RMG-Java
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ReactionMechanismGenerator
General speed optimization
This 'issue' is a place to collect thoughts about general speed and efficiency improvements.
There's a pretty minimal sampling java profiler at http://code.google.com/p/jsamp/wiki/Documentation that you can just attach to a running JVM on a compute node, leave it for a few hours, come back and kill it, and analyze the collected samples.
I sampled every 100ms for ~4 hours (5 enlargement iterations) on a job of mine with pdep, a large seed, and 32 reaction systems, but no pruning. Stats when I started sampling were:
The model core has 20524 reactions and 281 species. The model edge has 314641 reactions and 43038 species. There are 48093 partial pressure-dependent networks containing 50250 path and 13346 net reactions. The chem.inp file has 281 species (excluding inert gases). The chem.inp file has 20149 reactions (excluding duplicates). Running time: 2248.988 min Memory used: 1778.66 MB / 3585.67 MB (49.60%)
It spends roughly:
- 90% solving the reaction systems
jing.rxnSys.JDASSL.solve - 60% waiting for the unix proces (presumably mostly DASSL)
java.lang.UNIXProcess.waitForProcessExit - 26% checking if reaction structures are equal
jing.rxn.Structure.equals - 22% in
java.util.LinkedList.clone(possibly in the aboveStructure.equalscall?) - only 5% enlarging the model
jing.rxnSys.ReactionModelGenerator.enlargeReactionModel
First observation: solving all the reaction systems each time this way is incredibly wasteful - especially as 30 of my 32 reaction systems are valid and only 2 are being used to enlarge the model!
In your observation, I'm not sure what you mean by wasteful...the systems need to be solved to determine they are valid, no?
Here's the longer output (curtailed at 10 samples):
Self counts:
java.net.PlainSocketImpl.socketAccept 159333 37.8%
java.lang.UNIXProcess.waitForProcessExit 95934 22.8%
java.io.FileInputStream.readBytes 95847 22.7%
java.util.LinkedList.clone 34920 8.3%
jing.rxn.Structure.equals 7288 1.7%
java.lang.Object.wait 7094 1.7%
java.lang.UNIXProcess.forkAndExec 6929 1.6%
jing.chem.SpeciesDictionary.getSpeciesFromName 5263 1.2%
java.lang.StrictMath.floor 3457 0.8%
java.lang.StrictMath.acos 1603 0.4%
jing.rxn.PDepNetwork.contains 455 0.1%
java.lang.String.length 318 0.1%
java.util.LinkedList.indexOf 237 0.1%
jing.rxn.Reaction.calculateHrxn 214 0.1%
jing.rxn.Reaction.calculateTotalRate 183 0.0%
jing.chemUtil.Graph.getNodeList 163 0.0%
java.io.FileOutputStream.writeBytes 145 0.0%
jing.chemUtil.GraphComponent.isEquivalent 143 0.0%
jing.rxn.Reaction.calculateKeq 133 0.0%
java.util.Stack.push 130 0.0%
jing.chemUtil.Graph.addMissingHydrogen 117 0.0%
jing.chemUtil.Node.contentSub 102 0.0%
jing.chemUtil.Graph.isEquivalent 97 0.0%
jing.rxnSys.ReactionSystem.appendUnreactedSpeciesStatus 96 0.0%
