ColabFold Scripts

a few scripts to run ColabFold painlessly

Install on Compute Canada

# load necessary modules
module load gcc/9.3.0 openmpi/4.0.3 cuda/11.4 cudnn/8.2.0 kalign/2.03 hmmer/3.2.1 openmm-alphafold/7.5.1 hh-suite/3.3.0 python/3.8 mmseqs2
# create a python virtual environment
virtualenv --no-download ~/alphafold_env
source ~/alphafold_env/bin/activate
# install colabfold and alphafold
pip install --no-index --upgrade pip
pip install --no-index alphafold
pip install --no-deps alphafold-colabfold
pip install --no-deps "colabfold[alphafold]@git+https://github.com/sokrypton/ColabFold" appdirs py3Dmol tqdm urllib3 requests
# test wheter we succeeded or not
python -m colabfold.batch

Then clone this repository:

cd ~/scratch/  # or any other base directory you want
git clone https://github.com/alirezaomidi/colabfold-scripts.git
cd colabfold-scripts/

Run on Cedar

To use one GPU:

./slurm/cedar-single-gpu.sh path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME

and to use multiple GPUs:

./slurm/cedar-multi-gpu.sh path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME

Substitute EXPERIMENTNAME with an arbitrary experiment name. This is the directory where ColabFold will save all output files in.

Run on Graham:

To run on Graham, first install sshpass in your home (~) directory:

cd ~/
wget -O sshpass-1.10.tar.gz https://sourceforge.net/projects/sshpass/files/sshpass/1.10/sshpass-1.10.tar.gz/download
tar xvzf sshpass-1.10.tar.gz
cd sshpass-1.10
mkdir ./build
./configure --prefix=$PWD/build
make install

Run the following script to download AlphaFold model parameters. This needs to be run only once:

cd ~/scratch/colabfold-scripts/
module load gcc/9.3.0 openmpi/4.0.3 cuda/11.4 cudnn/8.2.0 kalign/2.03 hmmer/3.2.1 openmm-alphafold/7.5.1 hh-suite/3.3.0 python/3.8 mmseqs2
source ~/alphafold_env/bin/activate

python batch.py path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME --model-type alphafold2_multimer_v2 --only-download-params

If you want to use another AlphaFold version, change alphafol2_multimer_v2. A list of options can be found in batch.py file, under model_type argument.

To use one GPU:

cd ~/scratch/colabfold-scripts/
./slurm/graham-single-gpu.sh YOURPASSWORD path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME

and to use multiple GPUs:

./slurm/graham-multi-gpu.sh YOURPASSWORD path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME

Substitute:

YOURPASSWORD with your Compute Canada account's password
EXPERIMENTNAME with an arbitrary experiment name. This is the directory where ColabFold will save all output files in.

Array Jobs

The multi GPU run scripts use SLURM array jobs to simultaneously submit a few colabfold jobs. For example the following line will submit 8 parallel jobs:

#SBATCH --array=0-7

Since in each job we ask for full node allocations and make use of 4 GPUs in each node, we'll have 32 instances of ColabFold running in parallel. You can modify this number based on your needs. Suppose we want 8 instances of ColabFold in parallel. Then we need to modify 2 lines in the submission script:

Modify #SBATCH --array=0-7 to #SBATCH --array=0-1 to ask for 2 nodes
Modify --n-batch 32 to --n-batch 8 at the near bottom of the script.

MSA Public Server Rate Limit

ColabFold's public MSA server https://api.colabfold.com has a rate limit of a few request per minute. To avoid this rate limit, we can ask for MSAs before running the neural-network. To do so, Run the following in a login node:

cd ~/scratch/colabfold-scripts/
module load gcc/9.3.0 openmpi/4.0.3 cuda/11.4 cudnn/8.2.0 kalign/2.03 hmmer/3.2.1 openmm-alphafold/7.5.1 hh-suite/3.3.0 python/3.8 mmseqs2
source ~/alphafold_env/bin/activate

python batch.py path/to/fastafile.fasta ~/scratch/colabfold/exp/EXPERIMENTNAME --only-msa

This comamnd will request for MSAs one-by-one and save them in the ~/scratch/colabfold/exp/EXPERIMENTNAME/ directory. You can then submit the jobs as previously described. The jobs will automatically find the MSAs and use them instead of requesting new ones.

Permission denied when running scripts

If you get a Permission denied error when running the scripts, run the following command:

chmod +x ~/scratch/colabfold-scripts/slurm/*.sh

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