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Psi4 on Biowulf & Helix

Psi4 is an ab-initio electronic structure code that supports various methods for calculating energies and gradients of molecular systems. It is designed to be highly flexible and extensible, with performance-critical code implemented in C++ that can be accessed via either Python language bindings or a domain-specific input script language. Specific features include:

Psi4 is distributed under the GNU Lesser General Public License (LGPL) version 3.

Example input files may be found in /usr/local/apps/psi4/1.1/share/psi4/samples.

On Helix

Psi4 is a cpu-intensive program that is not allowed to be run on Helix.

Multithreaded Batch job on Biowulf

Sample batch script: (this file is called run_psi4)

#!/bin/bash
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --threads-per-core=1
#SBATCH --gres=lscratch:50
#SBATCH --partition=norm

cd $SLURM_SUBMIT_DIR

module load psi4

psi4 -n $SLURM_CPUS_PER_TASK saptest.in

Submit this job with

biowulf% sbatch run_psi4

where:

-n $SLURM_CPUS_PER_TASKtells Psi4 to run $SLURM_CPUS_PER_TASK threads. This is only defined if --cpus-per-task is specified to sbatch
--ntasks=1 Tells Slurm to allocate a single task
--cpus-per-task=4 tells Slurm how many CPUs to allocate to the task
--threads-per-core=1 specifies that one thread should be run on each physical core (i.e. ignore hyperthreading). This is usually recommended for cpu-intensive parallel jobs.
--gres=lscratch:100specifies that 100 GB of local scratch on the node should be allocated to this job. This parameter is required for all Psi4 job submissions, including interactive jobs.

The Psi4 module must be loaded from within a batch job. It sets the environment variable $PSI_SCRATCH to '/lscratch/$SLURM_JOBID'. This directory is only created if you submit the job with --gres=lscratch:#. (see the User Guide section on using local disk. If you do not allocate local scratch space, your job will fail.

Running Psi4 on the Biowulf login node or Helix is not permitted and will fail.

Documentation

Psi4 Manual