Long waiting during Result set building, leading to TimeoutE

Hello,

I am running some superstructure searches on a table called patterns. I use JchemWebServices 6.2 (the latest version). I have had a serious problem running some really large compounds.

One query example is: 

CCCCCCCCCCCCCCCCCC(=O)NCC(C(/C=C/CCCCCCCCCCCCC)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O[C@@H]2[C@H]([C@@H]([C@@H]([C@@H](O2)CO)O[C@@H]3[C@H]([C@@H]([C@@H]([C@@H](O3)CO)O)O[C@@H]4[C@H]([C@@H]([C@@H]([C@@H](O4)CO)O)O[C@]5(C[C@@H]([C@H]([C@@H](O5)C(C(O)O[C@]6(C[C@@H]([C@H]([C@@H](O6)C(C(CO)O)O)N)O)C(=O)O)O)N)O)C(=O)O)O)NC(=O)C)O[C@]7(C[C@@H]([C@H]([C@@H](O7)C(C(CO)O)O)N)O)C(=O)O)O)O)O

The search returns 149 hits. However, JchemWebServices takes a lot to build the result set. I am not sure why. It takes about 100 s with almost 100% CPU, as shown on the following line:

           c.j.w.MoleculeResultsetBuilder - HitResolvers completed in: 100.1 s

 

It took about 18 s to find 149 hits. 

18:00:02.063 [partitionExecutor-7] DEBUG c.j.w.m.jchem.JChemHitResolverSQL - JChemHitResolverSQL process for 149 hits: 21.08 ms

I am not sure if the searching operation is done at this point. You can find a part of the log is attached to the email.

 

Could you please check and help me out here?

Thank you in advance.

MrYan

 

Hi Yannick,

Thanks for the detailed report. We are investigating your issue.
Am I understand it right, the same query took only 18 sec on a previous version of the web services? 

Regards,
Peter

Hi Peter,

No, it did not take 18s on a previous version.

The following line in the file I attached tells me that 149 hits were found after 21.08 ms(actually not 18 s ).

18:00:02.063 [partitionExecutor-7] DEBUG c.j.w.m.jchem.JChemHitResolverSQL - JChemHitResolverSQL process for 149 hits: 21.08 ms

Wether the superstructure search process was over, I do not know. It also takes forever when I use the API.

I've got to say that I do not had issues with the same compound on a previous version of JChemWebServices though.

 

Thanks,

 

MrYan

Hi Yannick,

We found the cause in the web services and the superstructure search performance will be improved in the next minor version. (Displaying search results is very resource demanding method in this case, search will be still slow if you want to generate the highlighted hits, but your concrete example will be much faster.)
 
Regards,
Peter 

Thanks a lot,

Please let me know as soon as you have released the new version.

Regards,

 

MrYan

Hello,

 

Has the problem mentioned in my previous email been solved? PLease let me know.

Regards,

 

MrYan

Hi MrYan,

JChem Web Services 6.3.0 version is now available for download:
http://www.chemaxon.com/download/jchem-suite/#jcws />
It contains  many stability and performance fixes.

Regards,
Peter