jing.chemUtil.Graph.resetMatchedGC 73 0.0%
java.util.Stack.pop 73 0.0%
jing.rxn.PDepReaction.calculateForwardFlux 70 0.0%
jing.param.Temperature.<init> 61 0.0%
sun.misc.FloatingDecimal.multPow52 56 0.0%
java.util.ArrayList.iterator 52 0.0%
java.util.HashMap.getEntry 51 0.0%
sun.misc.FloatingDecimal.doubleValue 38 0.0%
java.lang.String.<init> 38 0.0%
jing.chemUtil.GraphComponent.isSubCentralMatched 34 0.0%
java.lang.Integer.hashCode 30 0.0%
java.util.LinkedList.access$200 29 0.0%
sun.misc.FloatingDecimal.readJavaFormatString 28 0.0%
jing.chemUtil.GraphComponent.isSub 25 0.0%
java.lang.Integer.getChars 24 0.0%
java.lang.Object.hashCode 23 0.0%
java.io.FileOutputStream.open 23 0.0%
jing.chemUtil.Graph.toStringWithoutCentralID 22 0.0%
java.lang.AbstractStringBuilder.append 22 0.0%
java.security.AccessController.doPrivileged 21 0.0%
jing.rxnSys.JDAS.getAutoEdgeReactionInfo 20 0.0%
java.util.LinkedList.addAll 19 0.0%
jing.chemUtil.Node.toStringWithoutCentralID 17 0.0%
java.util.HashMap.transfer 14 0.0%
jing.rxnSys.JDAS.generatePDepReactionList 13 0.0%
jing.chemUtil.Graph.getNodeNumber 13 0.0%
jing.chem.ChemElement.translateName 13 0.0%
jing.rxnSys.JDAS.generatePDepODEReactionList 11 0.0%
java.lang.StringBuilder.append 11 0.0%
java.lang.Integer.toString 11 0.0%
jing.rxnSys.CoreEdgeReactionModel.reactantsInCoreQ 10 0.0%
jing.rxn.PDepNetwork.getCoreReactions 10 0.0%
jing.chemUtil.Arc.neighborOk 10 0.0%
java.util.Arrays.copyOfRange 10 0.0%
Total counts:
jing.rxnSys.ReactionModelGenerator.modelGeneration 159334 37.8%
ca.evanjones.JSamp$1.run 159334 37.8%
RMG.main 159334 37.8%
java.net.ServerSocket.implAccept 159333 37.8%
java.net.ServerSocket.accept 159333 37.8%
java.net.PlainSocketImpl.socketAccept 159333 37.8%
java.net.AbstractPlainSocketImpl.accept 159333 37.8%
jing.rxnSys.ReactionSystem.solveReactionSystem 143926 34.1%
jing.rxnSys.JDASSL.solve 142437 33.8%
java.lang.UNIXProcess$1$1.run 102888 24.4%
java.lang.UNIXProcess.waitForProcessExit 95934 22.8%
java.lang.UNIXProcess.access$900 95934 22.8%
java.io.BufferedReader.readLine 95888 22.7%
sun.nio.cs.StreamDecoder.read 95848 22.7%
sun.nio.cs.StreamDecoder.implRead 95848 22.7%
java.io.InputStreamReader.read 95848 22.7%
java.io.BufferedReader.fill 95848 22.7%
sun.nio.cs.StreamDecoder.readBytes 95847 22.7%
java.io.FileInputStream.readBytes 95847 22.7%
java.io.FileInputStream.read 95847 22.7%
java.io.BufferedInputStream.read 95823 22.7%
java.io.BufferedInputStream.read1 95822 22.7%
jing.rxnSys.JDASSL.solveDAE 92272 21.9%
java.util.LinkedList.indexOf 42465 10.1%
java.util.LinkedList.contains 42465 10.1%
jing.rxn.Structure.equals 42248 10.0%
jing.rxn.Reaction.equals 42228 10.0%
jing.rxnSys.JDAS.generatePDepODEReactionList 41290 9.8%
jing.rxnSys.JDAS.generatePDepReactionList 41082 9.7%
jing.rxn.Structure.isCGListEquivalentAsSpecies 34960 8.3%
java.util.LinkedList.clone 34927 8.3%
