Comments (10)
This is still not working.
On Josh's branch at commit
125a79b
http://github.com/jwallen/RMG-Java/tree/125a79
we still run out of memory
Settings:
DynamicSimulator: DASSL
TimeStep: AUTOPRUNE
TerminationTolerance: 1E30
PruningTolerance: 1.0E-18
MinSpeciesForPruning: 1000
MaxEdgeSpeciesAfterPruning: 30000
As you can see, it is not pruning down to 30k species:
bfm_stijn]$ grep pruning RMG.log The number of species in the model's edge, after pruning: 521 The number of species in the model's edge, before pruning: 3033 The number of species in the model's edge, after pruning: 3010 The number of species in the model's edge, before pruning: 3563 The number of species in the model's edge, after pruning: 3540 The number of species in the model's edge, before pruning: 3721 The number of species in the model's edge, after pruning: 3698 The number of species in the model's edge, before pruning: 4849 The number of species in the model's edge, after pruning: 4826 The number of species in the model's edge, before pruning: 5782 The number of species in the model's edge, after pruning: 5759 The number of species in the model's edge, before pruning: 6286 The number of species in the model's edge, after pruning: 6266 The number of species in the model's edge, before pruning: 6901 The number of species in the model's edge, after pruning: 6881 The number of species in the model's edge, before pruning: 7657 The number of species in the model's edge, after pruning: 7635 The number of species in the model's edge, before pruning: 8043 The number of species in the model's edge, after pruning: 8017 The number of species in the model's edge, before pruning: 10365 The number of species in the model's edge, after pruning: 10339 The number of species in the model's edge, before pruning: 11681 The number of species in the model's edge, after pruning: 11659 The number of species in the model's edge, before pruning: 13441 The number of species in the model's edge, after pruning: 13418 The number of species in the model's edge, before pruning: 14973 The number of species in the model's edge, after pruning: 14952 The number of species in the model's edge, before pruning: 16096 The number of species in the model's edge, after pruning: 16077 The number of species in the model's edge, before pruning: 17307 The number of species in the model's edge, after pruning: 17240 The number of species in the model's edge, before pruning: 18391 The number of species in the model's edge, after pruning: 18376 The number of species in the model's edge, before pruning: 19994 The number of species in the model's edge, after pruning: 19979 The number of species in the model's edge, before pruning: 21575 The number of species in the model's edge, after pruning: 21553 The number of species in the model's edge, before pruning: 22672 The number of species in the model's edge, after pruning: 22655 The number of species in the model's edge, before pruning: 23528 The number of species in the model's edge, after pruning: 23505 The number of species in the model's edge, before pruning: 24823 The number of species in the model's edge, after pruning: 24805 The number of species in the model's edge, before pruning: 27016 The number of species in the model's edge, after pruning: 26959 The number of species in the model's edge, before pruning: 29355 The number of species in the model's edge, after pruning: 29319 The number of species in the model's edge, before pruning: 32774 The number of species in the model's edge, after pruning: 31669 The number of species in the model's edge, before pruning: 31980 The number of species in the model's edge, after pruning: 31738 The number of species in the model's edge, before pruning: 34223 The number of species in the model's edge, after pruning: 34004 The number of species in the model's edge, before pruning: 35491 The number of species in the model's edge, after pruning: 35237 The number of species in the model's edge, before pruning: 37562 The number of species in the model's edge, after pruning: 37329 The number of species in the model's edge, before pruning: 38735 The number of species in the model's edge, after pruning: 38473 The number of species in the model's edge, before pruning: 41671 The number of species in the model's edge, after pruning: 41464 The number of species in the model's edge, before pruning: 44865 The number of species in the model's edge, after pruning: 44656 The number of species in the model's edge, before pruning: 47356 The number of species in the model's edge, after pruning: 47106 The number of species in the model's edge, before pruning: 50701 The number of species in the model's edge, after pruning: 50417 The number of species in the model's edge, before pruning: 51693 The number of species in the model's edge, after pruning: 51496
logs currently on monch in ~/RMGruns/bfm_stijn
from rmg-java.
It looks like at most 922 species are elligible for pruning as of the last iteration based on the number of edge species being tracked.
from rmg-java.
OK, I think I've narrowed down the issue. If you look at the lines with DEBUG at the beginning (the reactions where RMG thinks the reactants are not in the core; I estimate there are about 6700 such reactions at the the last iteration before running out of memory), they all seem to involve a small molecule (probably a seed species). Also, I noticed that Stijn is using "GenerateReactions: no" . For some reason, it seems that RMG does not recognize these species as being in the core, even though in at least some cases, they should be recognized as such. Is there some reason to expect that these seed mechanism species would not be part of the core?
(Also I should clarify that although I may have stated earlier that the reaction set has both forward and reverse reactions; this is not correct, it only has one of them, but it seems to be the direction taking core to edge (cf. appendUnreactedSpeciesStatus in ReactionSystem.java))
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Another (probably unrelated) issue: Stijn's output contains many of the following type lines:
Warning: Attempted to read unreacted species flux for C10H14O5(55713), but there are only 54444 fluxes.
This is produced by RateBasedPDepRME and appears to reflect a mismatch between unreactedSpeciesFlux.length and the maximum species ID number.
from rmg-java.
The issue with the DEBUG lines turns out to be a non-issue, I think: RMG was iterating through all Pdep reactions (core and edge) and was identifying reactions that had no edge species. The unrelated issue of mismatch between unreactedSpeciesFlux.length and the maximum species ID number still remains, as far as I know. JWA and I think we have pinpointed the source of the bug that Stijn is observing and JWA has developed and implemented a fix which he will soon push for testing.
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Post-mortem analysis: I failed to incorporate the changes in eee9ce6 (in particular the change to getLeakFlux) into the code for writing auto edge reaction info. This is also likely the source of Issue #114 (http://github.com/GreenGroup/RMG-Java/issues#issue/114)
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the pruning seems to be working fine! It is keeping the amount of species in the model edge at 30000 and pruning some 1000 species on average every time it prunes.
from rmg-java.
This should be fixed now.
from rmg-java.
Clarification...this is fixed on PDepRMEMods branch...I've reopened and we can close once we bring it to master
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Merge branch 'PDepRMEMods' per discussion between grm, jwa, rhw
Conflicts:
source/RMG/jing/rxnSys/JDAS.java
closed by 61872e8 (temporarily)
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Related Issues (20)
- Populate reactions module does not read in reaction library rates
- No consistency check on thermo group adjlists
- RMG errors with new families HOT 1
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- Program hangs when running the make test example (waiting for GATPFit) HOT 10
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- Populate Reactions finds different rate from RMG job when there are multiple rate rules HOT 1
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- RMG Database Editor not present HOT 2
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- Seed mechanism, generateReactions on vs off
- RMGVE (viewer/editor GUI) should be available for download HOT 1
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