Benchmarks

Benchmark results for CYANA 3.0:

Computer system	Number of processors (cores)	Computation time (s)		Relative performance
		Basic	Auto
Laptop	1	813	?	0.26
Desktop (intel)	1	208	?	= 1
	4	57	2479	3.65
Desktop (gfortran)	1	258	?	0.81
Desktop (g95)	1	336	?	0.62
Mac mini (intel)	1	157	?	1.32
	2	87	4092	2.39
Cluster	1	146	6756	1.42
	10	16	745	13.0
	20	11	412	18.9
	50	4	209	52.0
	100	5	142	41.6

February 2010

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 (-O5) Fortran compiler 0.91.

• Mac mini: Mac mini with 1 Intel Core 2 Duo P8700 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.

• Cluster: 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.

Relative performance

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

Notes

• Running the 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., takes about 3.65 times as long as the Auto benchmark.

• Doubling the number of torsion angle dynamics steps from 4000 to 8000 in the Basic calculation requires about 1.8 times more computation time.

• Performance with the gfortran compiler is 80-85% of the performance achieved with the Intel Fortran compiler.

• Performance with the g95 compiler is 60-65% of the performance achieved with the Intel Fortran compiler.