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Octopus is currently available only on Lise. The standard pseudopotentials deployed with Octopus are located in $OCTOPUS_ROOT/share/octopus/pseudopotentials/PSF/. If you wish need to use a different set, please refer to the manual.
The most recent compiled version is 12.1, and it has been built using with the intel-oneapi compiler (v. 2021.2) and linked to Intel MKL (including FFTW).
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| Octopus version | Module files | Requirements | Optional features supported | Compute partitions | CPU/GPU |
|---|---|---|---|---|---|
| 12.1 | octopus/12.1 |
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| CentOS 7 |  / | |||
| 14.1 | octopus/14.1 | | NetCDF | Rocky Linux 9 | / |
Example Jobscripts
Assuming that your input file inp is located within the directory where you are submitting the jobscriptjob script, and that the output is written to out, one example of jobscript job script is given below
| Codeblock | ||||
|---|---|---|---|---|
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#!/bin/bash #SBATCH --time 12:00:00 #SBATCH --partition cpu-clx #SBATCH --nodes=1 #SBATCH --ntasks-per-node=24 #SBATCH --cpus-per-task=4 #SBATCH --job-name=octopus module load intelimpi/2021.2 impi/2021.7.113 module load octopus/1214.1 # Set the number of OpenMP threads as given by the SLURM parameter "cpus-per-task" export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK} # Adjust the maximum stack size of OpenMP threads export OMP_STACKSIZE=512m # Do not use the CPU binding provided by slurm export SLURM_CPU_BIND=none # Binding OpenMP threads export OMP_PLACES=cores export OMP_PROC_BIND=close # Binding MPI tasks export I_MPI_PIN=yes export I_MPI_PIN_DOMAIN=omp export I_MPI_PIN_CELL=core mpirun octopus |
Please, check carefully for your use cases the best parallelization strategies in terms of e. g. the number of MPI processes and OpenMP threads. Note that the variables ParStates, ParDomains and ParKPoints defined in the input file also impact the parallelization performance.
A similar example valid for the CPU partitions with CentOS 7 is
| Codeblock | ||||
|---|---|---|---|---|
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#!/bin/bash
#SBATCH --time 12:00:00
#SBATCH --partition standard96
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --cpus-per-task=4
#SBATCH --job-name=octopus
module load intel/2021.2 impi/2021.7.1 octopus/12.1
# Set the number of OpenMP threads as given by the SLURM parameter "cpus-per-task"
export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
# Adjust the maximum stack size of OpenMP threads
export OMP_STACKSIZE=512m
# Do not use the CPU binding provided by slurm
export SLURM_CPU_BIND=none
# Binding OpenMP threads
export OMP_PLACES=cores
export OMP_PROC_BIND=close
# Binding MPI tasks
export I_MPI_PIN=yes
export I_MPI_PIN_DOMAIN=omp
export I_MPI_PIN_CELL=core
mpirun octopus |