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| doku:gromacs [2023/11/23 11:50] – +links msiegel | doku:gromacs [2023/11/23 12:18] – [Many nodes with many GPUs] msiegel | ||
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| 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 253: | Line 253: | ||
| In most cases one node is **better** than more nodes. | In most cases one node is **better** than more nodes. | ||
| - | In some cases, for example a large molecule like Test 7, you might want to run GROMACS on multiple nodes in parallel using MPI, with multiple GPUs (one each node). We strongly encourage you to test if you actually benefit from running with GPUs on many nodes. GROMACS can perform worse on many nodes in parallel than on a single one, even considerably! | + | In some cases, for example a large molecule like Test 7, you might want to run GROMACS on multiple nodes in parallel using MPI, with multiple |
| Run GROMACS on multiple nodes with: | Run GROMACS on multiple nodes with: | ||
| 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 323: | Line 323: | ||
| } | } | ||
| </ | </ | ||
| + | |||
| + | 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. | ||