NAMD Benchmarks - Revision history

Tanthony@uab.edu: added category MD

2012-04-04T15:00:28Z

added category MD

← Older revision		Revision as of 15:00, 4 April 2012
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	[[Category:~~NAMD~~]]		[[Category:Molecular Dynamics]]

Tanthony@uab.edu: added category NAMD

2011-06-09T17:19:09Z

added category NAMD

← Older revision		Revision as of 17:19, 9 June 2011
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	The Cheaha outperforms the BG/L using only 32 cores on the gen 3 hardware. At equal processor count the Cheaha is roughly 8 times faster than the BG/L.		The Cheaha outperforms the BG/L using only 32 cores on the gen 3 hardware. At equal processor count the Cheaha is roughly 8 times faster than the BG/L.


			[[Category:NAMD]]

Tanthony@uab.edu: added Bluegene data

2011-05-31T16:31:42Z

added Bluegene data

← Older revision		Revision as of 16:31, 31 May 2011
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	\|}		\|}
	[[File:NAMD_benchmark_image_6_Effciency_combined_AM.png\|center]]		[[File:NAMD_benchmark_image_6_Effciency_combined_AM.png\|center]]

			=== Comparison to IBM BG/L ===
			NAMD comparison of job data between UAB IBM BlueGene/L and Cheaha.

			Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps (same as actual user job described above)

			{\| border="1" align="center" cellpadding="10" style="text-align:center;"
			\|+ NAMD Comparison to IBM BG/L
			! System
			! CPU count
			! Atoms
			! Days/ns
			\|-
			\|UAB BlueGene/L
			\|256
			\|246K
			\|0.80
			\|-
			\|Cheaha Gen3
			\|32
			\|246K
			\|0.6809
			\|-
			\|Cheaha Gen3
			\|256
			\|246K
			\|0.0982
			\|-
			\|Cheaha Gen3
			\|512
			\|246K
			\|0.0578
			\|}

			The Cheaha outperforms the BG/L using only 32 cores on the gen 3 hardware. At equal processor count the Cheaha is roughly 8 times faster than the BG/L.

Tanthony@uab.edu: added link to NAMD Cheaha user page

2011-05-31T16:15:48Z

added link to NAMD Cheaha user page

← Older revision		Revision as of 16:15, 31 May 2011
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	The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.		The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.

			Information on how to submit NAMD jobs to [[Cheaha]] is avaiable [[NAMD \|here]].

Tanthony@uab.edu: added Martins Segrest job data

2011-05-31T16:09:40Z

added Martins Segrest job data

← Older revision		Revision as of 16:09, 31 May 2011
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	Generation 2 hardware contains 192 cores. 3.06 GHz Intel Xeon Quad-core (24-2x4 core)		Generation 2 hardware contains 192 cores. 3.06 GHz Intel Xeon Quad-core (24-2x4 core)
	More information about the hardware used on [[Cheaha]] is available [[Cheaha#Hardware \|here]].		More information about the hardware used on [[Cheaha]] is available [[Cheaha#Hardware \|here]].


			== Actual job benchmarks (Segrest job) ==
			Actual NAMD job courtesy of Center for Computational and Structural Biology.

			STRUCTURE SUMMARY:
			Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps
			245956 ATOMS
			174192 BONDS
			130742 ANGLES
			84410 DIHEDRALS
			1622 IMPROPERS
			0 CROSSTERMS
			0 EXCLUSIONS
			232802 RIGID BONDS
			505063 DEGREES OF FREEDOM
			84698 HYDROGEN GROUPS
			4 ATOMS IN LARGEST HYDROGEN GROUP
			84698 MIGRATION GROUPS
			4 ATOMS IN LARGEST MIGRATION GROUP
			TOTAL MASS = 1.48179e+06 amu
			TOTAL CHARGE = 2.7746e-05 e
			MASS DENSITY = 1.01378 g/cm^3
			ATOM DENSITY = 0.101334 atoms/A^3


