2.8. MedeA Command-Line Tools: Execute Workflows Through the Command-Line

Contents

Introduction
Commands and Options

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2.8.1. Introduction

While MedeA is primarily intended to be used through a graphical user interface (GUI), there are instances for which access to a command-line interface would be helpful. In particular, executing existing MedeA Flowcharts without human intervention or the use of a GUI can be helpful for continuous integration and development efforts. While most MedeA users use MedeA itself as a workflow manager, some users may want to incorporate MedeA as a single step in a multi-physics workflow involving several other software packages. For these reasons, basic functionality for executing, but not constructing, MedeA Flowcharts through a command-line interface is provided.

2.8.2. Commands and Options

In order to submit a new Job, the syntax is the following if you run from e.g. a bash console:

./bin/Linux-x86_64/mdlauncher cmd jobsubmit --help

jobsumit options:
-dir value           The directory to save files to if the -wait option is set. Creation of directory will be attempted if it does not exist.  <>
-flow value          The workflow file (computational protocol). <>
-queue value         The JobServer queue to submit to. If omitted, the first available queue is used. <>
-title value         The Job title. <>
-description value   The Job description. <>
-nproc value         The requested number of processors/cores. If omitted, default queue value is used. <>
-priority value      The requested priority. If omitted, the default queue value is used. <>
-structure value     The initial structure file. <>
-server value        The JobServer to submit to. <local>
-v                   Verbose mode, print information to standard output.
-wait                Wait for job completion.

For example, a MedeA VASP job can be started like this:

./bin/Linux-x86_64/mdlauncher cmd jobsubmit -flow ~/MedeA/Flowcharts/simple_vaspAG.flow -structure ~/MD/Structures/Elements/Ag.sci -nproc 2 -priority 8 -title 'Command\ line\ submitted\ VASP\ on\ Ag'

Note

If the server is not specified, the server is the last one used from MedeA (loaded from MedeA.settings). If the server is specified, the -server value must be a registered name in MD/servers.dat (if not it will display the list of available servers).

The last forcefield used in MedeA is used (loaded from MedeA.settings). A “Set Forcefield” stage can be added to the Flowchart to ensure that a specific forcefield is used.

If you do not include -wait, the command will just submit and return. The -wait option adds more flexibility on how to submit several jobs and wait/process output.

To check whether a Job is finished, the “jobfinished” command and options may be used:

./bin/Linux-x86_64/mdlauncher cmd jobfinished --help

jobfinished options:
-job value           The Job number ( > 0) to query is a mandatory option. <>
-server value        The JobServer to query. <local>
-v                   Verbose mode, print information to standard output.

Example output of the “jobfinished” command is as follows:

./bin/Linux-x86_64/mdlauncher cmd jobfinished -job 1066
finished

To retrieve files from a Job in a local directory for further processing and inspection, the “jobget” command may be used:

./bin/Linux-x86_64/mdlauncher cmd jobget --help

jobget options:
-job value           The Job number ( > 0) to query is a mandatory option. <>
-dir value           The directory to save files to. Creation of directory will be attempted if it does not exist.  <.>
-server value        The JobServer to query. <local>
-v                   Verbose mode, print information to standard output.

Example output of the “jobget” command is as follows:

./bin/Linux-x86_64/mdlauncher cmd jobget -job 1066 -dir another_run_AG
24 files retrieved from Job 1066 in directory another_run_AG.

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