Gromacs Benchmark - Revision history

Tanthony@uab.edu: added category MD

2012-04-04T15:01:07Z

added category MD

← Older revision		Revision as of 15:01, 4 April 2012
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	Performance: 76.705 5.208 1.330 18.040		Performance: 76.705 5.208 1.330 18.040

	[[Category: ~~Gromacs~~]]		[[Category:Molecular Dynamics]]

Tanthony@uab.edu at 13:12, 15 June 2011

2011-06-15T13:12:34Z

← Older revision		Revision as of 13:12, 15 June 2011
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	~~This page is under construction!~~

	The efficiency of a parallel system describes the fraction of the time that is being used by the processors for a given computation. It is defined as		The efficiency of a parallel system describes the fraction of the time that is being used by the processors for a given computation. It is defined as
	<pre>		<pre>

Tanthony@uab.edu: added Gromacs version s for Cheaha and DMC

2011-06-15T13:10:33Z

added Gromacs version s for Cheaha and DMC

← Older revision		Revision as of 13:10, 15 June 2011
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	The above benchmarks were run using d.dppc benchmark [http://www.gromacs.org/About_Gromacs/Benchmarks ] from Gromacs.		The above benchmarks were run using d.dppc benchmark [http://www.gromacs.org/About_Gromacs/Benchmarks ] from Gromacs.

	On Cheaha, the second and third generation hardware was used for the above benchmarks. More information about the hardware used on [[Cheaha]] is available [[Cheaha#Hardware \|here]].		On Cheaha, the second and third generation hardware was used for the above benchmarks. More information about the hardware used on [[Cheaha]] is available [[Cheaha#Hardware \|here]]. Cheaha is running Gromacs 4.0.7

			All tests on the DMC are run on mixed generation hardware. DMC is running Gromacs 4.5.3

	The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/gromacs/bench-4.0.3.html. The Biowulf hardware used for comparison in the e2800 with Infiniband and o2800 with ethernet.		The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/gromacs/bench-4.0.3.html. The Biowulf hardware used for comparison in the e2800 with Infiniband and o2800 with ethernet.

Tanthony@uab.edu: added ns/day speedup image

2011-06-14T18:15:49Z

added ns/day speedup image

← Older revision		Revision as of 18:15, 14 June 2011
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	Benchmark parameters: 1024 DPPC lipids with 23 water molecules per lipid, totalling to 121856 atoms. A twin-range group based cut-off is used, 1.8 nm for electrostatics and 1.0 nm for Lennard-Jones interactions. The long-range contribution to electrostatics is updated every 10 steps. 5000 steps = 10ps.		Benchmark parameters: 1024 DPPC lipids with 23 water molecules per lipid, totalling to 121856 atoms. A twin-range group based cut-off is used, 1.8 nm for electrostatics and 1.0 nm for Lennard-Jones interactions. The long-range contribution to electrostatics is updated every 10 steps. 5000 steps = 10ps.

	===~~Cheaha, DMC, and Biowulf wall~~ clock and efficiency on Gromacs - Benchmark d.dppc===		===Wall clock and efficiency on Gromacs - Benchmark d.dppc===
	{\| border="1" align="center" cellpadding="10" style="text-align:center;"		{\| border="1" align="center" cellpadding="10" style="text-align:center;"
	\|+ Cheaha, DMC, and Biowulf wall clock and efficiency on Gromacs - Benchmark d.dppc		\|+ Cheaha, DMC, and Biowulf wall clock and efficiency on Gromacs - Benchmark d.dppc
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	===~~Cheaha, DMC, and Biowulf~~ ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc===		===ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc===
	{\| border="1" align="center" cellpadding="10" style="text-align:center;"		{\| border="1" align="center" cellpadding="10" style="text-align:center;"
	\|+ Cheaha, DMC, and Biowulf ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc		\|+ Cheaha, DMC, and Biowulf ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc
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	\|}		\|}

			[[File:Gromacs_benchmark_img3_Gromacs_ns.png\|center]]

Tanthony@uab.edu: added ns/day and speedup table

2011-06-14T18:12:53Z

added ns/day and speedup table

← Older revision		Revision as of 18:12, 14 June 2011
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	[[File:Gromacs_Benchmark_img1_Gromacs_wall.png\|center]]		[[File:Gromacs_Benchmark_img1_Gromacs_wall.png\|center]]
	[[File:Gromacs_Benckmark_img2_Gromacs_efficiency.png\|center]]		[[File:Gromacs_Benckmark_img2_Gromacs_efficiency.png\|center]]


