This is as a Lab Notebook which describes how to solve a specific problem at a specific time.
Please keep this in mind as you read and use the content. Please pay close attention to the date, version
information and other details.
The 2.3.1 version of the AlphaFold singularity image is currently non-functional on HPCC. As of Ocotober, 2023, the image is no longer able to find the current libcusolver share library file.
Please use the 2.3.2 version of the image from this point forward. Please see the new documentation
Lab Notebook --- Instructions for AlphaFold version 2.3.1, Singulairty (2023-07-18)(DEPCREATED, see warnings)
These instructions are a work in progression for running AlphaFold version 2.3.1 using the singularity container found at:
We also recommend disbaling local Python libraries with the following argument to avoid conflicts with the Python installation within the Singularity container
Both the database and Python library parameters will be set automatically if you load the module "alphafold/2.3.1"
To run Alphafold 2.3.1 via SLURM, please use the following template (for more
information about options/flags, please refer to
the README on Github).
In the script, input.fasta is your input data, and you need to set up
output_dir. Since the command /usr/bin/hhsearch inside the container
does not work on intel14 nodes (Illegal instruction), please use the
SBATCH option --constraint in the job script.