jing.rxnSys.ReactionModelGenerator.enlargeReactionModel 7300 1.7%
jing.rxnSys.RateBasedPDepRME.enlargeReactionModel 7295 1.7%
jing.rxnSys.RateBasedPDepRME.addSpeciesToCore 7168 1.7%
java.lang.Object.wait 7094 1.7%
java.lang.Runtime.exec 6993 1.7%
java.lang.ProcessImpl.start 6993 1.7%
java.lang.ProcessBuilder.start 6993 1.7%
java.lang.UNIXProcess.<init> 6991 1.7%
java.lang.UNIXProcess$Gate.waitForExit 6981 1.7%
java.lang.UNIXProcess.access$500 6930 1.6%
java.lang.UNIXProcess.forkAndExec 6929 1.6%
jing.rxn.TemplateReactionGenerator.react 6637 1.6%
jing.rxn.ReactionTemplate.reactTwoReactants 6626 1.6%
jing.chem.Species.make 6348 1.5%
jing.chem.Species.<init> 5807 1.4%
jing.chem.SpeciesDictionary.getSpeciesFromName 5263 1.2%
jing.rxnSys.JDAS.transferReaction 5015 1.2%
jing.chem.Species.generateInChI 4279 1.0%
jing.chem.ChemGraph.generateInChI 4279 1.0%
jing.rxnSys.JDAS.generateTROEReactionList 3999 0.9%
jing.rxnSys.JDAS.getAutoEdgeReactionInfo 3857 0.9%
jing.rxnSys.JDAS.getEdgeReactionString 3771 0.9%
java.lang.StrictMath.floor 3457 0.8%
java.lang.Math.floor 3457 0.8%
java.lang.StringBuilder.append 3392 0.8%
java.lang.AbstractStringBuilder.append 3357 0.8%
sun.misc.FloatingDecimal.<init> 3322 0.8%
sun.misc.FloatingDecimal.dtoa 3321 0.8%
jing.chem.Species.findStablestThermoData 3245 0.8%
jing.chem.ChemGraph.getThermoData 3245 0.8%
jing.chem.ChemGraph.generateThermoData 3245 0.8%
jing.chem.QMTP.generateThermoData 3057 0.7%
jing.rxnSys.ReactionModelGenerator.writeInChIs 2863 0.7%
jing.rxnSys.ReactionSystem.initializePDepNetwork 2549 0.6%
jing.rxn.FastMasterEqn.runPDepCalculation 2532 0.6%
jing.chem.Species.generateNASAThermoData 2502 0.6%
jing.chem.GATPFit.generateNASAThermoData 2502 0.6%
jing.chem.GATPFit.callGATPFit 2502 0.6%
jing.chem.QMTP.generateQMThermoData 2408 0.6%
jing.chem.ChemGraph.getModifiedInChIKeyAnew 2149 0.5%
jing.chem.ChemGraph.getModifiedInChIAnew 2131 0.5%
jing.rxn.PDepReaction.calculateRate 1605 0.4%
jing.rxn.PDepRateConstant.calculateRate 1605 0.4%
jing.rxn.ChebyshevPolynomials.calculateRate 1603 0.4%
jing.rxn.ChebyshevPolynomials.calculatePhi 1603 0.4%
java.lang.StrictMath.acos 1603 0.4%
java.lang.Math.acos 1603 0.4%
jing.rxnSys.Chemkin.writeChemkinInputFile 1594 0.4%
jing.chem.QMTP.getPM3MM4ThermoDataUsingCCLib 1577 0.4%
jing.rxnSys.Chemkin.writeChemkinPdepReactions 1560 0.4%
jing.rxnSys.ReactionSystem.appendUnreactedSpeciesStatus 1481 0.4%
jing.chem.QMTP.getQMFileName 1418 0.3%
jing.chem.QMTP.parseMopacPM3 898 0.2%
jing.rxnSys.JDAS.generateThirdBodyReactionList 866 0.2%
jing.chem.QMTP.parseGaussianPM3 680 0.2%
jing.rxn.PDepReaction.calculateForwardFlux 652 0.2%
jing.chemUtil.Graph.isEquivalent 601 0.1%
jing.chem.ChemGraph.isEquivalent 593 0.1%
jing.chem.ChemGraph.equals 593 0.1%
jing.rxn.Reaction.calculateTotalRate 582 0.1%
jing.rxn.TemplateReaction.calculateTotalPDepRate 581 0.1%
jing.rxn.PDepNetwork.getCoreReactions 546 0.1%
