Octopus

Installed versions

Resource	Version
Dardel-GH/cpe25.03.gh	16.3
Dardel-GPU/cpe24.11.gpu	16.3
Dardel/cpe24.11	15.1, 16.3
Dardel/cpe23.12	14.0

General information

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. https://octopus-code.org/

How to use

To use this module do ml PDC/ ml octopus/16.3-cpeGNU-24.11 Below follows an example job script for Octopus.

#!/bin/bash

# time allocation
#SBATCH -A <your-project-account>

# name of this job
#SBATCH -J octopus-job

# partition
#SBATCH -p main

# wall time for this job
#SBATCH -t 01:00:00

# number of nodes
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=128
#SBATCH --cpus-per-task=1

ml PDC/<version>
ml octopus/16.3-cpeGNU-24.11

srun octopus inp > out.log

Assuming the script is named jobscriptoctopus.sh, it can be submitted using:

sbatch jobscriptoctopus.sh

GPU Support

Below follows an example job script for Octopus, for running on one Dardel GPU node using 8 MPI tasks per node (corresponding to one MPI task per GPU) and 8 OpenMP threads. You need to replace pdc.staff with an active project that you belong to. Note: This script is a simple template. For efficient calculation the script needs to be augmented with settings to pin appropriately the computation threads to the CCDs and GCD.

#!/bin/bash
#SBATCH -A pdc.staff
#SBATCH -p gpu
#SBATCH -J octopus
#SBATCH -t 02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --cpus-per-task=8

# Number and placement of OpenMP threads
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK
export OMP_NUM_THREADS=8
export OMP_PLACES=cores
export OMP_PROC_BIND=false
export MPICH_GPU_SUPPORT_ENABLED=1

ml PDC/24.11
ml octopus/16.3-cpeGNU-24.11-gpu

echo "Script initiated at `date` on `hostname`"

srun --hint=nomultithread octopus inp > out.log

echo "Script finished at `date` on `hostname`"

Assuming the script is named jobscriptoctopus.sh, it can be submitted using

sbatch jobscriptoctopus.sh

Octopus is also available as builds for the NVIDIA Grace Hopper nodes. Here is an example job script for running on one node, with one task per GPU.

#!/bin/bash
#SBATCH -A pdc.staff
#SBATCH -J octopus
#SBATCH -t 02:00:00
#SBATCH -p gpugh
#SBATCH -N 1
#SBATCH -n 4
#SBATCH -c 72
#SBATCH --gpus-per-task 1

# Run time modules and executable paths
ml PDC/25.03
ml octopus/16.3

# Runtime environment
export MPICH_GPU_SUPPORT_ENABLED=1
export PMPI_GPU_AWARE=1
export OMP_NUM_THREADS=72
export OMP_PLACES=cores
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK

echo "Script initiated at `date` on `hostname`"
srun --hint=nomultithread octopus > out.log
echo "Script finished at `date` on `hostname`"

Please consult the official Octopus documentation for more details

How to build Octopus

The program was installed using EasyBuild. A build in your local file space can be done with

ml PDC/24.11
ml easybuild-user/4.9.4
eb octopus-16.3-cpeGNU-24.11.eb --robot

A build for NVIDIA Grace Hopper nodes can be done with

# Build instructions for Octopus on Dardel Grace Hopper nodes

# Download the Octopus source code
wget https://octopus-code.org/download/16.3/octopus-16.3.tar.xz
tar xf octopus-16.3.tar.xz
cd octopus-16.3

# Load dependencies
ml PDC/25.03
ml PrgEnv-gnu
ml gcc-native/13.2
ml cudatoolkit/24.11_12.6
ml craype-accel-nvidia90
ml cray-libsci/25.03.0
ml cray-fftw/3.3.10.10
ml cmake/4.1.2
ml ninja/1.12.1
ml gsl/2.8
ml libxc/7.0.0

export CXX=CC
export CC=cc
export FC=ftn

# Configure
cmake -B ./buildGH1 \
    -GNinja \
    -D CMAKE_BUILD_TYPE=Release \
    -D CMAKE_INSTALL_PREFIX=/pdc/software/25.03/other/octopus/16.3 \
    -D OCTOPUS_MPI=ON \
    -D OCTOPUS_OpenMP=ON \
    -D OCTOPUS_FFTW=ON \
    -D OCTOPUS_CUDA=ON \
    -D CMAKE_POLICY_VERSION_MINIMUM=3.5 \
    > ./buildGH1/BuildOctopus_cmake.txt 2>&1

# Compile and install
cmake --build ./buildGH1 > ./buildGH1/BuildOctopus_make.txt 2>&1
MPIEXEC=srun ctest --test-dir ./buildGH1 -L short-run > ./buildGH1/BuildOctopus_test.txt 2>&1
cmake --install ./buildGH1 > ./buildGH1/BuildOctopus_install.txt 2>&1

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