error messages with Bingo on Postgres 9.0

[Joanna Sharman]

Hi,

I've installed the Bingo cartridge 64 bit version on my Linux server
running Postgres 9.0.

I've been getting error messages for substructure searches with
certain molecules and I'm not sure what the cause is. Is it a problem
with my set-up, system, SMILES or a genuine bug?

Here are 2 examples:

EXAMPLE 1

select count(ligand_id) from ligand_structure where nonisomeric_smiles
@ ('CCCCCNC(C)=O', '')::bingo.sub;
ERROR: error: molecule search engine: Error while searching a
molecule: array: invalid index 536872524 (size=30210)

The same SMILES with the TAU property gives:

select count(ligand_id) from ligand_structure where nonisomeric_smiles
@ ('CCCCCNC(C)=O', 'TAU')::bingo.sub;
ERROR: error: molecule search engine: Error while searching a
molecule: CMF loader: cannot decode bond: code 35

EXAMPLE 2

If I run this next query immediately after the above query I see this
error:

select count(ligand_id) from ligand_structure where nonisomeric_smiles
@ ('Clc1cc2CCCCc2cc1Cl', '')::bingo.sub;
ERROR: error: molecule search engine: Error while searching a
molecule: CMF loader: cannot decode bond: code 6

If I wait some time, it runs OK.

The weird thing is the errors are not consistently reproducible
either.

Hope you can help.

Many thanks,

Joanna

[Michael Kvyatkovskiy]

Hello,

It looks like there is a bug in shared memory management. I'm trying
to reproduce your error, but haven't suссeeded yet. However I have
reproduced a similar error which might be caused by the same bug. We
will try to fix it.

Also we are going to add a possibility of outputting of ID's of the
molecules that produce errors. If such feature will be implemented,
would you be able to send us molecules, that produced your error?

Best regards,
Mikhail Kvyatkovskiy.

[joanna....@gmail.com]

Hi Mikhail,

Many thanks for looking into this. If it's possible to identify the molecules that produce the errors I can certainly send them to you.

I suspected a memory-related error, because some queries that produce these errors do work on other occasions, especially when first run.

Regards,

Joanna

[Mihail Kvyatkovskiy]

Hello Joanna,

 

We finally could reproduce the bug on our test data set. We will try to fix it as soon as possible.

 

Best regards,

Mikhail Kvyatkovskiy.

[Savelyev Alexander]

Dear Joanna,

We have figured out, that the issue can be related to a hung PostgreSQL process. Bingo cartridge is in beta testing at the moment. There are some important tasks to be done, e.g. if you cancel a query in PgAdmin, the cancellation may be handled not properly. I suspect, the bug was called by the following reason: there was an error which resulted a PostgreSQL process hanging. After that, you updated the bingo library (a newer version) and launched the given query. The PostgreSQL memory management system may not load user libraries or load it with unexpected effects if a hung process exists.
Anyway, the easy solution for the issue is the database restart. Please, could you restart your PostgreSQL database and retry the given queries. Let us know about a success or a fail. Such a solution is the temporary solution. We will try to resolve the issue in a more accurate way in the nearest future.


With best regards,
Alexander