Benchmarks

Benchmark results for CYANA 3.0:

Computer system	Number of processors (cores)	Computation time (s)		Relative performance
		Basic	Auto
Laptop	1	813	?	?
Desktop (intel)	1	208	?	?
	4	57	2479	8919
Desktop (gfortran)	1	258	?	?
Desktop (g95)	1	336	?	?
Mac mini (intel)	2	87	4092	14977
Mac mini (gfortran)	2	104	4894	?
Server	1	146	?	?
	10	16	745	2775
	20	11	412	1508
	50	4	209	734
	100	5	142	484

February 2010

Relative performance

• Normalized to 1.0 for the calculation with the 'Desktop' computer system using 1 processor core.
• Based on the computation time for the Auto calculation

Computer systems:

• Laptop: Laptop computer with 1 Intel Core 2 Duo L7800 dual-core CPU, 2.00 Ghz, 2 GB memory, Cygwin under Windows 7, gfortran (-O3) Fortran compiler 4.3.4.

• Desktop: Desktop computer with 1 Intel Core 2 Q9400 quad-core CPU, 2.66 Ghz, 4 GB memory, Ubuntu 8.10 Linux, Intel Fortran compiler 11.1, gfortran (-O3) Fortran compiler 4.3.2, or g95 Fortran compiler 0.91.

• Mac mini: Mac mini with 1 Intel Core 2 Duo dual-core CPU, 2.53 Ghz, 4 GB memory, Mac OS X 10.6.2, Intel Fortran compiler 11.1 or gfortran (-O3) Fortran compiler 4.5.0.

• Server: Linux cluster system with 20 nodes, each having 2 Intel Xeon E5462 quad-core CPUs, 2.80 Ghz, 16 GB memory, Ubuntu 8.04 Linux, Intel Fortran compiler 10.1, OpenMPI.

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, 4732 NOESY cross peaks, 88 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, including the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, structure calculations using RDCs, pseudocontact shifts, etc.