jing.rxn.PDepNetwork.contains 518 0.1%
jing.rxn.PDepNetwork.addReactionToNetworks 517 0.1%
java.util.Formatter.format 481 0.1%
java.lang.String.format 481 0.1%
jing.rxn.Reaction.toRestartString 450 0.1%
jing.rxnSys.ReactionModelGenerator.writeEdgeReactions 428 0.1%
jing.rxn.PDepReaction.calculateReverseFlux 409 0.1%
jing.chem.QMTP.determinePointGroupUsingSYMMETRYProgram 356 0.1%
jing.chem.QMTP.calculateThermoFromPM3MM4Calc 356 0.1%
java.util.HashMap.put 349 0.1%
jing.chemUtil.GraphComponent.isEquivalent 329 0.1%
java.util.Formatter.parse 321 0.1%
java.util.regex.Matcher.getTextLength 318 0.1%
java.lang.String.length 318 0.1%
java.util.HashMap.getEntry 304 0.1%
jing.chem.SpeciesDictionary.putSpecies 302 0.1%
jing.rxn.ReactionAdjList.reactChemGraph 300 0.1%
jing.chem.ChemGraph.make 292 0.1%
jing.chem.ChemGraph.<init> 286 0.1%
jing.chemUtil.Graph.resetMatchedGC 281 0.1%
jing.rxn.PDepNetwork.getSpeciesLeakFluxes 263 0.1%
java.util.LinkedHashMap.get 243 0.1%
jing.rxn.ArrheniusKinetics.toChemkinString 241 0.1%
jing.rxnSys.ReactionSystem.isModelValid 240 0.1%
jing.rxnSys.RateBasedPDepVT.isModelValid 240 0.1%
jing.rxnSys.FinishController.isModelValid 240 0.1%
jing.chem.SpeciesDictionary.getSpecies 233 0.1%
jing.chemUtil.Graph.isSub 228 0.1%
jing.rxn.Reaction.calculateHrxn 214 0.1%
jing.rxnSys.ReactionModelGenerator.writeCoreReactions 208 0.0%
jing.chem.Species.getFullName 197 0.0%
jing.chem.ChemGraph.isForbiddenStructure 191 0.0%
jing.chem.GATP.generateThermoData 188 0.0%
jing.rxn.ThirdBodyReaction.toRestartString 179 0.0%
jing.rxn.Structure.toRestartString 178 0.0%
java.util.regex.Matcher.find 171 0.0%
jing.rxnSys.JDASSL.readOutputFile 168 0.0%
jing.chemUtil.Graph.getNodeList 165 0.0%
java.util.regex.Matcher.reset 161 0.0%
java.util.regex.Pattern.matcher 150 0.0%
java.util.regex.Matcher.<init> 150 0.0%
java.util.Formatter$FormatSpecifier.print 150 0.0%
java.util.Formatter$FormatSpecifier.printFloat 147 0.0%
sun.misc.FormattedFloatingDecimal.dtoa 145 0.0%
sun.misc.FormattedFloatingDecimal.<init> 145 0.0%
java.io.FileOutputStream.writeBytes 145 0.0%
java.io.FileOutputStream.write 145 0.0%
sun.nio.cs.StreamEncoder.writeBytes 144 0.0%
jing.rxn.ThirdBodyReaction.toChemkinString 144 0.0%
jing.rxn.TROEReaction.toRestartString 143 0.0%
java.lang.Double.parseDouble 138 0.0%
java.io.Writer.write 136 0.0%
java.io.BufferedWriter.write 136 0.0%
jing.chemUtil.GraphComponent.isSub 135 0.0%
jing.chemUtil.Graph.addMissingHydrogen 135 0.0%
sun.nio.cs.StreamEncoder.write 133 0.0%
sun.nio.cs.StreamEncoder.implWrite 133 0.0%
jing.rxn.Reaction.calculateKeq 133 0.0%
java.util.Stack.push 133 0.0%
java.io.OutputStreamWriter.write 133 0.0%
java.io.BufferedWriter.flushBuffer 133 0.0%
jing.chem.PrimaryThermoLibrary.getThermoData 129 0.0%
jing.rxn.TROEReaction.toChemkinString 115 0.0%
jing.chemUtil.Node.contentSub 114 0.0%
java.lang.UNIXProcess.waitFor 114 0.0%
