Dalton

To use, add the dalton module to add it to your environment. You give this command to see how to load Dalton and its prerequisites:

ml spider dalton

Notes

• HPC2N has compiled the program with GCC compilers and Intel MPI (impi).
• This is an OpenMP + MPI hybrid build.
• Dalton provides a few environment variables that refers to various directories, please use them, if needed, and not hard coded pathnames as this will make your life easier when Dalton gets upgraded.

You can find most of the environment variables with

dalton -h

while a few (like path to the install directory) are found with

env | grep -i dalton

NOTE: that DALTON_TMPDIR needs to be defined by the userr.

DALTON

There are several options to the script, which can be viewed by typing dalton -h or just dalton. Some of the more important ones include:

• -b directory Prepend this directory to the list of directories where the program should look for basis sets. Needed in case you want to use local modifications of a given basis. The job directory and the basis set library will always be included in the basis set directory list (in that search order).
• -f dal_mol[_pot] extract dal_mol[_pot].tar.gz archive from WRKDIR into DALTON_TMPDIR before calculation starts
• -mb mem set dalton max usable work memory to mem Megabytes.
• -N num Use num MPI processes
• -o filename Redirect the output normally printed in the DALTON.OUT file in the temporary directory to the file “filename” in the WRKDIR directory. On a computer system with distributed scratch disk but a commonly mounted home directory, this allows you to follow the calculation without having to log into the compute nodes.
• -w wrkdir Change the working directory to “wrkdir”, that is, change the directory in which the program searches for input files and places the DALTON.OUT file to “wrkdir”.

Serial

To run the program, load the module, then use this command:

dalton [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]]

to run using the shell script dalton, which is the recommended way of running. 

Example: Say you have the input file myinput.dal, and the molecule input molinput.mol, you would type this to run

dalton myinput molinput

When the job is finished, the output is copied back as myinput_molinput.out. In addition, the program will copy back a file named myinput_nmolinput.tar.gz. This file contains, in tar'ed and gzip'ed form, a number of useful intergace and post-processing files which may be needed for post-DALTON programs, or for restarting calculations.

Note If it is anything but a short program, you should ALWAYS run it as a batch script.

Example, batch script

#!/bin/bash
# Change to your own project id
#SBATCH -A SNICXXXX-YY-ZZ
# Asking for 1 task
#SBATCH -n 1
# Asking for 30 minutes run time 
#SBATCH --time=00:30:00

#Load the Dalton moduleand its prerequisites
ml GCC/6.2.0-2.27  
ml impi/2017.1.132
ml DALTON/2016.2

dalton [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]]

Submit the script with

sbatch <jobscript>

MPI

Note srun and mpirun both works

Example script

Assuming you have an input file dalton_in.dal (if you have a molecule input file, add that one as well)

Change n and DALTON_NUM_MPI_PROCS accordingly.

#!/bin/bash
#SBATCH -J DALTON-test
#SBATCH -A SNICXXXX-YY-ZZ
#SBATCH -n 8
#SBATCH --time=10:30:00

#Load the Dalton moduleand its prerequisites
ml GCC/6.2.0-2.27 
ml impi/2017.1.132
ml DALTON/2016.2 

#You can call the tmp dir anything
export DALTON_TMPDIR=<what-you-want>

export DALTON_NUM_MPI_PROCS=8

dalton -N 8 -noappend -t `pwd`/<any tmpdir> [options] dalinp{.dal} [molinp{.mol} [potinp{.pot}]

Submit the script with

sbatch <jobscript>