Gromacs on ThetaGPU

What is Gromacs?

GROMACS is a versatile 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.

Using GROMACS at ALCF

ALCF offers assistance with building binaries and compiling instructions for GROMACS. For questions, contact us at [email protected].

Building Gromacs

Download latest source code: http://manual.gromacs.org/documentation/2022.1/download.html
tar -xzf gromacs-2022.1.tar.gz

Submit an interactive job to a ThetaGPU compute node from Theta login node:

user@thetalogin4:~>module load cobalt/cobalt-gpu
user@thetalogin4:~>qsub -I -n 1 -t 60 -q single-gpu -A PROJECT --attrs filesystems=home
Job routed to queue "single-gpu".
Wait for job 10108666 to start...
Opening interactive session to thetagpu06-gpu0
...
user@thetagpu06:~$

cd gromacs-2022.1
mkdir build
module load cmake

cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx \
      -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON \
      -DCMAKE_INSTALL_PREFIX=/path-to/gromacs-2022.1/build \
      -DGMX_MPI=ON -DGMX_OPENMP=ON -DGMX_GPU=CUDA \
      -DCUDA_TOOLKIT_ROOT_DIR=/user/local/cuda-11.4

make –j 16
make install
The installed binary is build/bin/gmx_mpi.

Running Gromacs on ThetaGPU

Prebuilt Gromacs binaries can be found in the directory /soft/applications/gromacs/gromacs_cuda.

A sample qsub script follows that will run GROMACS on a full node using all eight GPUs available.

#!/bin/bash -l
#COBALT -n 1
#COBALT -t 30 
#COBALT -q full-node 
#COBALT -project catalyst 
#COBALT --attrs filesystems=home,theta-fs0

NODES=`cat $COBALT_NODEFILE | wc -l`

mpirun -hostfile $COBALT_NODEFILE --np 8 \
      /soft/applications/gromacs/gromacs_cuda/gmx_mpi.2022.1 \
      mdrun -ntomp 8 -gputasks 01234567 -nb gpu -pme gpu -npme 1 \
      -dlb yes -resethway -pin on -v deffnm step5_1 -g test.log

We strongly suggest that users try combinations of different numbers of nodes, MPI ranks per node, number of GPU tasks/devices, GPU task decomposition between nonbonded and PME kernels, and OMP threads per rank to find the optimal throughput for their particular workload.

The following is a representative benchmark for a system with 30,000 atoms generated on a single ThetaGPU node with above example.

	Core time(sec)	Wall time(sec)	(%)
Time	691.769	10.810	6399.6

	ns/day	hour/ns
Performance	399.661	0.060