Atomistic MD simulations of biomolecules on Fugaku

Fugaku is a supercomputer at RIKEN Center for Computational Science and has 158, 976 nodes. This machine has been made available through the HPCI project.

GENESIS was selected as one of the target applications during the development of the Fugaku supercomputer, and has been co-designed to maximize its performance on this platform. The appendix provides instructions on how to run atomistic MD simulations on Fugaku.

The optimized GENESIS code for Fugaku is available on GitHub in version 2.x.

# Download the source code
$ git clone https://github.com/genesis-release-r-ccs/genesis.git
$ cd genesis
$ autoreconf
$ ./configure --enable-mixed --host=Fugaku
$ make
$ make install

To compile GENESIS on Fugaku, please do not forget to add --host=Fugaku.

A option --enable-single/mixed/double controls default precision of real type variables. 

We recommend using --enable-mixed for improved simulation stability and accuracy on Fugaku. In particular, it has been reported that simulations compiled with --enable-single may produce slightly different box sizes and temperatures compared to those with --enable-mixed or --enable-double.

Please refer to doc/GENESIS.pdf for more information.

After the compilation, please execute compile test.

$ cd ./tests/regression_test
(make a job script)
$ pjsub test_script.sh

Templates for pjsub scripts are available on the Fugaku portal site (accessible to registered users only). Please refer to the site to find a script configured for hybrid parallelization (MPI/OpenMP). Detailed explanations of the available pjsub options can also be found there.

Due to amount of memory, please assign at least 2 nodes for compile test.

./test.py "mpiexec ${bindir}/spdyn " fugaku > regression.log

For normal jobs, please write down the line for the execution of GENESIS.

mpiexec -stdout run_fep1.out ${bindir}/spdyn inp

Although not as fast as the optimized version, GENESIS 1.5.1 and later are compatible with Fugaku. If you wish to use these versions, please specify --host=Fugaku during configuration. Note, however, that only --enable-single or --enable-double are available in these versions, whereas --enable-mixed is not supported.

Written by Chigusa Kobayashi@RIKEN Center for Computational Science
July 29, 2022

Updated: