Gromacs on Theta
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 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 ```
We strongly suggest that users try combinations of different numbers of nodes, MPI ranks per node, and 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 |