jing.rxnSys.ReactionModelGenerator.writePDepNetworks 111 0.0%
jing.chemUtil.HierarchyTreeNode.findMatchedPath 110 0.0%
jing.chemUtil.HierarchyTree.findMatchedPath 110 0.0%
jing.chem.ChemGraph.isSubAtCentralNodes 110 0.0%
sun.misc.FloatingDecimal.doubleValue 108 0.0%
jing.chemUtil.Graph.isSubAtCentralNodes 108 0.0%
jing.chem.GATP.getGAGroup 103 0.0%
jing.rxnSys.JDAS.generateLindemannReactionList 96 0.0%
jing.rxnSys.ReactionModelGenerator.writeEdgeSpecies 91 0.0%
jing.rxnSys.RateBasedPDepRME.makeSpeciesIncluded 89 0.0%
jing.rxn.PDepNetwork.makeIsomerIncluded 87 0.0%
jing.chemUtil.GraphComponent.resetStack 80 0.0%
jing.chem.ChemGraph.toString 73 0.0%
java.util.Stack.pop 73 0.0%
jing.rxn.TemplateReactionGenerator.generatePdepReactions 72 0.0%
jing.rxn.ReactionTemplate.reactOneReactant 72 0.0%
jing.rxn.PDepIsomer.generatePaths 72 0.0%
jing.chemUtil.Graph.toStringWithoutCentralID 72 0.0%
jing.chemUtil.GraphComponent.isSubCentralMatched 68 0.0%
jing.chem.Species.equals 63 0.0%
java.util.HashSet.contains 63 0.0%
java.util.HashMap.containsKey 63 0.0%
jing.param.Temperature.<init> 61 0.0%
jing.rxn.PDepReaction.toRestartString 58 0.0%
sun.misc.FloatingDecimal.multPow52 57 0.0%
jing.chemUtil.Graph.getArcList 52 0.0%
java.util.ArrayList.iterator 52 0.0%
jing.chemUtil.Node.toStringWithoutCentralID 50 0.0%
jing.chem.ThermoGAGroupLibrary.findGAGroup 48 0.0%
java.lang.String.<init> 48 0.0%
jing.chem.Species.calculateTransportParameters 42 0.0%
jing.chem.GATransportP.generateTransportData 42 0.0%
jing.chem.ChemGraph.getTransportData 42 0.0%
jing.chem.ChemGraph.generateTransportData 42 0.0%
jing.rxnSys.ReactionModelGenerator.writeRatesAndParameters 39 0.0%
jing.chem.QMTP.successfulGaussianResultExistsQ 37 0.0%
jing.chem.ChemGraph.whichForbiddenStructures 37 0.0%
jing.rxn.ReactionTemplate.findRateConstant 35 0.0%
jing.chem.Species.generateSpectroscopicData 32 0.0%
jing.chem.FrequencyGroups.generateFreqData 32 0.0%
java.util.LinkedList$ListItr.remove 30 0.0%
java.security.AccessController.doPrivileged 30 0.0%
java.lang.Integer.hashCode 30 0.0%
java.util.LinkedList.access$200 29 0.0%
sun.misc.FloatingDecimal.readJavaFormatString 28 0.0%
java.lang.String.valueOf 27 0.0%
java.io.FileWriter.<init> 27 0.0%
java.io.FileOutputStream.<init> 27 0.0%
jing.rxn.StructureTemplate.getMatchedFunctionalGroup 26 0.0%
jing.rxnSys.Chemkin.writeGridOfRateCoeffs 25 0.0%
jing.chemUtil.GraphComponent.addNeighbor 25 0.0%
jing.rxn.ReactionAdjList.react 24 0.0%
jing.chem.Species.generateMolFileString 24 0.0%
java.lang.Integer.toString 24 0.0%
java.lang.Integer.getChars 24 0.0%
jing.chemUtil.Graph.copy 23 0.0%
jing.chemUtil.Arc.addNeighbor 23 0.0%
java.lang.Object.hashCode 23 0.0%
java.io.FileOutputStream.open 23 0.0%
jing.chemUtil.Graph.connect 22 0.0%
jing.chemUtil.Graph.addArcBetween 22 0.0%
jing.chemUtil.Arc.link 22 0.0%
jing.rxnSys.CoreEdgeReactionModel.categorizeReaction 21 0.0%
