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

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+---
+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
+## 2025.2
+### 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
+```
+## 2025.3
+### CPU nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.9-n4yf-A100-gpu gromacs/2025.3-6ken-omp
+```
+### A100 nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.9-xqhy-A100-gpu gromacs/2025.3-ohlj-A100-gpu-omp
+```
+### GH nodes
+```bash
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.9-inxi-GH200-gpu gromacs/2025.3-yqlu-GH200-gpu-omp
+```
+
+### SBATCH CPU, 4 MPI ranks, 16 OMP threads
+```bash
+#!/bin/bash
+#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
+#SBATCH --nodes=1            # requesting 1 compute node
+#SBATCH --ntasks=4           # use 4 MPI rank (task)
+#SBATCH --partition=hourly
+#SBATCH --cpus-per-task=16 # modify this number of CPU cores per MPI task
+#SBATCH --output=_scheduler-stdout.txt
+#SBATCH --error=_scheduler-stderr.txt
+
+unset PMODULES_ENV
+module purge
+module use Spack unstable
+module load gcc/12.3 openmpi/5.0.7-ax23-A100-gpu gromacs/2025.2-whcq-omp
+
+export FI_CXI_RX_MATCH_MODE=software
+
+# Add your input (tpr) file in the command below
+srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
+srun gmx_mpi mdrun -s step6.0_minimization.tpr -pin on -ntomp ${SLURM_CPUS_PER_TASK}
+```
+
+### SBATCH A100, 4 GPU, 16 OMP threads, 4 MPI ranks
+```bash
+#!/bin/bash
+#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
+#SBATCH --output=_scheduler-stdout.txt
+#SBATCH --error=_scheduler-stderr.txt
+#SBATCH --nodes=1             # number of GH200 nodes with each node having 4 CPU+GPU
+#SBATCH --ntasks-per-node=4  # 4 MPI ranks per node
+#SBATCH --cpus-per-task=16    # 16 OMP threads per MPI rank
+#SBATCH --cluster=gmerlin7
+#SBATCH --hint=nomultithread
+#SBATCH --partition=a100-hourly
+#SBATCH --gpus=4
+
+unset PMODULES_ENV
+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
+
+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
+
+# Add your input (tpr) file in the command below
+srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
+srun gmx_mpi mdrun -s step6.0_minimization.tpr -ntomp ${SLURM_CPUS_PER_TASK}
+```
+
+### SBATCH GH, 2 GPU, 18 OMP threads, 2 MPI ranks
+```bash
+#!/bin/bash
+#SBATCH --time=00:10:00      # maximum execution time of 10 minutes
+#SBATCH --output=_scheduler-stdout.txt
+#SBATCH --error=_scheduler-stderr.txt
+#SBATCH --nodes=1             # number of GH200 nodes with each node having 4 CPU+GPU
+#SBATCH --ntasks-per-node=2  # 2 MPI ranks per node
+#SBATCH --cpus-per-task=18    # 18 OMP threads per MPI rank
+#SBATCH --cluster=gmerlin7
+#SBATCH --hint=nomultithread
+#SBATCH --partition=gh-hourly
+#SBATCH --gpus=2
+
+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
+
+# Add your input (tpr) file in the command below
+srun gmx_mpi grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx
+srun gmx_mpi mdrun -s step6.0_minimization.tpr -ntomp ${SLURM_CPUS_PER_TASK}
+```
+
+## 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
+
+```
+