Environment variables

Mandatory variables

They must be defined for the pele_platform to work correctly:

• PELE: path to PELE installation

• SCHRODINGER: path to Schrodinger installation

Examples:

export PELE=/path/to/PELE-1.X/
export SCHRODINGER=/path/to/schrodinger/20XX/

Optional variables

PELE_EXEC

The PELE executable can be configured in several ways (from highest to lowest precedence):

1. Can be specified by input.yaml flag:

pele_exec: "/home/pele/bin/Pele_mpi"

2. Can be specified by environment variable:

export PELE_EXEC=/home/pele/bin/Pele_mpi

3. If no path is specified, the PELE executable must be /path/to/PELE-1.X/bin/Pele_mpi (according to the path specified by the environment variable PELE).

PELE_DATA

The PELE data folder can be configured in several ways (from highest to lowest precedence):

1. Can be specified by input.yaml flag:

pele_data: "/home/pele/Data/"

2. Can be specified by environment variable:

export PELE_DATA=/home/pele/Data/

3. If no path is specified, the PELE data folder must be /path/to/PELE-1.X/Data (according to the path specified by the environment variable PELE).

PELE_DOCUMENTS

The PELE documents folder can be configured in several ways (from highest to lowest precedence):

1. Can be specified by input.yaml flag:

pele_documents: "/home/pele/Documents/"

2. Can be specified by environment variable:

export PELE_DOCUMENTS=/home/pele/Documents/

3. If no path is specified, the PELE documents folder must be /path/to/PELE-1.X/Documents (according to the path specified by the environment variable PELE).

PELE_LICENSE

Licenses can be configured in several ways (from highest to lowest precedence):

1. Can be specified by input.yaml flag:

license: /path/to/licenses/folder/

2. Can be specified by environment variable:

export PELE_LICENSE=/path/to/licenses/folder/

3. If no path is specified, licenses must be under /path/to/PELE-1.X/licenses/ (according to the path specified by the environment variable PELE).

SINGULARITY_EXEC

Path of the singularity container that contains the PELE executable. It can be configured in two ways:

1. Can be specified by input.yaml flag:

singularity_exec: /path/to/singularity/container/

2. Can be specified by environment variable:

export SINGULARITY_EXEC=/path/to/singularity/container/

PELE_MPI_PARAMS

Custom MPI parameters, which can be used whenever additional command line arguments are required (for example when running PELE on AWS).

1. Can be specified by input.yaml flag:

pele_mpi_params: "--prefix /path/to/openmpi"

2. Can be specified by environment variable:

export PELE_MPI_PARAMS="--prefix /path/to/openmpi"