Generating Submission Scripts

orto can generate submission scripts for your job scheduler of choice. Currently, the following job schedulers are supported:

- slurm

Setup

To use the job submission script generation feature, you need to first set the orto_orca_load environment variable as the command to load the ORCA module - this is typically done using a module system like Lmod or Environment Modules. For example, if you are using Lmod, you might set this variable as

export orto_orca_load="orca/6.0.1"

We advise that you set this to the version of ORCA you use most frequently. To use a different version, you can override this variable using the --orca_load optional argument in orto gen job.

Example Submission

First, prepare an 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 bugs page.

The following example is a simple ORCA input file for a geometry optimisation of benzene using the BP86 functional and the def2-svp basis set.

benzene.inp

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

You must always have the number of cores and amount of memory specified in the input file. The above example uses 16 cores and 2000 MB of memory per core.

In this example the structure is located in a separate .xyz file - benzene.xyz.

benzene.xyz

 12
 Benzene
 H      1.2194     -0.1652      2.1600
 C      0.6825     -0.0924      1.2087
 C     -0.7075     -0.0352      1.1973
 H     -1.2644     -0.0630      2.1393
 C     -1.3898      0.0572     -0.0114
 H     -2.4836      0.1021     -0.0204
 C     -0.6824      0.0925     -1.2088
 H     -1.2194      0.1652     -2.1599
 C      0.7075      0.0352     -1.1973
 H      1.2641      0.0628     -2.1395
 C      1.3899     -0.0572      0.0114
 H      2.4836     -0.1022      0.0205

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. Run squeue or similar to check the status of your job - it might take a few minutes to start!

The job will be given the same name as your 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.6718675.o  benzene.inp  benzene.out  benzene.slm  benzene.xyz ...

Coordinates within .inp files

Instead of providing a separate .xyz file, it is possible to specify coordinates within the ORCA input file.

This feature is supported by orto and requires no additional effort on the part of the user.

Cores and Memory

You must always have the number of cores and amount of memory 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, you need to first set the orto_nbo_load environment variable as the command to load the NBO module - this is typically done using a module system like Lmod or Environment Modules.

For example, if you are using Lmod, you might set this variable as

export orto_nbo_load="nbo/6.0"

More

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

orto gen job -h