			=== Speedup (Actual Wall times, days/ns, efficiency)===
			{\| border="1" align="center" cellpadding="10" style="text-align:center;"
			\|+ Actual NAMD CSB job on Cheaha Gen 3 hardware
			!Processors
			! Wall Clock
			! Days/ns
			! Speedup
			\|-
			\|1
			\|357278 (99hrs 14mins)
			\|20.4950 (100%)
			\|1
			\|-
			\|8
			\|45784 (12hrs 42mins)
			\|2.6237 (97.64%)
			\|7.80
			\|-
			\|16
			\|23380 (6hrs 29mins)
			\|1.33205 (96.16%)
			\|15.28
			\|-
			\|32
			\|11871 (3hrs 17mins)
			\|0.6809 (94.04%)
			\|30.09
			\|-
			\|64
			\|6242 (1hr 43mins)
			\|0.3626 (88.30%)
			\|57.23
			\|-
			\|128
			\|3386 (56mins 26secs)
			\|0.1940 (82.51%)
			\|105.51
			\|-
			\|256
			\|1814 (30mins 14secs)
			\|0.0982 (81.51%)
			\|196.96
			\|-
			\|512
			\|1129 (18mins 49secs)
			\|0.0578 (69.21%)
			\|316.46
			\|}
			[[File:NAMD_benchmark_image_6_Effciency_combined_AM.png\|center]]

Tanthony@uab.edu: Added hardware notes from discussion

2011-05-31T14:35:23Z

Added hardware notes from discussion

← Older revision		Revision as of 14:35, 31 May 2011
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	The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.		The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.



	== Sample Benchmark using NAMD ==		== Sample Benchmark using NAMD ==
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	! Cheaha		! Cheaha
	! Biowulf		! Biowulf
	! DMC		! DMC <ref group="note" >No hardware control was possible for the ASC's DMC and as such it is possible that different runs might have run on different hardware. *Efficiency on DMC using 4 processors is above 100%. This could be probably because of an older generation processor being used to run the job serially i.e. using 1 processor, thus setting a lower baseline to begin with causing the efficiency to go up as better processors are available for the parallel jobs.</ref>
	\|-		\|-
	\|1		\|1
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	\|256		\|256
	\|0.0770 (78.09%)		\|0.0770 (78.09%)
			\|NA
			\|NA
			\|-
			\|512
			\|0.0439 (68.49%)
	\|NA		\|NA
	\|NA		\|NA
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	The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.		The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.

			;ASC-DMC
			<references group="note"/>



	== Comparison of Ethernet and IB ==		== Comparison of Ethernet and IB ==
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	\|0.0770 (78.09%)		\|0.0770 (78.09%)
	\|0.8632 (6.97%)		\|0.8632 (6.97%)
			\|-
			\|512
			\|0.0439 (68.49%)
			\|NA
	\|}		\|}
	[[File:NAMD_benchmark_img3_Ib_eth_days_ns_2.8.png\|center]]		[[File:NAMD_benchmark_img3_Ib_eth_days_ns_2.8.png\|center]]
	[[File:NAMD_benchmark_img4_Ib_eth_efficiency_2.8.png\|center]]		[[File:NAMD_benchmark_img4_Ib_eth_efficiency_2.8.png\|center]]

	== Comparison of different Generations of Cheaha hardware on NAMD with Infinband ==		== Comparison on different Generations of Cheaha hardware on NAMD with Infinband ==
	{\| border="1" align="center" cellpadding="10" style="text-align:center;"		{\| border="1" align="center" cellpadding="10" style="text-align:center;"
	\|+ Cheaha Gen 2 and Gen 3 hardware using NAMD 2.8 and Inifiband		\|+ Cheaha Gen 2 and Gen 3 hardware using NAMD 2.8 and Inifiband
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	\|256		\|256
	\|0.0770 (78.09%)		\|0.0770 (78.09%)
			\|NA
			\|-
			\|512
			\|0.0439 (68.49%)
	\|NA		\|NA
	\|}		\|}
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	[[File:NAMD_benchmark_img5_Days_gen2_gen3_infiniband.png\|center]]		[[File:NAMD_benchmark_img5_Days_gen2_gen3_infiniband.png\|center]]
	[[File:NAMD_benchmark_img6_Efficiency_gen2_gen3_ib.png\|center]]		[[File:NAMD_benchmark_img6_Efficiency_gen2_gen3_ib.png\|center]]

			===Hardware Notes===
			Generation 3 hardware contains 576 cores. 2.66 GHz Intel Xeon Hex-core (48-2x6 core)
			Generation 2 hardware contains 192 cores. 3.06 GHz Intel Xeon Quad-core (24-2x4 core)
			More information about the hardware used on [[Cheaha]] is available [[Cheaha#Hardware \|here]].

