2f10af2c0e43c0cc602ac70474e64d4cf15fcf38
examples/diffdock
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1 | -DiffDock Example |
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2 | -Mar. 9, 2023 |
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3 | - |
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4 | -Version 73ef67f |
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5 | - |
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6 | -``` |
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7 | - |
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8 | -#!/usr/bin/env bash |
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9 | - |
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10 | -## DiffDock example |
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11 | -## Args: none |
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12 | -## |
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13 | -## James Vincent - biogrids.org |
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14 | -## vincent@hkl.hms.harvard.edu |
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15 | -## Mar 9, 2023 |
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16 | - |
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17 | -:<<ACKNOWLEDGE |
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18 | - |
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19 | -If your use of BioGrids compiled software was an important element in |
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20 | -your publication, please include the following statement in your work: |
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21 | -"Software used in the project was installed and configured by BioGrids |
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22 | -(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.) |
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23 | - |
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24 | -ACKNOWLEDGE |
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25 | - |
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26 | -# Load cuda |
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27 | -module load cuda/11.5.2 |
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28 | -gpu_out=gpu_load.out # for monitoring gpu use |
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29 | - |
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30 | -# Verify we have a working GPU |
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31 | -echo -e "hostname: $HOSTNAME \n\n" |
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32 | -echo -e "nvidia-smi output \n\n" |
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33 | -nvidia-smi |
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34 | - |
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35 | -# Start nvidia-smi monitor of gpu |
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36 | -nvidia-smi --query-gpu=timestamp,name,utilization.gpu,utilization.memory,memory.total,memory.free,memory.used --format=csv -l 5 >& ${gpu_out} & |
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37 | - |
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38 | - |
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39 | -# Activate SBGrid env |
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40 | -export SBGRID_ALLOW=true |
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41 | -source /programs/sbgrid.shrc |
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42 | - |
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43 | -# Copy sample data |
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44 | -cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/data ./ |
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45 | -cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/workdir ./ |
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46 | -mkdir results |
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47 | - |
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48 | -out_dir="./results/user_predictions_small" |
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49 | -input_csv="./data/protein_ligand_example_csv.csv" |
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50 | - |
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51 | -# Run job |
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52 | -export SSL_CERT_FILE=/programs//x86_64-linux/diffdock/73ef67f/ssl/cacert.pem |
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53 | -python.diffdock -m inference --protein_ligand_csv ${input_csv} --out_dir ${out_dir} \ |
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54 | - --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise |
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55 | - |
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56 | - |
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57 | -``` |
examples/diffdock.md
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1 | +DiffDock Example |
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2 | +Mar. 9, 2023 |
|
3 | + |
|
4 | +Version 73ef67f |
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5 | + |
|
6 | +``` |
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7 | + |
|
8 | +#!/usr/bin/env bash |
|
9 | + |
|
10 | +## DiffDock example |
|
11 | +## Args: none |
|
12 | +## |
|
13 | +## James Vincent - biogrids.org |
|
14 | +## vincent@hkl.hms.harvard.edu |
|
15 | +## Mar 9, 2023 |
|
16 | + |
|
17 | +:<<ACKNOWLEDGE |
|
18 | + |
|
19 | +If your use of BioGrids compiled software was an important element in |
|
20 | +your publication, please include the following statement in your work: |
|
21 | +"Software used in the project was installed and configured by BioGrids |
|
22 | +(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.) |
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23 | + |
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24 | +ACKNOWLEDGE |
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25 | + |
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26 | +# Load cuda |
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27 | +module load cuda/11.5.2 |
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28 | +gpu_out=gpu_load.out # for monitoring gpu use |
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29 | + |
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30 | +# Verify we have a working GPU |
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31 | +echo -e "hostname: $HOSTNAME \n\n" |
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32 | +echo -e "nvidia-smi output \n\n" |
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33 | +nvidia-smi |
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34 | + |
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35 | +# Start nvidia-smi monitor of gpu |
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36 | +nvidia-smi --query-gpu=timestamp,name,utilization.gpu,utilization.memory,memory.total,memory.free,memory.used --format=csv -l 5 >& ${gpu_out} & |
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37 | + |
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38 | + |
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39 | +# Activate SBGrid env |
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40 | +export SBGRID_ALLOW=true |
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41 | +source /programs/sbgrid.shrc |
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42 | + |
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43 | +# Copy sample data |
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44 | +cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/data ./ |
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45 | +cp -r /programs//x86_64-linux/diffdock/73ef67f/DiffDock/workdir ./ |
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46 | +mkdir results |
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47 | + |
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48 | +out_dir="./results/user_predictions_small" |
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49 | +input_csv="./data/protein_ligand_example_csv.csv" |
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50 | + |
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51 | +# Run job |
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52 | +export SSL_CERT_FILE=/programs//x86_64-linux/diffdock/73ef67f/ssl/cacert.pem |
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53 | +python.diffdock -m inference --protein_ligand_csv ${input_csv} --out_dir ${out_dir} \ |
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54 | + --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise |
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55 | + |
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56 | + |
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57 | +``` |