• NAMD benchmarks (Jan 2009)
• Blast Benchmarks (Dec 2008)
• GROMACS benchmarks (May 2008)
• Amber 10 benchmarks (May 2008)
• WU-Blast benchmarks (Jun 2007)
• Charmm Benchmarks (Apr 2007)
• CNS benchmarks (Aug 2005)
• Sequence Analysis benchmark suite (2006)

CHARMM (c31b2) Benchmarks (Apr 2007)

Model: Myoglobin with CO in a cubic box of 4985 water molecules
Test : dynamics using pme (Particle Mesh Ewald) method, nstep = 2000

# proc.	Time in minutes
	p2800,gige 2.8 GHz Xeon, 1Gb/s ethernet	o2000,gige (2.0 GHz Opteron, 1Gb/s ethernet)	o2200,gige (2.2 GHz Opteron, 1Gb/s ethernet)	o2800,gige (2.8 GHz Opteron, 1Gb/s ethernet)	o2600,gige (2.6 GHz Opteron, dual-core(4p), 1Gb/s ethernet)
1	38.2	35.8	32.4	26.0	27.4
2	21.8	35.8	32.4	13.7	14.4
4	26.0	15.9	15.5	13.4	21.1

CHARMM (c28b3) Benchmarks (7/22/02)

Model: Myoglobin with CO in a cubic box of 4985 water molecules
Test : dynamics using pme (Particle Mesh Ewald) method, nstep = 1000

• AMD 1.4 GHz vs. Intel 866 MHz
• AMD 1.4 GHz, Myrinet vs. Ethernet
• CHARMM scalability

CHARMM (c28b3) Benchmarks (12/5/01)

Model: Myoglobin with CO in a cubic box of 4985 water molecules
Test : dynamics using pme (Particle Mesh Ewald) method, nstep = 1000

• Myrinet vs. Ethernet
• 2.2-tcpfix vs. 2.4 kernels
• Pentium vs. XP
• Athlon vs XP
• 2.4.12 vs 2.4.18 kernels

Test: QM using GAMESS, nstep = 1

• Pentium vs XP

CHARMM MPICH/GM Benchmarks (3/27/01)

These benchmarks are described in /usr/local/src/mpich-1.2..5/examples/perftest

• 2 x 866 MHz Pentium III, 256k full speed secondary cache, 512MB memory
• Myricom Myrinet-2000 PCI64B
• RedHat Linux 6.x/2.2.16 kernel
• MPICH-GM 1.2..5
• GM-1.4pre56

		Average latency (uS)	Average transfer rate (Mbytes/s)
p2p-short	blocking point-to-point message sizes 0 - 1k bytes	9.77	37.05
p2p-long	blocking point-to-point message sizes 16k - 64k bytes	118.33	193.95
nbpt2pt-long	non-blocking point-to-point message sizes 16k - 64k bytes	119.06	193.44
bisect8-short	bisectional bandwidth message sizes 0 - 1k bytes 8 procs on 8 nodes	9.77	148.47
bisect8-long	bisectional bandwidth message sizes 16k - 64k bytes 8 procs on 8 nodes	118.32	193.96
bw	Blocking bandwidth 0 - 4MBytes	9.96	218.12

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CHARMM MPICH/GM Benchmarks (3/27/00)

These benchmarks are described in /usr/local/src/mpich-1.1.2..13/examples/perftest.

• 2 x 450 MHz Pentium III, 512k secondary caches, 256MB memory
• Myricom Myrinet PCI32C (1MB)
• RedHat Linux 6.x/2.2.13 kernel
• MPICH-GM 1.1.2..13
• GM-1.1.3

		latency (uS)	transfer rate (Mbytes/s)	variance in fit
pt2ptshort	blocking point-to-point message sizes 0 - 1k bytes	24.55	25.29	0.000034
pt2ptlong	blocking point-to-point message sizes 16k - 64k bytes	119.77	50.16	0.001753
nbpt2ptlong	non-blocking point-to-point message sizes 16k - 64k bytes	121.85	50.03	0.001655
bisectshort8	bisectional bandwidth message sizes 0 - 1k bytes 8 procs on 8 nodes	24.53	25.30	0.000034
bisectlong8	bisectional bandwidth message sizes 16k - 32k bytes 8 procs on 8 nodes	125.30	50.63	0.001646

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CHARMM MPICH/GM Benchmarks (10/20/99)

These benchmarks are described in /usr/local/src/mpich-1.1.2..7/examples/perftest.

• 2 x 450 MHz Pentium II, 512k secondary caches, 256MB memory
• Myricom Myrinet PCI32C (1MB)
• RedHat Linux 6.0/2.2.12 kernel
• MPICH-GM 1.1.2..7
• GM-1.086 for Linux-2.2.12smp

		latency (uS)	transfer rate (Mbytes/s)	variance in fit
pt2ptshort	blocking point-to-point message sizes 0 - 1k bytes	32.05	24.47	0.000043
pt2ptlong	blocking point-to-point message sizes 16k - 64k bytes	143.91	50.73	0.001593
nbpt2ptlong	non-blocking point-to-point message sizes 16k - 64k bytes	147.85	51.02	0.001584
bisectshort16	bisectional bandwidth message sizes 0 - 1k bytes 16 procs on 16 nodes	32.06	24.37	0.000043
bisectlong16	bisectional bandwidth message sizes 16k - 32k bytes 16 procs on 16 nodes	132.76	49.83	0.001622
bisectshort32	bisectional bandwidth message sizes 0 - 1k bytes 32 procs on 16 nodes	32.06	24.37	0.000043
bisectlong32	bisectional bandwidth message sizes 16k - 32k bytes 32 procs on 16 nodes	142.69	50.73	0.001593

Performance testing a la Myricom: runex generates basic latency and bandwidth performance data.

	bandwidth	latency
blocking	50.85 Mbytes/s	32.11 usec
non-blocking	50.47 Mbytes/s	33.34 usec

Benchmarks published by Myricom for 64-bit and 32-bit interfaces.