Installation of VFVS
Last updated
Last updated
VFVS 2.0 on AWS uses an AWS Batch cluster and workload manager. Instructions on how to create the AWS Batch cluster, and how to access the AWS Batch login node can be found on the VFVS GitHub page.
To log in to the AWS Batch login node via ssh, follow the instructions . You will land in the home directory of the AWS Batch login node.
VFVS requires Python 3.x (it has been tested with Python 3.9.4). Additionally, it requires packages to be installed that are not included at many sites. As a result, we recommend that you create a virtualenv for VFVS that can be used to run jobs.
Make sure that virtualenv is installed:
Create a virtualenv (this example creates it under $HOME/vfvs_env):
Enter the virtualenv and install needed packages
Alternatively, all the above steps can be performed using conda instead of pip. Further information on setting up a conda style environment can be found .
To exit a virtual environment:
When running VFVS commands, you should enter the virtualenv that you have set up using:
For the remainder of the tutorial and for future use of VFVS, please ensure the virtual environment is activated.
After Python is set up, we can install VFVS 2.0. Normally this is done by cloning the GitHub repo, but for this tutorial, we provide a pre-configured folder for download. On the AWS Batch login node, you can download it by running the following command:
This preconfigured folder was prepared by:
Cloning the GitHub repo (branch vfvs-2)
Adding the docking input files to the input-files folder
Configuring the all.ctrl file. The following parameters are changed compared to the template file in the VFVS GitHub repo:
job_name
docking_scenario_names
docking_scenario_programs
docking_scenario_replicas
docking_scenario_batchsizes
Alternatively, all the above steps can be performed using conda instead of pip. Further information on setting up a conda style environment can be found .