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Benchmarks routine and bench faster_surface command
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@rdk
rdk committed Aug 3, 2024
1 parent 4a385cc commit 198d4ea
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Showing 3 changed files with 72 additions and 171 deletions.
7 changes: 6 additions & 1 deletion src/main/groovy/cz/siret/prank/program/Main.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ import cz.siret.prank.program.routines.Routine
import cz.siret.prank.program.routines.analyze.AnalyzeRoutine
import cz.siret.prank.program.routines.analyze.PrintRoutine
import cz.siret.prank.program.routines.analyze.TransformRoutine
import cz.siret.prank.program.routines.benchmark.Benchmarks
import cz.siret.prank.program.routines.predict.PredictPocketsRoutine
import cz.siret.prank.program.routines.predict.PredictResiduesRoutine
import cz.siret.prank.program.routines.predict.RescorePocketsRoutine
Expand Down Expand Up @@ -357,6 +358,10 @@ class Main implements Parametrized, Writable {
new PrintRoutine(args, this).execute()
}

private runBenchmark() {
new Benchmarks(args, this).execute()
}

void runHelp() {
println Futils.readResource('/help.txt')
}
Expand Down Expand Up @@ -411,7 +416,7 @@ class Main implements Parametrized, Writable {
break
case 'print': runPrint()
break
case 'run': runExperiment(args.unnamedArgs[0])
case 'bench': runBenchmark()
break
default:
runExperiment(command)
Expand Down
89 changes: 65 additions & 24 deletions src/main/groovy/cz/siret/prank/program/routines/benchmark/Benchmarks.groovy
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@@ -1,54 +1,95 @@
package cz.siret.prank.program.routines.benchmark

import cz.siret.prank.domain.Dataset
import cz.cuni.cusbg.surface.FasterNumericalSurface
import cz.siret.prank.domain.Protein
import cz.siret.prank.domain.loaders.electrostatics.DelphiCubeLoader
import cz.siret.prank.domain.loaders.electrostatics.GaussianCube
import cz.siret.prank.program.Main
import cz.siret.prank.program.routines.Routine
import cz.siret.prank.utils.Bench
import cz.siret.prank.utils.CdkUtils
import cz.siret.prank.utils.CmdLineArgs
import groovy.transform.CompileDynamic
import groovy.transform.CompileStatic
import groovy.util.logging.Slf4j
import org.openscience.cdk.geometry.surface.NumericalSurface
import org.openscience.cdk.interfaces.IAtomContainer

import static cz.siret.prank.utils.Bench.timeitLog
import static cz.siret.prank.utils.Futils.*

/**
* Old benchmarks moved from Experiments routine
* TODO revive
*
*/
@Slf4j
@CompileStatic
class Benchmarks extends Routine {

String command
Main main
CmdLineArgs args

Dataset trainDataset
Dataset evalDataset
boolean doCrossValidation = false
Benchmarks(CmdLineArgs args, Main main) {
super(null)
this.args = args
this.main = main

String outdirRoot
String datadirRoot

String label
}

Main main
CmdLineArgs cmdLineArgs
@CompileDynamic
void execute() {

public Benchmarks(CmdLineArgs args, Main main, String command) {
super(null)
this.cmdLineArgs = args
this.command = command
this.main = main
String subCommand = args.unnamedArgs[0]

log.info "executing bench $subCommand command"

this."$subCommand"()

}

//===========================================================================================================//

/**
* Benchmark FasterNumericalSurface against NumericalSurface
*/
void faster_surface() {

String structFile = args.get("f") ?: "$main.installDir/test_data/2W83.pdb"

log.info "Benchmarking faster surface o file [$structFile]"

Protein protein = Protein.load(structFile)


IAtomContainer cdkAtoms = CdkUtils.toAtomContainer(protein.proteinAtoms)


double solventRadius = 1.6
int outerReps = 5
int reps = 16

for(int tesslevel in 2..4) {
double oldTime = Bench.timeitLogWithHeatup("OLD tess:" + tesslevel, outerReps, {
reps.times {
NumericalSurface numericalSurface = new NumericalSurface(cdkAtoms, solventRadius, tesslevel)
numericalSurface.getAllSurfacePoints()
}
})

double newTime = Bench.timeitLogWithHeatup("NEW tess:" + tesslevel, outerReps, {
reps.times {
FasterNumericalSurface numericalSurface = new FasterNumericalSurface(cdkAtoms, solventRadius, tesslevel)
numericalSurface.getAllSurfacePoints()
}
})

double timeMult = oldTime / newTime
log.info("Tessellation $tesslevel SPEEDUP: {}", Math.round(timeMult * 1000)/1000 )
}

