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Optional: AlphaFold2 Batch Script

Log into the HPC cluster’s On Demand Interface

  • Open a Chrome browser and go to On Demand
  • Log in with your Tufts Credentials
  • On the top menu bar choose Clusters->Tufts HPC Shell Access

  • You'll see a welcome message and a bash prompt, for example for user tutln01:
[tutln01@login001 ~]$
  • This indicates you are logged in to the login node of the cluster. DO NOT run anything from this node as it is a shared login node. To complete jobs we either need to start an interactive session to get on to a compute node (more details can be found here about this option) or we can write a batch script to submit our job to a compute node.

AlphaFold2 Batch Script

A batch script can be broken into two parts - the header section with information on how to run the job and a command section where we use UNIX commnads to do a job. Here is our script:

#!/bin/bash
#SBATCH -p preempt                          # partition we submit to
#SBATCH -n 8                                # The number of cpu cores we would like
#SBATCH --mem=64g                           # The amount of RAM we would like
#SBATCH --time=2-0:00:00                    # The time we think our job will take       
#SBATCH -o output.%j                        # The name of the output file
#SBATCH -e error.%j                         # The name of the error file
#SBATCH -N 1                                # The number of nodes we would like
#SBATCH --gres=gpu:1                        # The number of GPUs
#SBATCH --exclude=c1cmp[025-026]            # The nodes to exclude when using AlphaFold2

# Load the AlphaFold2 and NVIDIA modules
module load alphafold/2.1.1
nvidia-smi

# Make the results direcory
mkdir /path/to/your/home/directory/af2

# Specify where your output directory and raw data are
outputpath=/path/to/your/home/directory/af2
fastapath=/path/to/your/home/directory/data/1AXC.fasta

# Date to specify if you want to avoid using template
maxtemplatedate=2020-06-10

source activate alphafold2.1.1

# Running alphafold 2.1.1
runaf2 -o $outputpath -f $fastapath -t $maxtemplatedate -m multimer

What do these commands mean?

  • module load alphafold/2.1.1: load the AlphaFold2 module
  • nvidia-smi: load the NVIDIA-SMI module
  • mkdir /path/to/your/home/directory/af2: make a directory for our outputs
  • outputpath=/path/to/your/home/directory/af2: specify where our outputs should go
  • fastapath=/path/to/your/home/directory/data/1AXC.fasta: specify our input FASTA file
  • maxtemplatedate=2020-06-10: specify our maximum template date
  • source activate alphafold2.1.1: activate our AlphaFold2 conda environment
  • runaf2 -o $outputpath -f $fastapath -t $maxtemplatedate -m multimer: run our AlphaFold2 program
    • -o: output path
    • -f: our input FASTA file path
    • -t: our maximum template date
    • -m: whether or not this is a multimeric protein

What's up with the maxtemplatedate?

The maxtemplatedate option is a bit more complicated. If we ask AlphaFold to predict the structure of a protein with a structure already in the Protein Data Bank (PDB) - then we have the option of using that structure in the prediction. If we do not want AlphaFold 2 to use this structure in the prediction we need to specify a date before the release date of that structure.

What do the SBATCH commands mean?
command description
#!/bin/bash specify our script is a bash script
#SBATCH -p ccgpu The partition we are requesting, and if you don't have ccgpu access, use "preempt"
#SBATCH -n 8 The number of cpu cores we would like - here it is 8
#SBATCH --mem=64g The amount of RAM we would like - here it is 64 Gigabytes
#SBATCH --time=2-0:00:00 The time we think our job will take - here we say 2 days (days-hours:minutes:seconds)
#SBATCH -o output.%j The name of the output file - here it is "output.jobID"
#SBATCH -N 1 The number of nodes we would like - here it is 1
#SBATCH --gres=gpu:1 The number of GPUs - here we ask for 1
#SBATCH --exclude=c1cmp[025-026] These are nodes to exclude when using AlphaFold2

Run the AlphaFold2 Batch Script

  • First save your batch script, here we will save it as runaf2.sh.
    • The bash script must end in .sh
  • Now submit your script with the command:
    • sbatch runaf2.sh
  • To check on the status of this script use the following command:
    • squeue -u your_utln
    • Be sure to swap out your_utln with your Tufts utln!