Predicting multiple protein structures using Alphafold on Notos
Setup
- Copy the alphafold folder from /mnt/beegfs/alphafold/alphafold to your home directory
- When you log in to notos you are automatically in your home directory
- Run the command below to copy the folder into your home directory
cp -r /mnt/beegfs/alphafold/alphafold/ .
- This folder has all the required updates to run alphafold successfully
- Locate the folder named docker by running the command
cd alphafold/docker
- Open run_docker.py by running the command
vi run_docker.py
- Press i to insert and make edits to the file
- Change the destination folder output_dir on line 49 to a folder you wish the results are saved into
- Make sure you have sufficient read and write permissions for the output_dir folder
Running multiple files on Alphafold in series on a single GPU
- Create a folder with all the sequences you want to run on a single GPU
- Check the status of the GPU’s by running the command
nvidia-smi
- cd into your home directory using the command
cd
- Locate and enter the folder GPU_scripts by running the command
cd alphafold/GPU_scripts
- List contents in the folder by using the command
ls
. The folders are namedGPU_[GPU_number].sh
. Choose the GPU number which isn’t being used (Following step 2) - Start a named screen session, by typing the following in your console
screen -S session_name
-
Run the following command to run the sequences on a single GPU
bash GPU_[GPU_number].sh path_to_the_folder_with_sequences
For example, if you want to run the sequences on GPU number 6:
bash GPU_6.sh ~\sequences\test_folder\
where~\sequences\test_folder\
is the folder with sequences.- These scripts run alphafold using full databases. For optimized performance use the preset reduced_dbs. Open the GPU_[number] script and add the preset
--db_preset=reduced_dbs
to line 9 - Other presets and options can be found here
- These scripts run alphafold using full databases. For optimized performance use the preset reduced_dbs. Open the GPU_[number] script and add the preset
- Detach from the linux screen session, by press
Ctrl+a d
- To get the list of current running sessions, type the following
screen -ls
- To reattach to a linux screen, type the following
screen -r session_name
- To get the list of current running sessions, type the following
Running multiple files on Alphafold in series on a multiple GPUs
- Create seperate folders for each set of sequences you want to run on the GPUs
- Repeat steps 2 to 8 for each of the folders on seperate GPUs