Hello,
>The first thing I'd suggest is to take the same code and write a simple
>wrapper outside of the database context, a test program that you can run
>against a few hundred molecules, and verify that it's growing. If it >seems to
>be leaking, use valgrind(1) to track down the problem. Valgrind is amazing.
yes, I’ll try that next. Since I cannot see that behavior e.g. with SVG
conversion, it is something special to _PNG2.
>Some databases (Postgres, I don't know about MySQL or Alice) strongly
>recommend that you use their built-in allocator rather than using malloc. It
>makes it difficult to link in code like OpenBabel. Postgres is >written in C,
>and OpenBabel in C++. I've had so many problems trying to get OpenBabel to
>behave inside of a Postgres executable that I gave up and now use OpenBabel in
>a Fast-CGI wrapper to provide a scalable, >parallelizable
>remote-procedure-call mechanism that I can access from Perl, PHP, C or C++.
Hm, I’m doing this for ten years now and this is the first time OpenBabel is
making real trouble. While it is true that you must use palloc() instead of
malloc() for _database_ objects that are returned from a _database_ function,
mainly because your code has no control over them afterwards so you cannot
free() them programmatically, malloc and palloc coexist just fine as long as
you don’t mix them! The code shown lives in a C++ wrapper I have to use because
- PostgreSQL has no C++ API.
>As much as I like OpenBabel, it's not reliable enough to trust inside the
>executable of a database. It's a good way to corrupt your entire database and
>lose everything. If your database has a public web site, you're >giving the
>public a loaded gun.
I cannot confirm that. While OpenBabel does strange things sometimes, it never
threatened my Databases. ☺ During my dissertation I’ve put literally millions
of structures through PostgreSQL+OpenBabel and many more since then. So I
became pretty confident in the two. But I’m not running eMolecules for a living
either… ☺
best regards,
Ernst-Georg
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