Tanthony@uab.edu at 16:55, 26 May 2011

2011-05-26T16:55:39Z

← Older revision		Revision as of 16:55, 26 May 2011
Line 20:		Line 20:

	The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.		The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.




	== Sample Benchmark using NAMD ==		== Sample Benchmark using NAMD ==

Tanthony@uab.edu at 16:55, 26 May 2011

2011-05-26T16:55:21Z

← Older revision		Revision as of 16:55, 26 May 2011
Line 20:		Line 20:

	The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.		The parameters for the benchmark used through out are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.

Tanthony@uab.edu: added section 2and 3

2011-05-26T16:54:07Z

added section 2and 3

← Older revision		Revision as of 16:54, 26 May 2011
Line 89:		Line 89:

	The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.		The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.

			== Comparison of Ethernet and IB ==
			{\| border="1" align="center" cellpadding="10" style="text-align:center;"
			\|+ Ethernet vs Infiniband interconnect on Cheaha Gen 3 hardware
			!Processors
			! Infiniband
			! Ethernet
			\|-
			\|1
			\|15.4054 (100%)
			\|15.4040 (100%)
			\|-
			\|2
			\|7.7119 (99.87%)
			\|7.7800 (98.99%)
			\|-
			\|4
			\|3.8933 (98.92%)
			\|3.9405 (97.72%)
			\|-
			\|8
			\|1.9653 (97.98%)
			\|2.2816 (84.39%)
			\|-
			\|16
			\|0.9950 (96.76%)
			\|1.2714 (75.74%)
			\|-
			\|32
			\|0.5101 (94.37%)
			\|0.6973 (69.03%)
			\|-
			\|64
			\|0.2592 (92.83%)
			\|0.6562 (36.67%)
			\|-
			\|128
			\|0.1360 (88.45%)
			\|0.8950 (13.44%)
			\|-
			\|256
			\|0.0770 (78.09%)
			\|0.8632 (6.97%)
			\|}
			[[File:NAMD_benchmark_img3_Ib_eth_days_ns_2.8.png\|center]]
			[[File:NAMD_benchmark_img4_Ib_eth_efficiency_2.8.png\|center]]

			== Comparison of different Generations of Cheaha hardware on NAMD with Infinband ==
			{\| border="1" align="center" cellpadding="10" style="text-align:center;"
			\|+ Cheaha Gen 2 and Gen 3 hardware using NAMD 2.8 and Inifiband
			!Processors
			! Generation 3
			! Generation 2
			\|-
			\|1
			\|15.4054 (100%)
			\|15.9300 (100%)
			\|-
			\|2
			\|7.7119 (99.87%)
			\|8.6620 (91.98%)
			\|-
			\|4
			\|3.8933 (98.92%)
			\|4.2560 (93.59%)
			\|-
			\|8
			\|1.9653 (97.98%)
			\|2.3450 (84.93%)
			\|-
			\|16
			\|0.9950 (96.76%)
			\|1.2060 (82.56%)
			\|-
			\|32
			\|0.5101 (94.37%)
			\|0.6420 (77.57%)
			\|-
			\|64
			\|0.2592 (92.83%)
			\|0.2750 (90.38%)
			\|-
			\|128
			\|0.1360 (88.45%)
			\|0.1620 (76.81%)
			\|-
			\|256
			\|0.0770 (78.09%)
			\|NA
			\|}

			[[File:NAMD_benchmark_img5_Days_gen2_gen3_infiniband.png\|center]]
			[[File:NAMD_benchmark_img6_Efficiency_gen2_gen3_ib.png\|center]]

Tanthony@uab.edu at 15:42, 26 May 2011

2011-05-26T15:42:35Z

← Older revision		Revision as of 15:42, 26 May 2011
Line 89:		Line 89:

	The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.		The data for the NIH-Biowulf benchmarks is available at: http://biowulf.nih.gov/apps/namd/namd_bench.html. The Biowulf hardware used for comparison in the e2800 with Infiniband.

	~~== Comparison of Ethernet and IB ==~~


	~~== Comparison on different nodes on Cheaha Gen 2 and Gen 3 with IB ==~~

	~~== Actual job benchmarks (Segrest job) ==~~

	~~== Perform Your Own Benchmarks ==~~