Talk:NAMD Benchmarks - Revision history

Tanthony@uab.edu: added category NAMD

2011-06-09T17:19:31Z

added category NAMD

2011-05-31T16:29:43Z

Actual job comparison to IBM BG/L

← Older revision		Revision as of 16:29, 31 May 2011
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	\|}		\|}

	The Cheaha outperforms the BG/L using ~~onlu~~ 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.

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

2011-05-31T16:28:54Z

added bluegene data

@@ Line 280: / Line 280: @@
 [[File:NAMD_benchmark_image_6_Effciency_combined_AM.png|center]]
 === Actual job comparison to IBM BG/L ===
-NAMD Comparison data to UAB IBM BlueGene/L
+NAMD Comparison data to UAB IBM BlueGene/L.
 == Perform Your Own Benchmarks ==

2011-05-31T16:20:31Z

Actual job comparison to IBM BG/L

← Older revision		Revision as of 16:20, 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]]
	=== Actual job comparison to IBM BG/L ===		=== Actual job comparison to IBM BG/L ===
			NAMD Comparison data to UAB IBM BlueGene/L

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

2011-05-31T16:08:29Z

added martins job data

← Older revision		Revision as of 16:08, 31 May 2011
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	\|316.46		\|316.46
	\|}		\|}
			[[File:NAMD_benchmark_image_6_Effciency_combined_AM.png\|center]]
	=== Actual job comparison to IBM BG/L ===		=== Actual job comparison to IBM BG/L ===

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

2011-05-31T15:24:31Z

Speedup (Actual Wall times, days/ns, efficiency): added speed up

← Older revision		Revision as of 15:24, 31 May 2011
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	! Wall Clock		! Wall Clock
	! Days/ns		! Days/ns
			! Speedup
	\|-		\|-
	\|1		\|1
	\|357278 (99hrs 14mins)		\|357278 (99hrs 14mins)
	\|20.4950 (100%)		\|20.4950 (100%)
			\|1
	\|-		\|-
	\|8		\|8
	\|45784 (12hrs 42mins)		\|45784 (12hrs 42mins)
	\|2.6237 (97.64%)		\|2.6237 (97.64%)
			\|7.80
	\|-		\|-
	\|16		\|16
	\|23380 (6hrs 29mins)		\|23380 (6hrs 29mins)
	\|1.33205 (96.16%)		\|1.33205 (96.16%)
			\|15.28
	\|-		\|-
	\|32		\|32
	\|11871 (3hrs 17mins)		\|11871 (3hrs 17mins)
	\|0.6809 (94.04%)		\|0.6809 (94.04%)
			\|30.09
	\|-		\|-
	\|64		\|64
	\|6242 (1hr 43mins)		\|6242 (1hr 43mins)
	\|0.3626 (88.30%)		\|0.3626 (88.30%)
			\|57.23
	\|-		\|-
	\|128		\|128
	\|3386 (56mins 26secs)		\|3386 (56mins 26secs)
	\|0.1940 (82.51%)		\|0.1940 (82.51%)
			\|105.51
	\|-		\|-
	\|256		\|256
	\|1814 (30mins 14secs)		\|1814 (30mins 14secs)
	\|0.0982 (81.51%)		\|0.0982 (81.51%)
			\|196.96
	\|-		\|-
	\|512		\|512
	\|1129 (18mins 49secs)		\|1129 (18mins 49secs)
	\|0.0578 (69.21%)		\|0.0578 (69.21%)
			\|316.46
	\|}		\|}

	=== Actual job comparison to IBM BG/L ===		=== Actual job comparison to IBM BG/L ===

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

2011-05-31T15:20:04Z

← Older revision		Revision as of 15:20, 31 May 2011
Line 207:		Line 207:

	== Actual job benchmarks (Segrest job) ==		== Actual job benchmarks (Segrest job) ==
	~~Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps~~.		Actual NAMD job courtesy of Center for Computational and Structural Biology.

	STRUCTURE SUMMARY:		STRUCTURE SUMMARY:
			Job parameters: 100,000 steps, 246K atoms, 12A cutoff + PME every 4 steps
	245956 ATOMS		245956 ATOMS
	174192 BONDS		174192 BONDS
Line 229:		Line 230:


	=== Speedup (Actual Wall ~~times,CPU~~ times,days/ns, efficiency)===		=== Speedup (Actual Wall times, days/ns, efficiency)===
	{\| border="1" align="center" cellpadding="10" style="text-align:center;"		{\| border="1" align="center" cellpadding="10" style="text-align:center;"
	\|+ Actual NAMD CSB job on Cheaha Gen 3 hardware		\|+ Actual NAMD CSB job on Cheaha Gen 3 hardware
Line 266:		Line 267:
	\|512		\|512
	\|1129 (18mins 49secs)		\|1129 (18mins 49secs)
	\|0.~~057840~~(69.21%)		\|0.0578 (69.21%)
	\|}		\|}
	=== Actual job comparison to IBM BG/L ===		=== Actual job comparison to IBM BG/L ===

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

2011-05-31T15:07:51Z

added MArtins CSB job table and data

@@ Line 19: / Line 19: @@
 Benchmark used for performance evaluation on the [[Cheaha]], [http://biowulf.nih.gov Biowulf], and [http://www.asc.edu/supercomputing/index.shtml DMC] is Apoa1 from the NAMD suite  and is available at: http://www.ks.uiuc.edu/Research/namd/utilities/
-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 throughout are: 500 steps, 92K atoms, 12A cutoff + PME every 4 steps.
@@ Line 207: / Line 207: @@
 == Actual job benchmarks (Segrest job) ==
-=== Speedup (Actual Wall times and CPU times)===
+STRUCTURE SUMMARY:
 === Actual job comparison to IBM BG/L ===
 == Perform Your Own Benchmarks ==

2011-05-31T14:34:51Z

← Older revision		Revision as of 14:34, 31 May 2011
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	[[File:NAMD_benchmark_img6_Efficiency_gen2_gen3_ib.png\|center]]		[[File:NAMD_benchmark_img6_Efficiency_gen2_gen3_ib.png\|center]]

	===Notes===		===Hardware Notes===
	Generation 3 hardware contains 576 cores. 2.66 GHz Intel Xeon Hex-core (48-2x6 core)		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)		Generation 2 hardware contains 192 cores. 3.06 GHz Intel Xeon Quad-core (24-2x4 core)

2011-05-31T14:19:10Z

added hardware notes in generation comparison

← Older revision		Revision as of 14:19, 31 May 2011
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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]]

			===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]].

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