first stab at mkdocs migration

refactor CSCS and Meg content add merlin6 quick start update merlin6 nomachine docs give the userdoc its own color scheme we use the Materials default one refactored slurm general docs merlin6 add merlin6 JB docs add software support m6 docs add all files to nav vibed changes #1 add missing pages further vibing #2 vibe #3 further fixes
2025-11-26 17:28:07 +01:00
parent 149de6fb18
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--- a/docs/merlin7/05-Software-Support/quantum-espresso.md
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+---
+title: Quantum Espresso
+keywords: Quantum Espresso software, compile
+summary: "Quantum Espresso code for electronic-structure calculations and materials modeling at the nanoscale"
+sidebar: merlin7_sidebar
+toc: false
+permalink: /merlin7/quantum-espresso.html
+---
+
+## Quantum ESPRESSO
+
+Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials:
+
+    PWscf (Plane-Wave Self-Consistent Field)
+    FPMD (First Principles Molecular Dynamics)
+    CP (Car-Parrinello)
+
+## Licensing Terms and Conditions
+
+Quantum ESPRESSO is an open initiative, in collaboration with many groups world-wide, coordinated by the Quantum ESPRESSO Foundation. Scientific work done using Quantum ESPRESSO should contain an explicit acknowledgment and reference to the main papers (see Quantum Espresso Homepage for the details).
+
+## How to run on Merlin7
+### 7.5
+### CPU nodes
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.9-xqhy-A100-gpu quantum-espresso/7.5-zfwh-omp
+```
+### GH nodes
+```bash
+module purge
+module use Spack unstable
+module load nvhpc/25.7 openmpi/4.1.8-l3jj-GH200-gpu quantum-espresso/7.5-2ysd-gpu-omp
+```
+### 7.4.1
+### A100 nodes
+```bash
+module purge
+module use Spack unstable
+module load nvhpc/25.3 openmpi/main-6bnq-A100-gpu quantum-espresso/7.4.1-nxsw-gpu-omp
+```
+### GH nodes
+```bash
+module purge
+module use Spack unstable
+module load nvhpc/25.3 openmpi/5.0.7-e3bf-GH200-gpu quantum-espresso/7.4.1-gxvj-gpu-omp
+```
+
+### SBATCH A100, 1 GPU, 64 OpenMP threads, one MPI rank example
+```bash
+#!/bin/bash
+#SBATCH --no-requeue
+#SBATCH --job-name="si64"
+#SBATCH --get-user-env
+#SBATCH --output=_scheduler-stdout.txt
+#SBATCH --error=_scheduler-stderr.txt
+#SBATCH --partition=a100-daily
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --time=06:00:00
+#SBATCH --cpus-per-task=64
+#SBATCH --cluster=gmerlin7
+#SBATCH --gpus=1
+#SBATCH --hint=nomultithread
+
+export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
+export OMP_PROC_BIND=spread
+export OMP_PLACES=threads
+
+# Load necessary modules
+module purge
+module use Spack unstable
+module load nvhpc/25.3 openmpi/main-6bnq-A100-gpu quantum-espresso/7.4.1-nxsw-gpu-omp
+
+"srun" '$(which pw.x)' '-npool' '1' '-in' 'aiida.in'  > "aiida.out"
+```
+
+## Developing your own GPU code
+### Spack
+2. ```spack config edit ```
+3. Add granularity: microarchitectures to your config (if you use nvhpc compiler! Not needed for CPU builds!)
