Generating Submission Scripts

orto can generate submission scripts for your job scheduler of choice

Currently, only SLURM is supported, though support for additional schedulers may be added in future releases.

Setup

To use the job submission script generation feature, you need to first set the orto_orca_load environment variable - this specifies the command used to load the ORCA module on your system.

Typically a module system like Lmod or Environment Modules is used to manage software on HPC systems, and you will need to set this variable accordingly - for example, when using Environment Modules, this may be set as

export orto_orca_load="orca/6.0.1"

We advise that you set this to the version of ORCA you use most frequently.

Alternatively, you can provide the --orca_load optional argument in orto gen job to specify the command to load ORCA for each job submission script - this overrides the environment variable and so can be used to submit jobs with different versions of ORCA.

Usage

To submit a job run

orto gen job <input_file>

where <input_file> is the path to your ORCA input file.

Caution

You must always have the number of cores and amount of memory specified in the input file.

Note

orto is fairly agnostic to the contents of the input file, but edge-cases might not work as expected. If you encounter any problems, please head to the Reporting Bugs page to find how to report them to us.

Cores and Memory

The number of cores and amount of memory must be specified in the input file and, by default, orto will read these numbers and use them when submitting a job.

To override this, use the --n_procs and --memory optional arguments in orto gen job - This may be useful if your submission system imposes per-core memory limits.

NBO

If you wish to use NBO within an orca calculation, the orto_nbo_load environment variable must contain the command to used to load an NBO module - this is typically done using a module system like Lmod or Environment Modules - for example, when using Environment Modules, this may be set as

export orto_nbo_load="nbo/6.0"

Optional Arguments

Additional command line arguments for orto gen job can be listed by running

orto gen job -h

Example

The following minimal example is a simple ORCA input file for a geometry optimisation of benzene using the BP86 functional and the def2-svp basis set, with 16 cores and 2000 MB of memory per-core.

benzene.inpbenzene.xyz

!BP86 def2-svp OPT
%PAL NPROCS 16 END
%maxcore 2000
*xyzfile 0 1 benzene.xyz

In this example the structure is located in a separate .xyz file, but it could equally be specified directly within the input file itself.

To submit a job for this calculation, simply run

orto gen job benzene.inp

You should then see an message informing you that a submission script was created and subsequently submitted.

and run squeue or similar to check the status of the job.

The job will be given the same name as the input file, and the output file(s) for this calculation should appear in the current directory when the job starts running - for example

user@computer ~/benzene $ ls
benzene.6718675.e  benzene.123456.o  benzene.inp  benzene.out  benzene.slm  benzene.xyz ...