Perlmutter

The NERSC user guide can be found  here .

Setup

General Tips

  • Fill out the  VASP License Confirmation Request  form to get access to system-level VASP modules.
  • It is recommended that you install  sshproxy  to make multi-factor authentication less annoying.
  • NERSC has a  dedicated workflow queue  for long-running background processes that is accessible upon request. Perpetual processes should not be run on the login node.

Bashrc

Add the following to your ~/.bashrc. Here, it assumes we are operating out of the m5034 project directory.
export CFS=/global/cfs/cdirs/m5034/$USER
export COMMON=/global/common/software/m5034/common
export SOFTWARE=$COMMON/software
module use --append $COMMON/modulefiles

Filesystems

The NERSC documentation does a thorough job describing the different  file systems .
  • Run calculations out of $SCRATCH, which is available without defining anything in your ~/.bashrc. Data may be purged after 8 weeks, so this is for temporary storage.
  • Store data medium-term in $CFS. It is not backed up but is also not purged.
  • Compiled codes can be found in $SOFTWARE
  • You have a home directory that is meant for storing small software and scripts, but calculations are not to be run here.

Job Submission

VASP

The following parallelization flags have been reasonably well-optimized for usage on Perlmutter. For the account ID, check  Iris platform  or  💰⁠⁠Grant Details⁠ .
#!/bin/bash
#SBATCH -N 1
#SBATCH -C gpu
#SBATCH -G 4
#SBATCH -q debug
#SBATCH -J test
#SBATCH -t 00:30:00
#SBATCH -A AccountID_g

module load python
module load vasp/6.5.1_gpu

export OMP_NUM_THREADS=8
export OMP_PLACES=threads
export OMP_PROC_BIND=spread

srun -n 4 -c 32 --cpu_bind=cores -G 4 --gpu-bind=none vasp_std # or vasp_gam

Databases

If you would like to use MongoDB on NERSC,  fill out a ticket  and the NERSC staff will host one for you that you can access from the machine. Make sure to select MongoDB and Production-quality. For the description you can put: "Workflows carried out using Jobflow and Jobflow-Remote to orchestrate DFT calculations with VASP. The database needs to be accessible from the login and compute nodes."