Tuesday, August 27, 2013

Fink: coot and coot-pre alternate packages now available

Dear OS X Coot users:

I've updated coot to use a stand-alone refmac, as well as the CCP4 open-source libraries, so all dependencies on proprietary parts of CCP4 should no longer be present.

If you want a recent pre-release, just install "coot".  If it isn't recent enough, either email me, or just grab a pre-compiled nightly version.

You can also do it yourself, if you are in a hurry, just by editing the file

/sw/fink/dists/stable/main/finkinfo/sci/coot.info, changing line 3 (the Revision number) and the corresponding checksum (line 8).

The stand-alone packages will continue to be based upon automatic nightly builds, available here:

or here:  http://psbmini.ucsc.edu/~wgscott/coot/?C=M;O=D

Please let me know if any of these are problematic.

Sunday, July 28, 2013

The future of Fink's CCP4 package

Now that CCP4 plans to distribute 64-bit binaries for OS X, and has its own update system, the need for a fink package of CCP4 seems less compelling.  I am thinking of creating some sort of "system-ccp4" fink placeholder, and might augment that with a version of the ccp4_setup.xsh files that the user can optionally install.

Any objections?

Coot 0.7.1 stable is now available

The OS X fink and pre-build Coot packages for Coot 0.7.1 are now available.

Fairly recently, I created a fink package for rdkit, which coot now depends upon (and makes good use of).

See further details here.

Tuesday, January 1, 2013

Tuesday, October 2, 2012

Coot 0.7 stable is now available

Congratulations to Paul Emsley, both for COOT 0.7 and for the new position at the MRC-LMB.  He has certainly earned it.

The OS X fink and pre-build Coot packages are now available.

See further details here.

Tuesday, September 18, 2012

More changes to the Fink CCP4 package

The main change is to move /sw/share/xtal/ccp4-6.3.0 to /sw/opt/ccp4-6.3.0.  This change of location is to remove a 10 year old violation of fink packaging policy. Briefly, packages with their own unix-like filesystem hierarchy (bin, lib, include, share, etc), should go into /sw/opt/packagename, whereas /sw/share is for platform-indepenent files (text files and so on).

Saturday, September 15, 2012

Phaser MPI on OS X: Fink package phaser-mpi

I am trying to get phaser to use all my processors

I've created a fink package called phaser-mpi that does the following automatically:

1. Phaser uses c++ by default (clang++ on OS X).  If you compile phaser using an untouched ccp4-phaser-N.tgz package distributed by CCP4, this works.  If you compile cctbx first, it will fail to compile with clang++.  So you either need to compile both with g++, which you can do by issuing the


directive.  (No other such directive will work, fwiw.)  This is why I had such troubles building phaser for 10.8.1.

2.  Phaser can be tricked into linking the openmpi library by doing the following:

(a)  Install Fink's gcc47 compiler package.

(b)  Unpack CCP4's cctbx/phaser source code.

(c) cd into the ccp4-6.3.0 directory, and issue the following (one-line) command:

perl -pi.orig -e \
"s|cxx \= cc.replace\('gcc', 'g\+\+'\)|cxx \= cc.replace\('gcc', 'sw/bin/g\+\+-4'\)|g" \

(d) Issue the following commands within the phaser src directory:

export CXXFLAGS="-L/sw/lib"
export CFLAGS="-I/sw/include"

mv bin bin.orig

/usr/bin/python \
../../lib/cctbx/cctbx_sources/cctbx_project/libtbx/configure.py \
--repository=source phaser \ 
--build-boost-python-extensions=False \ 
--enable-openmp-if-possible=True \ 
--static-exe \ 
--use-environment-flags \ 

source setpaths.sh  

libtbx.scons -j 8 .  

(e) Restore the original /usr/bin/g++ and /usr/bin/gcc.

(I have 8 processors.  This speeds up the build, but has nothing to do with the outcome.)

(3) Run it using the following KeyWord (in this case for 8 processors):

   JOBS  8  

Thanks to Kaspar Hollenstein for help, advice and encouragement.