Benchmarks: Difference between revisions
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03-Dec-2008 | 03-Dec-2008 | ||
==== Computer systems: ==== | ===== 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. | * '''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. | ||
| Line 45: | Line 45: | ||
* '''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. | * '''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. | ||
==== Benchmark types: ==== | ===== 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. | * '''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. | ||
Revision as of 13:34, 4 December 2008
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.
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.