On Tue, May 27, 2014 at 6:51 AM, Craig James <cja...@emolecules.com> wrote:
> Jeff,
>
>
> On Mon, May 26, 2014 at 5:34 PM, Jeff Janes <jeff.ja...@gmail.com> wrote:
>
>> I've succeeded in building Chemistry::OpenBabel, but only with great
>> difficulty and a lot of random flailing around. I decided to go back and
>> take it step by step to figure out what is going on.
>>
>
> Even after compiling it, I was never able to get anything to link and work
> correctly. I encountered the same set of problems when I tried to link
> OpenBabel into an extension to the Postgres database, which (like Perl) is
> also written in C. In both cases, when the main program is written in C, it
> fails proper execution of C++ initializers in OpenBabel's dynamically
> linked file-format modules.
>
I've not had those problems that I know of. What are the symptoms you see?
After getting it to compile and install (and playing around with
LD_LIBRARY_PATH or /etc/ld.so.conf so that it can find the .so files) it
pretty much worked. But I also haven't used many of the features, mostly
just ReadString, WriteString, GetMolWt, and GetExactMass, so maybe that is
why I don't encounter problems. Also I never reuse a
"Chemistry::OpenBabel::OBMol" object, but always create a new one each
time--I don't recall exactly why I adopted that policy, and now when I do
reuse them it seems to work.
I use it from PostgreSQL just by writing plperl wrappers which in turn use
Chemistry::OpenBabel.
>
> I never had the time nor the expertise to investigate and solve all the
> compiler/linker/dynaloader issues. I just needed something that works year
> after year. If you get Chemistry::OpenBabel to compile, link and actually
> execute, that would be a good thing.
>
I think the first step is to get a script to build cleanly on a common
platform that anyone can use, and then try to figure out how to simplify it
and make it work on other platforms. Right now I'm using Amazon Linux but
I'm thinking of switching to Ubuntu on AWS, because Amazon Linux's "user
data" cloud-init script is too buggy.
The benefits of using the cloud servers are that anyone can obtain the same
environment for testing purposes, and it is easy to throw away an instance
and get a clean one. The second part is important, because OpenBabel seems
to be pretty sensitive about whether you have a previous installation in
place when you build a new one.
If I can come up with a recipe, would you be willing to test it in that
environment?
Cheers,
Jeff
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