Benchmarks: Difference between revisions

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Revision as of 20:10, 3 December 2008

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.

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.

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	-	Desktop	4	x	-

@@ Line 7: / Line 7: @@
 * '''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.
-=== Desktop: ===
+=== Computer systems: ===
-Benchmarks run on a desktop computer with 1 Intel Core2 Quad CPU Q6600, 2.40 Ghz, 3.0 GB memory, Ubuntu 8.04 Linux, gfortran (-O3) Fortran compiler
+* '''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.
-Using 4 processors: basic = 16 s, auto = 762 s, test suite = 2997 s
+* '''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 1 processor: basic = 5 s, auto = 152 s, test suite = 529 s
-=== Server: ===
-Benchmarks run on a 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
 Using 100 processors: basic = 5 s, auto = 152 s, test suite = 529 s
@@ Line 28: / Line 29: @@
 Using 1 processor: basic = 5 s, auto = 152 s, test suite = 529 s
+{| border="1" cellpadding="2"
+|-
+|System
+|processors
+|basic
+|auto
+|test suite
+|-
+|Desktop || 1 || x || x |-
+|Desktop || 4 || x || x |-
+|}