Benchmarks

CYANA Benchmarks

Benchmark calculations:

• basic: Structure calculation of a protein with 114 amino acid residues, 1737 NOE distance restraints, 110 torsion angle restraints. 50 conformers are calculated using 4000 torsion angle dynamics steps per conformer.

• auto: Structure calculation with automated NOESY assignment of a protein with 114 amino acid residues, 1737 NOE distance restraints, 110 torsion angle restraints. 8 x 100 = 800 conformers are calculated using 10000 torsion angle dynamics steps per conformer.

• test suite: Complete CYANA 3.0 test suite, comprising the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, using RDCs, pseudocontact shifts, etc.

Desktop:

Benchmarks run on a desktop computer with 1 Intel Core2 Quad CPU Q6600, 2.40 Ghz, 3.0 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler

Using 4 processors: basic = 16 s, auto = 762 s, test suite = 2997 s

Using 1 processor: basic = 5 s, auto = 152 s, test suite = 529 s

Server:

Benchmarks run on a Linux cluster system with 20 nodes, each having 2 Intel Xeon Quad CPU E5462, 2.80 Ghz, 16 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler

Using 100 processors: basic = 5 s, auto = 152 s, test suite = 529 s

Using 50 processors: basic = 5 s, auto = 152 s, test suite = 529 s

Using 20 processors: basic = 5 s, auto = 152 s, test suite = 529 s

Using 10 processors: basic = 16 s, auto = 762 s, test suite = 2997 s

Using 1 processor: basic = 5 s, auto = 152 s, test suite = 529 s