Merge pull request #617 from RuiApostolo/20240704_gromacs_gpu

Instructions on how to use the gromacs/2022.4-GPU module

docs/research-software/gromacs.md

@@ -17,12 +17,18 @@ non-biological systems, e.g. polymers.
 ## Using GROMACS on ARCHER2
 
 GROMACS is Open Source software and is freely available to all users.
-Three versions are available:
+Three executable versions are available on the normal (CPU-only) modules:
 
   - Parallel MPI/OpenMP, single precision: `gmx_mpi`
   - Parallel MPI/OpenMP, double precision: `gmx_mpi_d`
   - Serial, single precision: `gmx`
 
+We also provide a GPU version of GROMACS that will run on the MI210 GPU nodes, it's named `gromacs/2022.4-GPU` and can be loaded with
+
+```bash
+module load gromacs/2022.4-GPU
+```
+
 !!! important
     The `gromacs` modules reset the CPU frequency to the highest possible value
     (2.25 GHz) as this generally achieves the best balance of performance to 
@@ -33,8 +39,7 @@ Three versions are available:
 
 ### Running MPI only jobs
 
-The following script will run a GROMACS MD job using 4 nodes (128x4
-cores) with pure MPI.
+The following script will run a GROMACS MD job using 4 nodes (128x4 cores) with pure MPI.
 
 ```slurm
 #!/bin/bash
@@ -89,6 +94,30 @@ export OMP_NUM_THREADS=8
 srun --distribution=block:block --hint=nomultithread gmx_mpi mdrun -s test_calc.tpr
 ```
 
+### Running GROMACS on the AMD MI210 GPUs
+
+The following script will run a GROMACS MD job using 1 GPU with 1 MPI process 8 OpenMP threads per MPI process.
+
+```slurm
+#!/bin/bash
+#SBATCH --job-name=mdrun_gpu
+#SBATCH --gpus=1
+#SBATCH --time=00:20:00
+#SBATCH --hint=nomultithread
+#SBATCH --distribution=block:block
+
+# Replace [budget code] below with your project code (e.g. t01)
+#SBATCH --account=[budget code]
+#SBATCH --partition=gpu
+#SBATCH --qos=gpu-shd  # or gpu-exc
+
+# Setup the environment
+module load gromacs/2022.4-GPU
+
+export OMP_NUM_THREADS=8
+srun --ntasks=1 --cpus-per-task=8 gmx_mpi mdrun -ntomp 8 --noconfout -s calc.tpr
+```
+
 ## Compiling Gromacs
 
 The latest instructions for building GROMACS on ARCHER2 may be found in