544.nab_r
SPEC CPU2017 Benchmark Description

Benchmark Name

544.nab_r

Benchmark Author

Russ Brown <russ.brown[at] yahoo.com>, et al

Benchmark Program General Category

Molecular Modeling

Benchmark Description

544.nab_r is based on Nucleic Acid Builder (NAB), which is a molecular modeling application that performs the types of floating point intensive calculations that occur commonly in life science computation. The calculations range from relatively unstructured "molecular dynamics" to relatively structured linear algebra.

Input Description

544.nab_r's input consists molecules with varying numbers of atoms.

To simulate a molecule, two files are required.

One is a PDB format text file that specifies the atomic (x,y,z) coordinates; most of those were taken from the Brookhaven Protein Data Bank. Information at that site details how those files were created.

The other is a PRM format text file that specifies, among other characteristics, the "force field" that indicates how the atoms interact with one another. Generating the PRM file involves using the full version of NAB to read the PDB file, add protons to the molecule, and output the PRM file.

A small NAB program is required that reads the PDB file, adds H atoms if necessary, and outputs new PDB and PRM files. That program, as well as the steps necessary to run it, have been encapsulated in the shell script makeprm.sh in the benchmark Docs directory. The script requires access to a full installation of NAB, as well as working C and Fortran compilers.

Output Description

The outputs are summaries of the state of the molecular dynamics simulation every 100 iterations and at the end.

Programming Language

ANSI C

Known portability issues

None

Sources and Licensing

The benchmark is drawn from AmberTools 12, under GPL. SPEC added a BSD-licensed random number generator, and Henry Spencer's regexp.

Please see details in the document SPEC CPU2017 Licenses.

References

Last updated: $Date: 2017-05-01 13:34:29 -0400 (Mon, 01 May 2017) $