			===Cheaha, DMC, and Biowulf ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc===
			{\| border="1" align="center" cellpadding="10" style="text-align:center;"
			\|+ Cheaha, DMC, and Biowulf ns/day (speedup)and GFlops rating on Gromacs -Benchmark d.dppc
			! Processors
			! Cheaha ns/day(speedup)
			! Cheaha GFlops
			! DMC ns/day (speedup)
			! DMC GFlops
			! Biowulf IB ns/day (speedup)
			! Biowulf Ethernet ns/day(speedup)
			\|-
			\|1
			\|0.523
			\|2.482
			\|0.303
			\|1.428
			\|0.498
			\|0.325
			\|-
			\|2
			\|1.329 (2.5)
			\|6.307
			\|0.688 (2.2)
			\|3.234
			\|1.146 (2.7)
			\|0.832 (2.6)
			\|-
			\|4
			\|2.603 (4.9)
			\|12.326
			\|1.359 (4.4)
			\|6.381
			\|2.262 (5.3)
			\|1.701 (5.2)
			\|-
			\|8
			\|4.774 (9.1)
			\|22.613
			\|2.183 (7.2)
			\|10.266
			\|4.257 (10.3)
			\|2.939 (9.0)
			\|-
			\|16
			\|8.909 (17.0)
			\|42.341
			\|3.922 (12.9)
			\|18.442
			\|8.472 (17.0)
			\|5.879 (18.1)
			\|-
			\|32
			\|19.64 (37.5)
			\|93.496
			\|6.442 (21.2)
			\|30.352
			\|16.305 (32.7)
			\|9.933 (30.6)
			\|-
			\|64
			\|32.006 (61)
			\|152.524
			\|9.432 (31.1)
			\|44.509
			\|30.863 (62)
			\|NA
			\|-
			\|128
			\|61.727 (118)
			\|294.303
			\|NA
			\|NA
			\|50.834 (102)
			\|NA
			\|-
			\|256
			\|108.022 (207)
			\|516.398
			\|NA
			\|NA
			\|72.014 (144)
			\|NA
			\|}

Tanthony@uab.edu at 18:01, 14 June 2011

2011-06-14T18:01:14Z

← Older revision		Revision as of 18:01, 14 June 2011
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	==Other Benchmarks ==		==Other Benchmarks ==
	These benchmarks have been performed by Mike Hanby at ~~REsearch~~ Computing after ~~2011~~ Hardware upgrade to the Cheaha.		These benchmarks have been performed by Mike Hanby at Research Computing after 2007 Hardware upgrade to the Cheaha.

	~~=== 2011 Hardware ===~~

	Benchmark data for running Gromacs on [[Cheaha]] will be developed leveraging the benchmark foundation of the [http://biowulf.nih.gov/apps/gromacs NIH's Biowulf cluster Gromacs] testing suite combined with local work flow characteristics.

	=== 2007 Hardware and Gromacs 3.x ===		=== 2007 Hardware and Gromacs 3.x ===

Tanthony@uab.edu at 18:00, 14 June 2011

2011-06-14T18:00:09Z

← Older revision		Revision as of 18:00, 14 June 2011
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	The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/gromacs/bench-4.0.3.html. The Biowulf hardware used for comparison in the e2800 with Infiniband and o2800 with ethernet.		The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/gromacs/bench-4.0.3.html. The Biowulf hardware used for comparison in the e2800 with Infiniband and o2800 with ethernet.

			==Other Benchmarks ==
			These benchmarks have been performed by Mike Hanby at REsearch Computing after 2011 Hardware upgrade to the Cheaha.

	=== 2011 Hardware ===		=== 2011 Hardware ===

Tanthony@uab.edu: added efficeicny image

2011-06-14T17:57:52Z

added efficeicny image

← Older revision		Revision as of 17:57, 14 June 2011
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	\|}		\|}
	[[File:Gromacs_Benchmark_img1_Gromacs_wall.png\|center]]		[[File:Gromacs_Benchmark_img1_Gromacs_wall.png\|center]]
			[[File:Gromacs_Benckmark_img2_Gromacs_efficiency.png\|center]]

Tanthony@uab.edu at 17:43, 14 June 2011

2011-06-14T17:43:38Z

← Older revision		Revision as of 17:43, 14 June 2011
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	\|NA		\|NA
	\|}		\|}
			[[File:Gromacs_Benchmark_img1_Gromacs_wall.png\|center]]

Tanthony@uab.edu: added benchmark parameters

2011-06-14T17:40:44Z

added benchmark parameters

← Older revision		Revision as of 17:40, 14 June 2011
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	== Sample Benchmark using Gromacs ==		== Sample Benchmark using Gromacs ==

			Benchmark parameters: 1024 DPPC lipids with 23 water molecules per lipid, totalling to 121856 atoms. A twin-range group based cut-off is used, 1.8 nm for electrostatics and 1.0 nm for Lennard-Jones interactions. The long-range contribution to electrostatics is updated every 10 steps. 5000 steps = 10ps.

	===Cheaha, DMC, and Biowulf wall clock and efficiency on Gromacs - Benchmark d.dppc===		===Cheaha, DMC, and Biowulf wall clock and efficiency on Gromacs - Benchmark d.dppc===