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 offer assistance with building binaries and compiling instructions for GROMACS. For questions, contact us at support@alcf.anl.gov.
Building Gromacs
Download latest source code http://manual.gromacs.org/documentation/2018.5/download.html
Tar xzf gromacs-2018.5.tar.gz
Cd gromacs-2018.5
Mkdir build
Cd ../
Make sure use Intel compiler suite
CmakeCC=cc CXX=CC CFLAGS=” -xMIC-AVX512 -g -static-intel” CXXFLAGS=” -xMIC-AVX512 -g -static-intel” -DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=mkl DCMAKE_INSTALL_PREFIX=/PATH-to-Gromacs-Build-directory/ -DGMX_MPI=ON DGMX_OPENMP=ON -DGMX_CYCLE_SUBCOUNTERS=ON -DGMX_GPU=OFF DGMX_BUILD_HELP=OFF -DGMX_HWLOC=OFF -DGMX_SIMD=AVX_512_KNL DGMX_OPENMP_MAX_THREADS=256
Make –j 16
Make install
Cd build
The Gromacs binary is exe/gmx_mpi
Running Gromacs
A prebuilt Gromacs binary can be found in directory /soft/applications/gromacs
A sample qsub script:
#!/bin/bash #COBALT -t 30 #COBALT --project catalyst #COBALT --attrs mcdram=cache:numa=quad #COBALT -n 1& #COBALT -q debug-cache-quad #export I_MPI_DEBUG=5 #export I_MPI_FABRICS=shm #export I_MPI_PIN_MODE=lib #export KMP_AFFINITY=verbose,compact,1 exportGMX_MAXBACKUP=-1 aprun -n64-N64--envOMP_NUM_THREADS=2-ccdepth -d2-j2 /lus/theta-fs0/home/user_name/gromacs-2018.5/build/bin/gmx_mpi\ mdrun -dlbyes-resethway-pinon -v-deffnmstep5_1 -gtest.log
User is strongly suggested to try combinations of number of nodes, number of MPI ranks per node and number of Number of OMP threads per rank to find the optimal throughput for the application.
This is a benchmark for a 30,000 atoms system generated on 1 single Theta node with above qprun:
| Core time(sec) | Wall time(sec) | ||
|
Time |
8497.278(ns/day) | 12800.0(hour/ns) | |
| Performance | 65.078 | 0.369 |