jing.rxn.LibraryReactionGenerator.dupreaction 20 0.0%
jing.rxn.LibraryReactionGenerator.RemoveDuplicateReac 20 0.0%
jing.rxnSys.Logger.log 19 0.0%
jing.rxnSys.Logger.info 19 0.0%
jing.chem.GATransportP.getGAGroup 19 0.0%
java.util.LinkedList.addAll 19 0.0%
jing.rxnSys.ReactionModelGenerator.printModelSize 18 0.0%
jing.chem.ThermoGAGroupLibrary.findRadicalGroup 18 0.0%
jing.chem.Species.generateResonanceIsomers 18 0.0%
jing.rxnSys.CoreEdgeReactionModel.reactantsInCoreQ 17 0.0%
jing.rxnSys.CoreEdgeReactionModel.containsAsUnreactedSpecies 16 0.0%
jing.rxn.PDepNetwork.getNumCoreReactions 16 0.0%
jing.chem.PrimaryTransportLibrary.getTransportData 16 0.0%
jing.chem.ChemElement.make 15 0.0%
java.util.LinkedList.<init> 15 0.0%
jing.rxnSys.SystemSnapshot.getSpeciesStatus 14 0.0%
jing.rxn.TemplateReaction.makeTemplateReaction 14 0.0%
jing.chemUtil.Graph.combine 14 0.0%
java.util.HashMap.transfer 14 0.0%
java.util.HashMap.resize 14 0.0%
java.util.HashMap.addEntry 14 0.0%
java.io.PrintStream.println 14 0.0%
jing.rxnSys.JDAS.setupInputFile 13 0.0%
jing.rxnSys.JDAS.generateSpeciesStatus 13 0.0%
jing.rxn.PDepReaction.toChemkinString 13 0.0%
jing.chemUtil.Graph.getNodeNumber 13 0.0%
jing.chem.TransportGALibrary.findGroup 13 0.0%
jing.chem.ThermoGAGroupLibrary.findGaucheGroup 13 0.0%
jing.chem.ChemElement.translateName 13 0.0%
java.io.PrintStream.write 13 0.0%
java.io.BufferedOutputStream.flushBuffer 13 0.0%
sun.nio.cs.StreamEncoder.implFlushBuffer 12 0.0%
sun.nio.cs.StreamEncoder.flushBuffer 12 0.0%
java.io.OutputStreamWriter.flushBuffer 12 0.0%
java.io.BufferedOutputStream.flush 12 0.0%
jing.rxnSys.CoreEdgeReactionModel.containsAsReactedSpecies 11 0.0%
jing.rxn.Structure.hashCode 11 0.0%
jing.rxn.PDepReaction.toStringWithRate 11 0.0%
jing.rxn.StructureTemplate.identifyReactedSites 10 0.0%
jing.rxn.FastMasterEqn.writeInputString 10 0.0%
jing.chemUtil.Node.getOtherNode 10 0.0%
jing.chemUtil.Graph.setCentralNode 10 0.0%
jing.chemUtil.Graph.identifyAllOrderedMatchedSites 10 0.0%
jing.chemUtil.Graph.getCycleNumber 10 0.0%
jing.chemUtil.Arc.neighborOk 10 0.0%
jing.chemUtil.Arc.getOtherNode 10 0.0%
jing.chem.ChemGraph.resetThermoSite 10 0.0%
jing.chem.ChemGraph.identifyReactionMatchedSite 10 0.0%
jing.chem.ChemGraph.getSymmetryNumber 10 0.0%
jing.chem.ChemGraph.getCycleNumber 10 0.0%
java.util.HashSet.add 10 0.0%
java.util.Arrays.copyOfRange 10 0.0%
java.lang.StringBuilder.toString 10 0.0%
I mean that it spends a large majority of the CPU time, not generating reaction mechanisms, but checking that the reaction systems that have been converged for the last 100 iterations are still converged on the 101st iteration, which, by my observations, they usually are. Perhaps something like 'once a system has been valid for two iterations in a row, stop checking it until everything is valid (or N iterations have passed), then check them all again' would be safe?