// if (!commandRegister.containsKey(command)) {
// throw new PrankException("Invalid command: " + command)
// }
//
// //if (command in ['traineval', 'ploop', 'hopt']) {
// prepareDatasets(main)
// //}
}

//===========================================================================================================//

/**
* for jvm profiler
Expand Down
147 changes: 1 addition & 146 deletions src/test/groovy/cz/siret/prank/geom/cdksurface/FasterNumericalSurfaceTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ class FasterNumericalSurfaceTest {
static String dataDir = 'src/test/resources/data'

/**
* Test for protein loader as well
* TODO implement meaningful FasterNumericalSurface test
*/
@Test
@Disabled
Expand Down Expand Up @@ -59,151 +59,6 @@ class FasterNumericalSurfaceTest {

}

/*
[INFO] Bench - OLD tess:2 (heatup): 1390
[INFO] Bench - OLD tess:2 (run 1): 1214
[INFO] Bench - OLD tess:2 (run 2): 1237
[INFO] Bench - OLD tess:2 (run 3): 1237
[INFO] Bench - OLD tess:2 (run 4): 1214
[INFO] Bench - OLD tess:2 (run 5): 1240
[WARN] Bench - OLD tess:2 (AVG): 1228
[INFO] Bench - NEW tess:2 (heatup): 968
[INFO] Bench - NEW tess:2 (run 1): 929
[INFO] Bench - NEW tess:2 (run 2): 894
[INFO] Bench - NEW tess:2 (run 3): 942
[INFO] Bench - NEW tess:2 (run 4): 922
[INFO] Bench - NEW tess:2 (run 5): 929
[WARN] Bench - NEW tess:2 (AVG): 923
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.33
[INFO] Bench - OLD tess:3 (heatup): 3224
[INFO] Bench - OLD tess:3 (run 1): 3230
[INFO] Bench - OLD tess:3 (run 2): 3343
[INFO] Bench - OLD tess:3 (run 3): 3269
[INFO] Bench - OLD tess:3 (run 4): 3288
[INFO] Bench - OLD tess:3 (run 5): 3306
[WARN] Bench - OLD tess:3 (AVG): 3287
[INFO] Bench - NEW tess:3 (heatup): 2498
[INFO] Bench - NEW tess:3 (run 1): 2339
[INFO] Bench - NEW tess:3 (run 2): 2460
[INFO] Bench - NEW tess:3 (run 3): 2587
[INFO] Bench - NEW tess:3 (run 4): 2463
[INFO] Bench - NEW tess:3 (run 5): 2489
[WARN] Bench - NEW tess:3 (AVG): 2467
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.332
[INFO] Bench - OLD tess:4 (heatup): 10819
[INFO] Bench - OLD tess:4 (run 1): 10759
[INFO] Bench - OLD tess:4 (run 2): 10883
[INFO] Bench - OLD tess:4 (run 3): 10989
[INFO] Bench - OLD tess:4 (run 4): 10803
[INFO] Bench - OLD tess:4 (run 5): 10806
[WARN] Bench - OLD tess:4 (AVG): 10848
[INFO] Bench - NEW tess:4 (heatup): 7921
[INFO] Bench - NEW tess:4 (run 1): 7903
[INFO] Bench - NEW tess:4 (run 2): 7928
[INFO] Bench - NEW tess:4 (run 3): 7888
[INFO] Bench - NEW tess:4 (run 4): 7979
[INFO] Bench - NEW tess:4 (run 5): 7810
[WARN] Bench - NEW tess:4 (AVG): 7901
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.373
+ primitive collections
[INFO] Bench - OLD tess:2 (heatup): 1400
[INFO] Bench - OLD tess:2 (run 1): 1262
[INFO] Bench - OLD tess:2 (run 2): 1250
[INFO] Bench - OLD tess:2 (run 3): 1283
[INFO] Bench - OLD tess:2 (run 4): 1257
[INFO] Bench - OLD tess:2 (run 5): 1234
[WARN] Bench - OLD tess:2 (AVG): 1257
[INFO] Bench - NEW tess:2 (heatup): 953
[INFO] Bench - NEW tess:2 (run 1): 867
[INFO] Bench - NEW tess:2 (run 2): 842
[INFO] Bench - NEW tess:2 (run 3): 847
[INFO] Bench - NEW tess:2 (run 4): 826
[INFO] Bench - NEW tess:2 (run 5): 878
