Benchmarks: Difference between revisions
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Revision as of 19:12, 3 December 2008
Benchmark types:
- 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.
Computer systems:
- Desktop: Desktop computer with 1 Intel Core2 Quad CPU Q6600, 2.40 Ghz, 3.0 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler.
- Server: 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.
Benchmark results:
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
| System | processors | basic | auto | test suite |
| Desktop | 1 | x | x | x |
| Desktop | 4 | x | x | x |