Environment class

Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>

This file contains the Environment object which represents the computational environment.

class Environment(qsub_command, jid_pos, qstat_command, jid_flag, wham_executable)

This class represents the computational environment in which the software is run. It defines the functions used to communicate with the queuing system and the path to the WHAM executable.

Parameters:

• qsub_command (str) – Command used to submit a job to the queuing system. On SGE this should be “qsub”
• jid_pos (int) – Position of the job ID in the string returned by the qsub_command
• qstat_command (str) – Command used to check the status of a job. On SGE this should be “qstat”
• jid_flag (str) – Flag that should be added to the qstat_command to check the status of a job with a specific job ID. On SGE this should be “-j”
• wham_executable (str) – Path to the wham executable (either the 1D wham or 2D wham, depending on the number of CVs in the system)

DefineQstat(qstat_command, jid_flag)

DefineQsub(qsub_command, jid_pos)