application is silently dying on transform or gives access violaiton exception

[Karen Karapetyan]

Weird issue and hard to catch. In my application I get indigo exception below (both under debugger and from command line, Win7, 64 bit, VS2012).

AccessViolationException was unhandled

Attempted to read or write protected memory. This is often an indication that other memory is corrupt.

   at com.ggasoftware.indigo.Indigo.transform(IndigoObject reaction, IndigoObject monomer)

I tried to separate a sequence of events in the code to reproduce this under debugger but can't do it.

Can you provide me with indigo version that would spit out more debugging info?

Ken 

[Mikhail Rybalkin]

Hello Ken,

We will try to resolve this but can you answer the following questions:

Does it happen frequently? Do you use a specific transformation or a set of transformations? Can it happen because of parallel execution? 

Mikhail

[Kenneth (Karen) Karapetyan]

Hi, Mikhail,

In my application it happens every time (both under debugger and when running from command line). Basically I apply 50+ transformations to each molecule in sdf file. My app fails on very first record and always on specific reaction. However, when I separate reactions and molecule into unit test it works fine. 

Ken

Thanks,
Ken

phone: (240) 205-2004

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[Mikhail Rybalkin]

Hi Ken,

Can you share your transformations so that we can run tests on them?

Best regards,

Mikhail

[Karen Karapetyan]

Here are the part of transformations that I use. My app throws accessviolation on the last reaction  (molecule is irrelevant)

System.AccessViolationException: Attempted to read or write protected memory. Th

is is often an indication that other memory is corrupt.

   at com.ggasoftware.indigo.Indigo.transform(IndigoObject reaction, IndigoObject monomer)

Here are my test with transformations:

[N-,P-,As-,Sb-,O-,S-,Se-,Te-:1][C:2]=[N+,P+,As+,Sb+,O+,S+,Se+,Te+:3]>>[N,P,As,Sb,O,S,Se,Te:1]=[C:2][N,P,As,Sb,O,S,Se,Te:3]

[O-,S-,Se-,Te-:1][P+;D4:2][O-,S-,Se-,Te-:3]>>[O,S,Se,Te:1]=[P;D5:2][O-,S-,Se-,Te-:3]

[F-,Cl-,Br-,I-,At-:1]=[O:2]>>[F,Cl,Br,I,At:1][O-:2]

[S-;v7:1]=[O:2]>>[S:1][O-:2]

[Se-;v7:1]=[S,O:2]>>[Se:1][S-,O-:2]

[Te-;v7:1]=[Se,S,O:2]>>[Te:1][Se-,S-,O-:2]

[*:1][C+,S+:2]([N:3][*:4])[N:5]([H:6])[*:7]>>[*:1][C,S:2]([N:3][*:4])=[N+:5]([H:6])[*:7]

[*:1][P+:2]([*:7])([N:3][*:4])[N:5]([H:6])[*:7]>>[*:1][P:2]([*:7])([N:3][*:4])=[N+:5]([H:6])[*:7]

[C;v2:1][N,P,As:2]=[O,S,Se,Te:3]>>[C:1]#[N,P,As:2]=[O,S,Se,Te:3]

[C;v2:1][N,P,As:2]=[O,S,Se,Te:3]>>[C:1]#[N,P,As:2]=[O,S,Se,Te:3]

[O,S,Se,Te:1]=[O+,S+,Se+,Te+:2][C-;v3:3]>>[O,S,Se,Te:1]=[O,S,Se,Te:2]=[C:3]

[O-,S-,Se-,Te-:1][O+&v3,S+&v3,Se+&v3,Te+&v3:2]>>[O,S,Se,Te:1]=[O,S,Se,Te:2]

[O-,S-,Se-,Te-:1][O,S,Se,Te:2][C+;v3]>>[O,S,Se,Te:1]=[O,S,Se,Te:2]=[C]

[N&v3,P&v3,As&v3,Sb&v3:1]#[N&v4,P&v4,As&v4,Sb&v4:2]>>[N-,P-,As-,Sb-:1]=[N+,P+,As+,Sb+:2]

[N-,P-,As-,Sb-:1]=[O+&v3,S+&v3,Se+&v3,Te+&v3:2]>>[N,P,As,Sb:1]#[O,S,Se,Te:2]

[N-,P-,As-,Sb-:1]=[C+;v3:2]>>[N,P,As,Sb:1]#[C:2]

[P+&X4,As+&X4,Sb+&X4:1][O-,S-,Se-,Te-:2]>>[P,As,Sb:1]=[O,S,Se,Te:2]

[N+&v4,P+&v4,As+&v4,Sb+&v4:1][C-;v3:2]>>[N,P,As,Sb:1]=[C:2]

[N+&v4,P+&v4,As+&v4,Sb+&v4:1]=[C-;v3:2]>>[N,P,As,Sb:1]#[C:2]

[N+&v4,P+&v4,As+&v4,Sb+&v4:1][N-&v2,P-&v2,As-&v2,Sb-&v2:2]>>[N,P,As,Sb:1]=[N,P,As,Sb:2]

[O+&v3,S+&v3,Se+&v3,Te+&v3:1][C-&v3:2]>>[O,S,Se,Te:1]=[C:2]

[O+&v3,S+&v3,Se+&v3,Te+&v3:1]=[C-&v3:2]>>[O,S,Se,Te:1]#[C:2]

[O+&v3,S+&v3,Se+&v3,Te+&v3:1][N-&v2,P-&v2,As-&v2:2]>>[O,S,Se,Te:1]=[N,P,As:2]

