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Jobs via Command-line Interface

The user may want more control over the workflow execution, or run a type of calculation we have yet to implement. For that purpose, we provide access to our platform through Command Line Interface (CLI), were simulation Jobs can be executed.

Complete instructions on how to operate job submission via CLI can be found in this section. We also provide a tutorial dedicated to this topic, including on how to retrieve and inspect the final results of the simulation.

Command-line Interface

We provide an an incorporated Web Terminal to conveniently access the CLI. Alternatively, the user can use the SSH protocol.

To use the former Web Terminal interface, open the right-hand sidebar and click Terminal.

The simulations that have been submitted through the main Web Interface are under the data/<username> sub-directory under the main Login Home directory.

Our queuing system is controlled through the use of batch scripts. The reader can find batch script templates under the job templates directory.

Create job

Prepare subdirectory

To create a job under the CLI, we recommend working inside the aforementioned ~/data/<username> sub-directory. The user should create a new working directory under this sub-directory (called test_job, for example).

mkdir test_job

A convenient way to get acquainted with our CLI is to start by copying the template batch script file from within the ~/job-script-templates folder, and rename it as job.script. These actions can be performed with the following command, for the example case of the Quantum ESPRESSO template.

cp ~/job_script_templates/espresso/job.pbs ~/data/<username>/test_job/job.script

Copy any necessary simulation input files or executables into this current working directory as well.

Edit submission script

The user may need to edit the batch script if he/she wants to use a simulation software other the default. Directions on how to set resource manager variables can be found in the batch script examples. A comprehensive list of the resource manager options is available here.

In addition, if the user would like to alter runtime environment for the calculation, can may consult modules environment section of our documentation.

Lastly, the options for choosing the queue to submit the job can be found here.

Accounting Project Parameter

In order to specify a project that the job should belong to and should be charged upon, the instructions contained in this page should be followed.

In the present tutorial we will proceed with the default submission script template, without modification.

Submit job

As a next step, the user can submit the batch script for job execution using the qsub resource manager command:

 qsub job.script

Our resource management system will respond with a message letting know that the job was accepted.

Monitor job

In order to check on the current status of the job, type the following command.

qstat

Once the job starts running, all the output will be placed in the working directory where the qsub command was originally executed from (unless the "directory" line was changed within the batch script file).

Animation

The animation below demonstrates the above steps in action.