Skip to main content

AlphaFold

  1. INCD Local Installation
    1. Environment
    2. Data Base Location
    3. run_udocker.py
  2. How to Run
  3. Run Examples
  4. References

1. INCD Local Installation

The INCD team prepare a local installation of AlphaPhold using a container based on UDOCKER (instead of DOCKER) and includes the Genetic Database.

The local installation provide the AlphaFold version 2.1.1 over a container based on Ubuntu 18.04 distribution with cuda-11.0 and cudnn-8.

The main resource target of AlphaFold is the GPU but the application also execute only on the CPU although the performance is substantially worst, see the Run Exemples section bellow.

1.1 Environment

The environment is activate with command

$ module load udocker/alphaphold/2.1.1

this will activate automatically a virtual environment ready to start the AlphaFold container throught the python script run_udocker.py.

1.2 Data Base Location

The Genetic Database is installed bellow the filesystem directory

/users3/data/alphafold

on read-only mode, upgrades may be requested using the helpdesk@incd.pt address.

1.3 run_udocker.py Script

The run_udocker.py script was adapted from the run_docker.py script normally used by AlphaFold with the docker container technology.

The run_udocker.py accept the same options as the run_docker.py script with a few minor changes that we hope it will facilitate user interaction:

interaction.
  • environment variable DOWNLOAD_DIR points to the default local genetic database, theThe user may change the content,script behavour throught environment variables or command line options, we can see only the optionchanges bellow:

    Optional environment variables:

    Variable NameDefault ValueComment
    DOWNLOAD_DIRnoneGenetic database location
    OUPTPUT_DIRnoneOutput results directory

    Command line options:

    Command OptionMandatoryDefault ValueComment
    --data_dirno/users3/data/alphafoldGenetic database location, takes precedence over thisDOWNLOAD_DIR environmentwhen variable;both
  • optionare selected
    • --data_dir:output_dirno<working_dir>/outputOutput results directory, takes precedence over OUTPUT_DIR when both are selected

    The AlphaFold standard output results directory location is optional/tmp/alphafold andby pointsdefault, please note that we change this location to the local geneticworking database by default, takes prececence overdirectory, the environmentuser variabal DOWNLOAD_DIR;

  • the output dir points to a subdirectory output on the working directory by default instead of /tmp/alphafold/output;
  • environment variable OUTPUT_DIR may be used to overwirte the default output directory;
  • option --output_dir may be used tocan select a different outputpath directory and takes precedence overthrought the environment variable OUTPUT_DIR andor the defaultcommand outputline location.
    • option
--output_dir.

2. How to Run

3. Run Examples

4. References

Back to top