Gromacs Benchmark: Difference between revisions

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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
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In general, parallel jobs should scale to at least 70% efficiency. The ASC's DMC  recommends a scaling efficiency of 75% or greater. For Gromacs the efficiency of a parallel job can be calculated with wither the Wall clock parameter or the ns/day parameter. We use the wall clock and efficiency is calculated as (where N is processors committed to the job):
In general, parallel jobs should scale to at least 70% efficiency. The ASC's DMC  recommends a scaling efficiency of 75% or greater. For Gromacs the efficiency of a parallel job can be calculated with either the Wall clock parameter or the ns/day parameter. We use the wall clock and efficiency is calculated as (where N is processors committed to the job):
 


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Benchmark used for performance evaluation on [[Cheaha]] ,[http://biowulf.nih.gov Biowulf], and [http://www.asc.edu/supercomputing/index.shtml DMC]is the d.dppc which is available from the Gromacs benchmark suite and is available at: http://www.gromacs.org/About_Gromacs/Benchmarks  
Benchmark used for performance evaluation on [[Cheaha]], [http://biowulf.nih.gov Biowulf], and [http://www.asc.edu/supercomputing/index.shtml DMC]is the d.dppc which is available from the Gromacs benchmark suite and is available at: http://www.gromacs.org/About_Gromacs/Benchmarks  
 
Information on how to submit Gromacs jobs to [[Cheaha]] is available [[Gromacs |here]].
 
== 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.
 
===Wall clock and efficiency  on Gromacs - Benchmark d.dppc===
{| border="1" align="center" cellpadding="10" style="text-align:center;"
|+ Cheaha, DMC, and Biowulf wall clock and efficiency  on Gromacs - Benchmark d.dppc
!Processors
! Cheaha
! DMC
! Biowulf IB
! Biowulf Ethernet
|-
|1
|1562 (100%)
|2848 (100%)
|1734 (100%)
|2656 (100%)
|-
|2
|650 (127%)
|1256 (113%)
|754 (115%)
|1039 (128%)
|-
|4
|332 (124%)
|636 (112%)
|382 (114%)
|508 (131%)
|-
|8
|181 (114%)
|396 (90%)
|203 (107%)
|294 (113%)
|-
|16
|97 (106%)
|220 (81%)
|102 (106%)
|200 (83%)
|-
|32
|44 (117%)
|134 (66%)
|53 (102 %)
|147 (56%)
|-
|64
|27 (96%)
|92 (49%)
|28 (97%)
|NA
|-
|128
|14 (92 %)
|NA
|17 (80%)
|NA
|-
|256
|8 (81%)
|NA
|12 (56%)
|NA
|}
[[File:Gromacs_Benchmark_img1_Gromacs_wall.png|center]]
[[File:Gromacs_Benckmark_img2_Gromacs_efficiency.png|center]]
 
 
===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
|}
 
[[File:Gromacs_benchmark_img3_Gromacs_ns.png|center]]




Information on how to submit Gromacs jobs to [[Cheaha]] is available [[Gromacs |here]].
===Bench mark notes===
 
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]]. 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


=== 2011 Hardware ===
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.


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.
==Other Benchmarks ==
These benchmarks have been performed by Mike Hanby at Research Computing after 2007 Hardware upgrade to the Cheaha.


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

Latest revision as of 15:01, 4 April 2012

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 

        Execution time using one processor       ts
E(n)= --------------------------------------  = ----
      N * Execution time using N processors     N tn

In general, parallel jobs should scale to at least 70% efficiency. The ASC's DMC recommends a scaling efficiency of 75% or greater. For Gromacs the efficiency of a parallel job can be calculated with either the Wall clock parameter or the ns/day parameter. We use the wall clock and efficiency is calculated as (where N is processors committed to the job): 

        Wall Clock where N = 1
 ------------------------------------- * 100 = Efficiency
      N * Wall Clock on N processors

Benchmark used for performance evaluation on Cheaha, Biowulf, and DMCis the d.dppc which is available from the Gromacs benchmark suite and is available at: http://www.gromacs.org/About_Gromacs/Benchmarks

Information on how to submit Gromacs jobs to Cheaha is available here.

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.

Wall clock and efficiency on Gromacs - Benchmark d.dppc

Cheaha, DMC, and Biowulf wall clock and efficiency on Gromacs - Benchmark d.dppc
Processors Cheaha DMC Biowulf IB Biowulf Ethernet
1 1562 (100%) 2848 (100%) 1734 (100%) 2656 (100%)
2 650 (127%) 1256 (113%) 754 (115%) 1039 (128%)
4 332 (124%) 636 (112%) 382 (114%) 508 (131%)
8 181 (114%) 396 (90%) 203 (107%) 294 (113%)
16 97 (106%) 220 (81%) 102 (106%) 200 (83%)
32 44 (117%) 134 (66%) 53 (102 %) 147 (56%)
64 27 (96%) 92 (49%) 28 (97%) NA
128 14 (92 %) NA 17 (80%) NA
256 8 (81%) NA 12 (56%) NA
Gromacs Benchmark img1 Gromacs wall.png
Gromacs Benckmark img2 Gromacs efficiency.png


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
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
Gromacs benchmark img3 Gromacs ns.png


Bench mark notes

The above benchmarks were run using d.dppc benchmark [1] 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 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.

Other Benchmarks

These benchmarks have been performed by Mike Hanby at Research Computing after 2007 Hardware upgrade to the Cheaha.

2007 Hardware and Gromacs 3.x

Note: The Gromacs 3.x code base was severely limited in spanning multiple compute nodes. The limit for 1GigE network fabrics was 4 nodes. The following performance data is provided for historical reference only and does not reflect performance of the Gromacs 4.x code base currently install on Cheaha.

Two identical 4 CPU Gromacs runs and the jobs spread out as follows based on current queue load (the new nodes are using Infiniband, the old TCP for message passing):

Dell Blades: 4 cpu job running on 4 compute nodes 

Job ID:    71566
Submitted: 14:11:40
Completed: 17:06:03
Wall Clock: 02:54:23

              NODE (s)   Real (s)      (%)
      Time:  10462.000  10462.000    100.0
                      2h54:22
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    238.044     16.164      4.129      5.812

Verari: 4 cpu job running on 2 compute nodes 

Job ID:    71567
Submitted: 14:11:44
Completed: 23:13:01
Wall Clock: 09:01:17

              NODE (s)   Real (s)      (%)
      Time:  32473.000  32473.000    100.0
                      9h01:13
              (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     76.705      5.208      1.330     18.040
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