A follow-up analysis on Richard's work, that will systematically expanded to more features, such as Pdep, QMTP, restart,etc...
Introduction: RMG-Java, at commit 8574cb8a6cbb5a250648de79921c552e2d3d4158 is used. The GUI plugin for Eclipse called “JVM Monitor” is used for the CPU Profiling. CPU Sampling technique is used.
Settings: A simulation of JP10 (C10H16) pyrolysis for 1 reaction system (1 set of conditions) without QMTP, without P-Dep activated, with one small seed mechanism, without pruning, without reading restart. A Intel Core 2 Duo CPU P9600 @ 2.66Ghz is used for this purpose. This is the state of the RMG generated model: The model core has 172 reactions and 73 species. The model edge has 43345 reactions and 4459 species. The chem.inp file has 73 species (excluding inert gases). The chem.inp file has 172 reactions (excluding duplicates). Running time: 35.795 min Memory used: 251.22 MB / 259.52 MB (96.80%)
Results After 3.5 K seconds of sampling at 50ms of all the RMG core packages, the following order of total method invocation time is observed at ReactionModelGenerator.modelGeneration as base method: • 78% : ReactionModelGenerator.enlargeReactionModel • 3% : ReactionSystem.solveReactionSystem • 13% : ReactionModelGenerator.writeEdgeReactions • 5% : ReactionModelGenerator.writeEdgeSpecies
In ReactionModelGenerator.enlargeReactionModel the majority (69% ) of the time is spent in ReactionTemplate.reactTwoReactants. The majority in that method is spent to species comparison during the creation of a new species: ChemGraph.equals(): 21% (SpeciesDictionary.getSpecies() + 5% (SpeciesDictionary.putSpecies()). Another great portion is the initialization of a chemgraph (ChemGraph.init()) ( 20 %) in the ChemGraph.make() method. 13% abs. is consumed by the verification to check for a forbidden structure.
Conclusion: for large molecules for which many possible reaction possibilities exist, writing the edge reactions/species already becomes an important bottleneck and consumes roughly 20% of the CPU.
ps: all % are absolute, compared to the total CPU time (3.5K sec)
Check the snapshot i took in Eclipse from the JVM monitor: http://cloud.github.com/downloads/nickvandewiele/RMG-Java/CPU%20profiling.bmp
On second thoughts, the observations I made are significantly different from what @rwest saw during his trial. The main differences at Richard's run are the larger profiling time (> 4h compared to my < 1h), Pdep on and the large seed. I started with Leeds methane combustion. I am not sure if the profiling application influences these results, but that might be a culprit too.
Very interesting, thanks Nick. I had some ideas for potential opportunities for speedup, which I put on a new branch: https://github.com/GreenGroup/RMG-Java/commit/a75660378885f95a1a9ec55e2d0dc164b881db5a Haven't gotten around to testing them yet, but I'll update this issue if the potential changes are useful/safe.
Another possible difference: I had 32 reaction systems (this is partly why it spent a long time simulating them)