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benchmarking_linux.md
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1 | +# Linux Benchmarking |
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2 | + |
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3 | +<!-- TOC --> |
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4 | + - [Benchmark Summaries](#bench-summary) |
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5 | + - [Benchmarking Systems](#bench-systems) |
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6 | + - [Benchmarking Datasets](#bench-dataset) |
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7 | + |
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8 | +<!-- /TOC --> |
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9 | + |
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10 | +## Benchmark Summaries |
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11 | + |
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12 | +### Relion 2D classification |
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13 | + |
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14 | +System | Runtime | Notes |
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15 | +______ | _______ | _____ |
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16 | +Workstation 1 | 712s | |
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17 | +Workstation 2 | 398 | 2x GPU |
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18 | +GPU Node 1 | 281s | 4x GPU |
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19 | + |
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20 | + |
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21 | + |
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22 | +## Benchmarking Systems |
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23 | + |
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24 | +<!-- pm-linux0 --> |
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25 | +### Workstation 1 |
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26 | + - 8x Xeon E5-1630 v4 |
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27 | + - 128G RAM |
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28 | + - 1x GeForce RTX 2080 |
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29 | + - 1 Gb/s network |
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30 | + |
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31 | +<!-- haumea --> |
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32 | +### Workstation 2 |
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33 | + - 48x Xeon E5-268W v4 |
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34 | + - 128G RAM |
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35 | + - 2x GeForce GTX 1080 Ti |
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36 | + - 10 Gb/s network |
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37 | + |
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38 | +<!-- sbgrid-gpu1 --> |
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39 | +### GPU Node 1 |
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40 | + - 64x AMD EPYC 7502 |
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41 | + - 256G RAM |
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42 | + - 4x RTX A5000 |
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43 | + - 10 Gb/s network |
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44 | + |
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45 | +#### Notes |
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46 | +Core counts determined via "nproc" output, and include hyperthreading where enabled. |
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47 | + |
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48 | + |
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49 | + |
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50 | +## Benchmarking Datasets |
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51 | + |
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52 | +### Dataset 1 |
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53 | +Plasmodium ribosome data set from [Wong et al, 2014](http://dx.doi.org/10.7554/eLife.03080) ( [EMD 2660](https://www.ebi.ac.uk/emdb/EMD-2660) , [EMPIAR-10028](https://www.ebi.ac.uk/empiar/EMPIAR-10028/); courtesy of the [Relion Wiki](https://www3.mrc-lmb.cam.ac.uk/relion/index.php?title=Benchmarks_%26_computer_hardware). |
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54 | + |
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55 | +To allow for shorter runtimes during 2D classification benchmarks, input STAR files were truncated by removal of partical entries. |
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56 | + |
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57 | + |
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58 | + |