Re: [Rdkit-devel] Cartridge and PostgreSQL 9.1

[Adrian S. <am...@ca...>]

Hi Greg,

Just a couple of comments:

SET search_path = 'public' is not required in 9.1 and will throw an
error if I remember correctly - the schema can be set at any time with
ALTER EXTENSION SET SCHEMA = <schema> if the relocatable = true flag
is set in the extension control file.

It is possible to have only one Makefile for 9.1 and <9.1. The only
thing that is necessary is to have a conditional inside the Makefile
to change the DATA variable to the rdkit--3.1.sql file. Here is an
example from the pair extension Makefile
(http://api.pgxn.org/src/pair/pair-0.1.3/Makefile):

PG91 = $(shell $(PG_CONFIG) --version | grep -qE " 8\.| 9\.0" && echo
no || echo yes)

ifeq ($(PG91),yes)
all: sql/$(EXTENSION)--$(EXTVERSION).sql

sql/$(EXTENSION)--$(EXTVERSION).sql: sql/$(EXTENSION).sql
	cp $< $@

DATA = $(wildcard sql/*--*.sql) sql/$(EXTENSION)--$(EXTVERSION).sql
EXTRA_CLEAN = sql/$(EXTENSION)--$(EXTVERSION).sql
endif

9.1 Also introduces the ability to upgrade extensions in place with
ALTER EXTENSION UPDATE (using update scripts) without dropping all
data types and functions. This is especially useful I think if the
data types haven't changed and only new functions were introduced,
avoiding the need to recreate all molecules, fingerprints and indexes
again. This might be something for a future version.

I have added the -march=native flag to my Makefile, I'm not sure if
this would cause problems for people creating packages for RDKit. Have
you tried this flag for compiling RDKit itself? I would be curious
about the performance gains, if any.

Best Regards,

Adrian

On Sun, Oct 23, 2011 at 15:28, Greg Landrum <gre...@gm...> wrote:
> Adrian,
>
> On Wed, Oct 12, 2011 at 2:30 PM, Adrian Schreyer <am...@ca...> wrote:
>>
>> I made some small changes to the database cartridge code in order to
>> compile it under 9.1 and also to use the new extension infrastructure.
>> The exact changes are probably the easiest to see in my bitbucket
>> repository changesets
>> (https://bitbucket.org/aschreyer/rdkit/changesets). It's currently
>> running on our 9.1 server without any problems.
>
> I just merged your changes in along with some tweaks to allow the
> cartridge to still build under older versions of postgresql. Thanks
> for figuring out how to do this!
>
> The build instructions have changed, the new version is here:
> http://code.google.com/p/rdkit/wiki/BuildingTheCartridge
>
> Best Regards,
> -greg
>