRYSTAL and the Car Parrinello codes, CPMD and CASTEP), and computational Engineering (ANGUS and SBLI). Benchmark data on thirteen commodity-based systems (CS1-CS13) featuring Intel, AMD Athlon and Alpha CPU architectures coupled to traditional Beowulf interconnect, such as Myrinet and Ethernet, are presented. We include performance data on systems utilising the Quadrics QSNet and SCALI/SCI interconnect technologies. This extends earlier comparisons through the inclusion of four new clusters (CS10-CS13) and additional applications (SBLI and DLMULTI). This presentation is also available in PDF format (August 2003).
• The Performance of Various Computers in Computational Chemistry are earlier versions of the above report as presented at;
  1. the 13th Daresbury Machine Evaluation Workshop in December 2002. Copies of the associated MS powerpoint presentation are available in both HTML and PDF format (December 2002).
  2. the 14th Daresbury Machine Evaluation Workshop in December 2003. Copies of the associated MS powerpoint presentation are available in both HTML and PDF format (March 2004).
• GAMESS-UK Parallel Benchmarks are presented in the report "Massive Parallelism: The Hardware for Computational Chemistry?". Detailed timings on both MPP (the IBM SP and Cray T3E) and SMP hardware are given in Part 16 of the GAMESS-UK User Manual and Reference Guide. Recent developments on Beowulf Systems are available in the presentation "Scientific Applications on High-End and Commodity-Type Computers". (October 2001)
• DL_POLY Serial Benchmarks, extracted from the full report above, including six typical applications (2000).