Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
Last revisionBoth sides next revision
doku:gromacs [2023/06/14 11:31] – variants msiegeldoku:gromacs [2023/11/23 12:19] – [Many nodes with many GPUs] msiegel
Line 101: Line 101:
 benchmark various scenarios: benchmark various scenarios:
  
-  - a VSC users test case (50,897 atoms) 
   - R-143a in hexane (20,248 atoms) with very high output rate   - R-143a in hexane (20,248 atoms) with very high output rate
   - a short RNA piece with explicit water (31,889 atoms)   - a short RNA piece with explicit water (31,889 atoms)
   - a protein inside a membrane surrounded by explicit water (80,289 atoms)   - a protein inside a membrane surrounded by explicit water (80,289 atoms)
 +  - a VSC users test case (50,897 atoms)
   - a protein in explicit water (170,320 atoms)   - a protein in explicit water (170,320 atoms)
   - a protein membrane channel with explicit water (615,924 atoms)   - a protein membrane channel with explicit water (615,924 atoms)
Line 274: Line 274:
     }, {     }, {
         name: 'Test 3',         name: 'Test 3',
-        data: [ 0, 0, 0, 0, 0, 0 ]+        data: [ 94.069, 99.788, 97.9, 100.509, 95.666, 83.485 ]
     }, {     }, {
         name: 'Test 4',         name: 'Test 4',
-        data: [ 0, 0, 0, 0, 0, 0 ]+        data: [ 115.179, 117.999, 115.028, 114.967, 103.8, 0 ]
     }, {     }, {
         name: 'Test 5',         name: 'Test 5',
Line 299: Line 299:
     },     },
     title: {     title: {
-        text: 'GROMACS Benchmarks: Performance on multiple Nodes via MPI'+        text: 'GROMACS Benchmarks: Performance on multiple Nodes with dual A100 GPUs each via MPI'
     },     },
     xaxis: {     xaxis: {
Line 323: Line 323:
 } }
 </achart> </achart>
 +
 +Note: the computation timed out for 4 with 32 nodes, before gromacs was able to estimate a performance. We can safely assume this example case is going to be less performant on 32 than on fewer nodes too.
  
  
Line 407: Line 409:
 } }
 </achart> </achart>
 +
 +===== Links =====
 +
 +The benchmarks are based on three articles of NHR@FAU, featuring in
 +depth analysis on GROMACS Performance on various GPU systems, multi
 +GPU setups and comparison with CPU:
 +
 +https://hpc.fau.de/2022/02/10/gromacs-performance-on-different-gpu-types/
 +
 +https://hpc.fau.de/2021/08/10/gromacs-shootout-intel-icelake-vs-nvidia-gpu/
 +
 +https://hpc.fau.de/2021/06/18/multi-gpu-gromacs-jobs-on-tinygpu/
 +
  
  
  • doku/gromacs.txt
  • Last modified: 2023/11/23 12:27
  • by msiegel