ac2088fd8e5bf7b1ba07b84664939845d8a2e163
examples/opennucleome.md
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1 | 1 | ``` |
2 | 2 | #!/usr/bin/env bash |
3 | 3 | |
4 | - |
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6 | 4 | ## SBGrid OpenNucleome Example |
7 | 5 | |
8 | 6 | ## https://github.com/ZhangGroup-MITChemistry/OpenNucleome |
9 | - |
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10 | 7 | ## |
11 | - |
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12 | 8 | ## Run three tutorials from tutorials/init_configs dir |
13 | - |
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14 | -## Takes ~ 40 minutes on one NVIDIA GeForce GTX 1080 Ti |
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15 | - |
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16 | 9 | ## |
17 | - |
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18 | 10 | ## James Vincent help@sbgrid.org |
19 | - |
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20 | 11 | ## Jan 6, 2025 |
21 | 12 | |
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23 | - |
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24 | -export SBGRID_ALLOW=true # sbgrid internal only |
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25 | - |
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26 | - |
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27 | - |
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28 | 13 | echo "SBGrid OpenNucleome Example" |
29 | 14 | |
30 | - |
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31 | - |
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32 | 15 | ## Start SBGrid environment |
33 | - |
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34 | 16 | export SBGRID_ALLOW=true ## sbgrid dev only |
35 | - |
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36 | 17 | source /programs/sbgrid.shrc |
37 | - |
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38 | - |
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39 | - |
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18 | + |
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40 | 19 | ## Set OpenNucleome version - from command: $ sbgrid-info -l opennucleome |
41 | - |
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42 | 20 | export OPENNUCLEOME_X=1.3.0 |
43 | 21 | |
44 | - |
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45 | - |
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46 | 22 | ## Verify CUDA GPU for OpenNucleome |
47 | - |
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48 | 23 | python.opennucleome -m testInstallation |
49 | 24 | |
50 | - |
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51 | - |
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52 | 25 | ## Get repo |
53 | - |
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54 | 26 | rm -rf ./OpenNucleome |
55 | - |
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56 | 27 | git clone https://github.com/ZhangGroup-MITChemistry/OpenNucleome.git |
57 | 28 | |
58 | - |
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59 | - |
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60 | 29 | ## configs_generation |
61 | - |
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62 | 30 | cd ./OpenNucleome/tutorials/init_configs/configs_generation/ |
63 | - |
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64 | 31 | jupyter.opennucleome nbconvert --to script ConfigsGeneration.ipynb |
65 | - |
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66 | 32 | python.opennucleome ./ConfigsGeneration.py |
67 | 33 | |
68 | - |
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69 | - |
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70 | 34 | ## configs_relaxation |
71 | - |
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72 | 35 | cd ../configs_relaxation/ |
73 | - |
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74 | 36 | jupyter.opennucleome nbconvert --to script ConfigsRelaxation.ipynb |
75 | - |
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76 | 37 | python.opennucleome ./ConfigsRelaxation.py |
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78 | - |
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79 | - |
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38 | + |
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80 | 39 | ## configs_selection |
81 | - |
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82 | 40 | cd ../configs_selection |
83 | - |
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84 | 41 | jupyter.opennucleome nbconvert --to script ConfigsSelection.ipynb |
85 | - |
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86 | 42 | python.opennucleome ./ConfigsSelection.py |
87 | 43 | ``` |
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