GC overhead limit exceeded and some transport groups are not found

[rajeshdparmar]

One of the runs with "PM3 and Pdep OFF" has given memory error. Also it is showing some of the transport groups are not found. This was running for last few weeks. Heap dump file is created so it may be useful.

File location:

~/Rajesh/New_jobs/MultiT_Prun_15000$

Error Message:

--> C14H13O2JJJ(2511217)
Warning: Transport group not found: 2
Created new species: C14H13O2JJJ(2511218)
Ea raised by 10.2 from 5.2 to dHrxn(298K)=15.4 kcal/mol.
Created new R_Addition_MultipleBond reaction: C6H5O2J(626926) + C8H8JJ(1204506) --> C14H13O2JJJ(2511218)
Ea raised by 2.6 from 5.2 to dHrxn(298K)=7.8 kcal/mol.
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Created new species: C14H13O2JJJ(2511219)
Ea raised by 3.9 from 5.2 to dHrxn(298K)=9.1 kcal/mol.
Created new R_Addition_MultipleBond reaction: C6H5O2J(626926) + C8H8JJ(1204506) --> C14H13O2JJJ(2511219)
Ea raised by 2.6 from 5.2 to dHrxn(298K)=7.8 kcal/mol.
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Created new species: C14H13O2JJJ(2511220)
Ea raised by 3.9 from 5.2 to dHrxn(298K)=9.1 kcal/mol.
Created new R_Addition_MultipleBond reaction: C6H5O2J(626926) + C8H8JJ(1204506) --> C14H13O2JJJ(2511220)
Ea raised by 3.4 from 5.2 to dHrxn(298K)=8.6 kcal/mol.
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Created new species: C14H13O2JJJ(2511221)
Ea raised by 4.7 from 5.2 to dHrxn(298K)=9.9 kcal/mol.
Created new R_Addition_MultipleBond reaction: C6H5O2J(626926) + C8H8JJ(1204506) --> C14H13O2JJJ(2511221)
Ea raised by 3.4 from 5.2 to dHrxn(298K)=8.6 kcal/mol.
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 2
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Warning: Transport group not found: 21
Created new species: C14H13O2JJJ(2511222)
Ea raised by 4.7 from 5.2 to dHrxn(298K)=9.9 kcal/mol.
Created new R_Addition_MultipleBond reaction: C6H5O2J(626926) + C8H8JJ(1204506) --> C14H13O2JJJ(2511222)
Created new species: C14H13O2JJJ(2511223)
Created new R_Addition_MultipleBond reaction: C8H8JJ(1204506) + C6H5O2J(626926) --> C14H13O2JJJ(2511223)
java.lang.OutOfMemoryError: GC overhead limit exceeded
Dumping heap to java_pid29301.hprof ...
Heap dump file created [13881007472 bytes in 180.851 secs]
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
        at java.util.ArrayList.iterator(ArrayList.java:737)
        at jing.chemUtil.Graph.getArcList(Graph.java:1150)
        at jing.chemUtil.Graph.resetMatchedGC(Graph.java:1984)
        at jing.chemUtil.Graph.isSubAtCentralNodes(Graph.java:1646)
        at jing.chem.ChemGraph.isSubAtCentralNodes(ChemGraph.java:2234)
        at jing.chem.ChemGraph.isSubAtCentralNodes(ChemGraph.java:2179)
        at jing.chemUtil.HierarchyTreeNode.findMatchedPath(HierarchyTreeNode.java:182)
        at jing.chemUtil.HierarchyTreeNode.findMatchedPath(HierarchyTreeNode.java:191)
        at jing.chemUtil.HierarchyTreeNode.findMatchedPath(HierarchyTreeNode.java:191)
        at jing.chemUtil.HierarchyTreeNode.findMatchedPath(HierarchyTreeNode.java:191)
        at jing.chemUtil.HierarchyTree.findMatchedPath(HierarchyTree.java:87)
        at jing.chem.ThermoGAGroupLibrary.findGAGroup(ThermoGAGroupLibrary.java:232)
        at jing.chem.GATP.getGAGroup(GATP.java:177)
        at jing.chem.GATP.generateThermoData(GATP.java:95)
        at jing.chem.ChemGraph.generateThermoData(ChemGraph.java:1317)
        at jing.chem.ChemGraph.getThermoData(ChemGraph.java:1828)
        at jing.chem.Species.findStablestThermoData(Species.java:344)
        at jing.chem.Species.(Species.java:117)
        at jing.chem.Species.make(Species.java:877)
        at jing.rxn.ReactionTemplate.reactTwoReactants(ReactionTemplate.java:1196)
        at jing.rxn.TemplateReactionGenerator.react(TemplateReactionGenerator.java:219)
        at jing.rxnSys.RateBasedRME.enlargeReactionModel(RateBasedRME.java:164)
        at jing.rxnSys.ReactionModelGenerator.enlargeReactionModel(ReactionModelGenerator.java:3894)
        at jing.rxnSys.ReactionModelGenerator.modelGeneration(ReactionModelGenerator.java:1464)
        at RMG.main(RMG.java:96)

[rwest]

Oooh - a 13 GB heap dump file - that's going to be interesting to analyze! We may need to use the new server. Hang on to it for now. @gmagoon, do you want to take http://www.eclipse.org/mat/ for a spin on your new 96GB machine, and see where we're leaking memory?

[rajeshdparmar]

It will be really good if we can solve this problem. I realized that if I use conversion criteria 0.9999 then I get around 3999 core reaction but reaction time is in milliseconds. However my actual reaction time is 0.3 to 0.6 sec. So when I use these 3999 reactions for simulation, I get around 3% of C7 to C13 species which otherwise should decompose to give smaller hydrocarbons at high temperature and at higher residence time. This gives a good mismatch between predicted vs experimental data. So for me an ideal solution is the one that is obtained by 0.6 s criteria.

[rwest]

We should return something useful for transport estimates.