[cctbxbb] Debian Package

Richard Gildea rgildea at gmail.com
Tue Aug 7 17:55:10 PDT 2012


Here are the patches to the ANTLR 3.4 C runtime to which I referred in my
previous email:

http://cctbx.svn.sourceforge.net/viewvc/cctbx?view=revision&revision=14622

With this patch we saw approximately 30% reduction in memory usage during
parsing of large CIF files.

Cheers,

Richard

On 7 August 2012 14:43, Richard Gildea <rgildea at gmail.com> wrote:

> Hi Radostan,
>
> I think the integration with distutils would be A Good Thing to increase
> accessibility of the cctbx to users.
>
> One addition to Nat's comments:
>
> I noticed this commit with the log "fix cif parser to work with antlr3c
> 3.2":
>
> http://anonscm.debian.org/gitweb/?p=debian-science/packages/cctbx.git;a=blob;f=debian/patches/0015-fix-cif-parser-to-work-with-antlr3c-3.2.patch
>
> This is essentially a revert of the cctbx svn revision 14621 ("ucif:
> upgrade to antlr3.4"):
>
> http://cctbx.svn.sourceforge.net/viewvc/cctbx/trunk/ucif/parser.h?r1=14583&r2=14621
>
> The ANTLR C runtime changed its interface slightly between 3.2 and 3.4,
> hence the changes in revision 14621. From what I remember it isn't trivial
> to determine the ANTLR runtime version at compile time which was why we
> made no attempt to support both versions of the runtime. If you wish to be
> able to compile against 3.2 in addition to 3.4 we will need to figure out
> how to determine the runtime version. We also use a slightly modified
> version of the ANTLR C runtime in order to obtain savings on memory
> (particularly when reading large ribosome data files).
>
> Cheers,
>
> Richard
>
>
> On 7 August 2012 14:27, Nathaniel Echols <nechols at lbl.gov> wrote:
>
>> On Tue, Aug 7, 2012 at 11:19 AM, Radostan Riedel
>> <raybuntu at googlemail.com> wrote:
>> > But we don't want to overlook you and give some of our work back into
>> the main
>> > project.
>> >
>> > We have a few patches to give back upstream that would really help us
>> and
>> > hopefully help to increase the cctbx user community.
>>
>> Thanks for investing your time in this.  We agree that it would be
>> very helpful in making CCTBX more accessible - our main concern is
>> that any changes not impact the existing projects which depend on it
>> (Phenix, Olex2, CCP4, LABELIT, etc.), including the ability to support
>> these on all current platforms*.  Within this constraint, in principle
>> we're happy to accept any changes that you feel would be worth
>> incorporating.  This should be done slowly and incrementally;
>> conservative modifications that don't modify the default behavior
>> should go first, but I suspect you will eventually need access to our
>> testing systems in Berkeley in order to run tests.  Obviously you
>> should be working from the trunk when you do this.  I noticed that
>> you've also modified the ccp4io_adaptbx tree, which is kept on our
>> local SVN (for reasons that are obscure to me); we can deal with that
>> later**.
>>
>> A random aside: we will be switching to building against the Boost
>> release branch very soon.  Not sure if this affects you or not.
>>
>> > But if we can count on the shlib versioning as mentioned here[5] it
>> would help
>> > us and other developers a lot. Libtool should be available on most
>> systems,
>> > works with common compilers and it provides the quasi standard for
>> versioning
>> > shlibs.
>>
>> This is one point that came up in discussion here: how will this
>> impact Mac?  Apple's libtool appears to be an entirely different
>> beast.  Or will your changes only affect Linux right now?
>>
>> -Nat
>>
>> (* At the moment, this means Fedora 3 or newer using gcc [and Intel's
>> compiler, I guess, but we're less firm on this]; Mac OS 10.4 or later
>> using Xcode 2.4 or later, including both PPC and Intel; and Windows XP
>> or newer using VC++ 8.0 or newer.  And Python 2.4-2.7 in any case.)
>> (** It looks like you're building against gpp4 instead of the ccp4
>> libs - or is it in addition to ccp4?  I suspect this may be
>> problematic in the long term.)
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>>
>
>
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