[WARN] Bench - NEW tess:2 (AVG): 852
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.475
[INFO] Bench - OLD tess:3 (heatup): 3352
[INFO] Bench - OLD tess:3 (run 1): 3415
[INFO] Bench - OLD tess:3 (run 2): 3532
[INFO] Bench - OLD tess:3 (run 3): 3415
[INFO] Bench - OLD tess:3 (run 4): 3342
[INFO] Bench - OLD tess:3 (run 5): 3436
[WARN] Bench - OLD tess:3 (AVG): 3428
[INFO] Bench - NEW tess:3 (heatup): 2486
[INFO] Bench - NEW tess:3 (run 1): 2349
[INFO] Bench - NEW tess:3 (run 2): 2486
[INFO] Bench - NEW tess:3 (run 3): 2451
[INFO] Bench - NEW tess:3 (run 4): 2423
[INFO] Bench - NEW tess:3 (run 5): 2325
[WARN] Bench - NEW tess:3 (AVG): 2406
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.425
[INFO] Bench - OLD tess:4 (heatup): 11796
[INFO] Bench - OLD tess:4 (run 1): 11680
[INFO] Bench - OLD tess:4 (run 2): 11596
[INFO] Bench - OLD tess:4 (run 3): 11612
[INFO] Bench - OLD tess:4 (run 4): 11627
[INFO] Bench - OLD tess:4 (run 5): 11684
[WARN] Bench - OLD tess:4 (AVG): 11639
[INFO] Bench - NEW tess:4 (heatup): 7961
[INFO] Bench - NEW tess:4 (run 1): 7733
[INFO] Bench - NEW tess:4 (run 2): 7995
[INFO] Bench - NEW tess:4 (run 3): 7897
[INFO] Bench - NEW tess:4 (run 4): 8104
[INFO] Bench - NEW tess:4 (run 5): 8162
[WARN] Bench - NEW tess:4 (AVG): 7978
[INFO] MyNumericalSurfaceTest - SPEEDUP: 1.459
1.0
[INFO] Bench - OLD tess:2 (heatup): 1414
[INFO] Bench - OLD tess:2 (run 1): 1243
[INFO] Bench - OLD tess:2 (run 2): 1249
[INFO] Bench - OLD tess:2 (run 3): 1248
[INFO] Bench - OLD tess:2 (run 4): 1235
[INFO] Bench - OLD tess:2 (run 5): 1247
[WARN] Bench - OLD tess:2 (AVG): 1244
[INFO] Bench - NEW tess:2 (heatup): 959
[INFO] Bench - NEW tess:2 (run 1): 875
[INFO] Bench - NEW tess:2 (run 2): 860
[INFO] Bench - NEW tess:2 (run 3): 857
[INFO] Bench - NEW tess:2 (run 4): 875
[INFO] Bench - NEW tess:2 (run 5): 857
[WARN] Bench - NEW tess:2 (AVG): 864
[INFO] FasterNumericalSurfaceTest - SPEEDUP: 1.44
[INFO] Bench - OLD tess:3 (heatup): 3359
[INFO] Bench - OLD tess:3 (run 1): 3365
[INFO] Bench - OLD tess:3 (run 2): 3420
[INFO] Bench - OLD tess:3 (run 3): 3357
[INFO] Bench - OLD tess:3 (run 4): 3395
[INFO] Bench - OLD tess:3 (run 5): 3453
[WARN] Bench - OLD tess:3 (AVG): 3398
[INFO] Bench - NEW tess:3 (heatup): 2510
[INFO] Bench - NEW tess:3 (run 1): 2329
[INFO] Bench - NEW tess:3 (run 2): 2458
[INFO] Bench - NEW tess:3 (run 3): 2571
[INFO] Bench - NEW tess:3 (run 4): 2557
[INFO] Bench - NEW tess:3 (run 5): 2575
[WARN] Bench - NEW tess:3 (AVG): 2498
[INFO] FasterNumericalSurfaceTest - SPEEDUP: 1.36
[INFO] Bench - OLD tess:4 (heatup): 17770
[INFO] Bench - OLD tess:4 (run 1): 22138
[INFO] Bench - OLD tess:4 (run 2): 20347
[INFO] Bench - OLD tess:4 (run 3): 18072
[INFO] Bench - OLD tess:4 (run 4): 11325
[INFO] Bench - OLD tess:4 (run 5): 11322
[WARN] Bench - OLD tess:4 (AVG): 16640
[INFO] Bench - NEW tess:4 (heatup): 8608
[INFO] Bench - NEW tess:4 (run 1): 8473
[INFO] Bench - NEW tess:4 (run 2): 8544
[INFO] Bench - NEW tess:4 (run 3): 8603
[INFO] Bench - NEW tess:4 (run 4): 8717
[INFO] Bench - NEW tess:4 (run 5): 8428
[WARN] Bench - NEW tess:4 (AVG): 8553
[INFO] FasterNumericalSurfaceTest - SPEEDUP: 1.946
*/


}

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