ADD: GROMACS docu

_data/sidebars/merlin7_sidebar.yml

@@ -68,6 +68,8 @@ entries:
             url: /merlin7/ansys.html
           - title: ANSYS RSM
             url: /merlin7/ansys-rsm.html
+          - title: GROMACS
+            url: /merlin7/gromacs.html
           - title: Quantum ESPRESSO
             url: /merlin7/quantum-espresso.html
           - title: OPAL-X

pages/merlin7/05-Software-Support/gromacs.md

@@ -0,0 +1,91 @@
+---
+title: GROMACS
+keywords: GROMACS software, compile
+summary: "GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics"
+sidebar: merlin7_sidebar
+toc: false
+permalink: /merlin7/gromacs.html
+---
+
+## GROMACS
+
+GROMACS (GROningen Machine for Chemical Simulations) is a versatile and widely-used open source package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
+
+It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.)
+
+## Licensing Terms and Conditions
+
+GROMACS is a joint effort, with contributions from developers around the world: users agree to acknowledge use of GROMACS in any reports or publications of results obtained with the Software (see GROMACS Homepage for details).
+
+## How to run on Merlin7
+### CPU nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-ax23-A100-gpu gromacs/2025.2-whcq-omp
+```
+### A100 nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-omp
+```
+### GH nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp
+```
+
+### SBATCH GH, 4 GPU, 32 OMP threads, 4 MPI ranks
+```bash
+#!/bin/bash
+#SBATCH --get-user-env
+#SBATCH --output=_scheduler-stdout.txt
+#SBATCH --error=_scheduler-stderr.txt
+#SBATCH --job-name="Testing GROMACS GH"
+#SBATCH --nodes=1             # number of GH200 nodes with each node having 4 CPU+GPU
+#SBATCH --ntasks-per-node=4  # 8 MPI ranks per node
+#SBATCH --cpus-per-task 32    # 32 OMP threads per MPI rank
+#SBATCH --cluster=gmerlin7
+#SBATCH --hint=nomultithread 
+#SBATCH --partition=gh-hourly
+#SBATCH --gpus=4
+#SBATCH --gpus-per-task=1
+
+unset PMODULES_ENV
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-blxc-GH200-gpu gromacs/2025.2-cjnq-GH200-gpu-omp
+
+export FI_CXI_RX_MATCH_MODE=software
+
+export GMX_GPU_DD_COMMS=true
+export GMX_GPU_PME_PP_COMMS=true
+export GMX_FORCE_UPDATE_DEFAULT_GPU=true
+export GMX_ENABLE_DIRECT_GPU_COMM=1
+export GMX_FORCE_GPU_AWARE_MPI=1
+
+srun gmx_mpi mdrun -s input.tpr -ntomp 32 -bonded gpu -nb gpu -pme gpu -pin on -v -noconfout -dlb yes -nstlist 300 -npme 1 -nsteps 10000 -update gpu
+```
+
+## Developing your own GPU code
+#### A100
+```bash
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-3vzj-A100-gpu gromacs/2025.2-vbj4-A100-gpu-omp cmake/3.31.6-o3lb python/3.13.1-cyro
+
+git clone https://github.com/gromacs/gromacs.git
+cd gromacs 
+
+mkdir build && cd build
+cmake -DCMAKE_C_COMPILER=gcc-12 \
+    -DCMAKE_CXX_COMPILER=g++-12 \
+    -DGMX_MPI=on \
+    -DGMX_GPU=CUDA \
+    -GMX_CUDA_TARGET_SM="80" \ # 90 for the Hopper GPUs
+    -DGMX_DOUBLE=off \ # turn on double precision only if useful
+    ..
+
+make
+
+```
+