+```bash
+spack:
+  concretizer:
+    unify: false
+    targets:
+      granularity: microarchitectures
+```
+4. ```spack add quantum-espresso@develop +cuda +mpi +mpigpu hdf5=parallel %nvhpc arch=linux-sles15-zen3 # GPU```
+5. ```spack add quantum-espresso@develop +mpi hdf5=parallel %gcc # CPU```
+6. ```spack develop quantum-espresso@develop # clone the code under /afs/psi.ch/sys/spack/user/$USER/spack-environment/quantum-espresso```
+7. Make changes in /afs/psi.ch/sys/spack/user/$USER/spack-environment/quantum-espresso
+8. Build: ```spack install [-jN] -v --until=build quantum-espresso@develop```
+
+### Environment modules
+#### CPU
+[![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/q-e_cpu_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi)
+
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/main-syah fftw/3.3.10.6-qbxu-omp hdf5/1.14.5-t46c openblas/0.3.29-omp cmake/3.31.6-oe7u
+
+cd <path to QE source directory>
+mkdir build
+cd build
+
+cmake -DQE_ENABLE_MPI:BOOL=ON -DQE_ENABLE_OPENMP:BOOL=ON -DCMAKE_C_COMPILER:STRING=mpicc -DCMAKE_Fortran_COMPILER:STRING=mpif90 -DQE_ENABLE_HDF5:BOOL=ON ..
+make [-jN]
+```
+#### A100
+[![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/q-e_gpu_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi)
+
+```bash
+module purge
+module use Spack unstable
+module load nvhpc/25.3 openmpi/main-6bnq-A100-gpu fftw/3.3.10.6-qbxu-omp hdf5/develop-2.0-rjgu netlib-scalapack/2.2.2-3hgw cmake/3.31.6-oe7u
+
+cd <path to QE source directory>
+mkdir build
+cd build
+
+cmake -DQE_ENABLE_MPI:BOOL=ON -DQE_ENABLE_OPENMP:BOOL=ON -DQE_ENABLE_SCALAPACK:BOOL=ON -DQE_ENABLE_CUDA:BOOL=ON -DQE_ENABLE_MPI_GPU_AWARE:BOOL=ON -DQE_ENABLE_OPENACC:BOOL=ON -DCMAKE_C_COMPILER:STRING=mpicc -DCMAKE_Fortran_COMPILER:STRING=mpif90 -DQE_ENABLE_HDF5:BOOL=ON ..
+make [-jN]
+
+```
+#### GH200
+[![Pipeline](https://gitea.psi.ch/HPCE/spack-psi/actions/workflows/q-e_gh_merlin7.yml/badge.svg?branch=main)](https://gitea.psi.ch/HPCE/spack-psi)
+
+```bash
+salloc --partition=gh-daily --clusters=gmerlin7 --time=08:00:00 --ntasks=4 --nodes=1 --gpus=1 --mem=40000 $SHELL
+ssh <allocated_gpu>
+module purge
+module use Spack unstable
+module load nvhpc/25.3 openmpi/5.0.7-e3bf-GH200-gpu fftw/3.3.10-sfpw-omp hdf5/develop-2.0-ztvo nvpl-blas/0.4.0.1-3zpg nvpl-lapack/0.3.0-ymy5  netlib-scalapack/2.2.2-qrhq cmake/3.31.6-5dl7
+
+
+cd <path to QE source directory>
+mkdir build
+cd build
+
+cmake -DQE_ENABLE_MPI:BOOL=ON -DQE_ENABLE_OPENMP:BOOL=ON -DQE_ENABLE_SCALAPACK:BOOL=ON -DQE_ENABLE_CUDA:BOOL=ON -DQE_ENABLE_MPI_GPU_AWARE:BOOL=ON -DQE_ENABLE_OPENACC:BOOL=ON -DCMAKE_C_COMPILER:STRING=mpicc -DCMAKE_Fortran_COMPILER:STRING=mpif90 -DQE_ENABLE_HDF5:BOOL=ON ..
+make [-jN]
+```
+
+## Q-E-SIRIUS
+
+SIRIUS enabled fork of QuantumESPRESSO
+
+### CPU
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.8-mx6f q-e-sirius/1.0.1-dtn4-omp
+```
+
+### A100 nodes
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.8-lsff-A100-gpu q-e-sirius/1.0.1-7snv-omp
+```
+### GH nodes
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.8-tx2w-GH200-gpu q-e-sirius/1.0.1-3dwi-omp
+```