Benchmarks

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Benchmark results for CYANA 3.0:

Computer system Number of processors (cores) Computation time (s)
Basic Auto Test suite
Laptop (gfortran) 1 ? ? ?
2 ? ? ?
Desktop (intel) 1 228 ? ?
4 ? ? ?
Desktop (gfortran) 1 326 ? ?
4 ? ? ?
Server 1 144 ? ?
10 16 762 2997
20 10 420 1623
50 5 221 807
100 5 152 529

03-Dec-2008

Computer systems:

  • Laptop: Laptop computer with 1 Intel Core 2 Duo L7800 dual-core CPU, 2.00 Ghz, 2.0 GB memory, Cygwin under Windows Vista, gfortran (-O3) Fortran compiler.
  • Desktop: Desktop computer with 1 Intel Core 2 Q6600 quad-core CPU, 2.40 Ghz, 3.0 GB memory, Ubuntu 8.04 Linux, Intel or gfortran (-O3) Fortran compiler.
  • 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, OpenMPI.

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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, comprising the 'basic' and 'auto' calculations, as well as structure calculations for homodimers, structure calculations using RDCs, pseudocontact shifts, etc.