[N-&v2,P-&v2,As-&v2,Sb-&v2:1][O:2][C+&v3:3]>>[N,P,As,Sb:1]=[O:2]=[C:3]

[C-&v3:1][N,P,As,Sb:2]([*:3])[C+&v3:4]>>[C:1]=[N,P,As,Sb:2]([*:3])=[C:4]

[C-&v3:1][N,P,As,Sb:2]=[C+&v3:3]>>[C:1]=[N,P,As,Sb:2]#[C:3]

[C;v4:1]=[N,P,As,Sb:2][C;v2:3]>>[C:1]=[N,P,As,Sb:2]#[C:3]

[*:1][N,P,As,Sb:2](=[O,S,Se,Te:3])=[O,S,Se,Te:4]>>[*:1][N+,P+,As+,Sb+:2]([O-,S-,Se-,Te-:3])=[O,S,Se,Te:4]

[n:1]=[O:2]>>[n+:1][O-:2]

[*,H:1][N:2]=[N:3]#[N:4]>>[*,H:1][N:2]=[N+:3]=[N-:4]

[*:1]=[N:2]#[N:3]>>[*:1]=[N+:2]=[N-:3]

[!O:1][S+0;X3:2](=[O:3])[!O:4]>>[!O:1][S+1;X3:2]([O-:3])[!O:4]

[H:1][S:2][c:3]1[n:8][c:7]([H,*:13])[n:6][c:5]2[c:4]1[n:11][c:10]([H,*:12])[n:9]2>>[H:1][N:8]1[C:7]([H,*:13])=[N:6][C:5]2=[C:4]([N:11]=[C:10]([H,*:12])[N:9]2)[C:3]1=[S:2]

[H:1][#7:8]-1-[#6:7](-[*:9])=[#7:6]-[#6:5]-2=[#6:4]-1-[#6:12](=[S:13])-[#7:11]-[#6:10](-[*:2])=[#7:3]-2>>[H:1][#7:8]-1-[#6:7](-[*:9])=[#7:6]-[#6:5]-2=[#6:4]-1-[#7:3]=[#6:10](-[*:2])-[#7:11]-[#6:12]-2=[S:13]

[H:1][S:9][C:6]1=[N:5][C:4]([H,*:12])=[C:3]([H,*:11])[C:8](=[O:10])[N:7]1[H:2]>>[H:1][N:5]1[C:4]([H,*:12])=[C:3]([H,*:11])[C:8](=[O:10])[N:7]([H:2])[C:6]1=[S:9]

[H:2][O:10][C:8]1=[N:7][C:6](=[S:9])[N:5]([H:1])[C:4]([H,*:12])=[C:3]1[H,*:11]>>[H:1][N:5]1[C:4]([H,*:12])=[C:3]([H,*:11])[C:8](=[O:10])[N:7]([H:2])[C:6]1=[S:9]

[H:2][O:3][c:4]1[n:5][c:6]([S:7][H:1])[n:8][c:9]([H,*:10])[c:11]1[H,*:12]>>[H:1][N:8]1[C:9]([H,*:10])=[C:11]([H,*:12])[C:4](=[O:3])[N:5]([H:2])[C:6]1=[S:7]

[H:23][C:13]1([H,*:25])[C:12](=[O:24])-[C:11](-[H,*:26])[C:10]2([H,*:27])[C:9]([H,*:28])([H,*:29])[C:8]3([H,*:30])[C:17]([H:21])([C:18](=[O:19])-[C:1]-4=[C:6](-[C:5](-[H,*:33])=[C:4](-[H,*:34])-[C:3](-[H,*:35])=[C:2]-4-[H,*:36])[C:7]3([H,*:32])[H,*:31])[C:16](=[O:20])[C:15]2([H,*:37])[C:14]1=[O:22]>>[H:23][O:24]-[C:12]-1=[C:13](-[H,*:25])-[C:14](=[O:22])[C:15]2([H,*:37])[C:16](-[O:20][H:21])=[C:17]3-[C:18](=[O:19])-[C:1]-4=[C:6](-[C:5](-[H,*:33])=[C:4](-[H,*:34])-[C:3](-[H,*:35])=[C:2]-4-[H,*:36])[C:7]([H,*:32])([H,*:31])[C:8]3([H,*:30])[C:9]([H,*:29])([H,*:28])[C:10]2([H,*:27])[C:11]-1-[H,*:26]

[Mikhail Rybalkin]

Hello Ken,

Thank you for these examples! We tested our development version on them, and there are no issues anymore, while our tests fails with Indigo 1.1.11. 

Can you check this version and confirm that it works fine?

Universal: http://ggasoftware.com/accept?file=indigo-1.1.12dev%2Findigo-dotnet-1.1.12dev-universal.zip

Windows: http://ggasoftware.com/accept?file=indigo-1.1.12dev%2Findigo-dotnet-1.1.12dev-win.zip

If everything is fine we make a new release.

Best regards,

Mikhail

[Karen Karapetyan]

I did test the universal dev version and I no longer encounter the issue. Great!!

Hope to see 1.1.12 released soon as we were not able to update from 1.1.10 due to 1.1.11 issues.

Ken

[Mikhail Rybalkin]

Hello Ken,

Thank you for send us report for the transformation method. Your issue with access violation has been fixed in Indigo 1.1.12. Could you confirm that you cannot reproduce this bug?

Mikhail

[Kenneth Karapetyan]

so far it is working fine. Thanks.

Ken

Thanks,
Ken

phone: (240) 205-2004

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