One reason to compile refmac on Linux is that it can be faster.
I've just run $CEXAM/unix/runnable/refmac5-simple.exam example
with refmac from CCP4 6.3.0, from Garib's website and compiled with
GCC 4.7.2 only with -O3 option (all are 64-bit versions).
Running times were, correspondingly, 32.2s, 35.1s and 18.7s.
I'd speculate that most of the difference was caused by different
compiler version (GCC 4.7 vs 4.4). Times are avg of two runs, on i7
(sandy bridge), Fedora 18.
It's good for us if some users test new versions before they are in
ccp4 release, so we try to make compilation of individual programs easy.
If you like to try what's in bazaar repository, here is instruction
http://devtools.fg.oisin.rc-harwell.ac.uk/
I'm also putting repository snapshot here:
http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/ccp4-latest-source.tar.bz2
with all programs/modules in a separate top-level directory.
Have a look at the build-all.sh script there to see how it can be built.
For example, in case of refmac, with $HOME local as installation dir,
in mmdb and libccp4 subdirectories do:
./configure --prefix=$HOME/local && make install
and in lapack and refmac directories:
cmake -DCMAKE_INSTALL_PREFIX=$HOME/local . && make install
compiler options can be passed through env vars, e.g.
export CFLAGS="-O2"
export CXXFLAGS="-O2"
export FFLAGS="-O2"
Marcin
On Fri, Mar 01, 2013 at 10:39:30PM +0100, Tim Gruene wrote:
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> Hello Ed,
>
> did you try creating a ccp4 tree from source and replacing the refmac
> source? Maybe that ccp4 environment will help you compile refmac - at
> least with refmac I had the least trouble compiling when I got the
> ccp4 source.
>
> Why are you trying to do this anyhow? Do Garib's binaries not work
> under this Ubuntu installation?
>
> Best,
> Tim
>
> On 02/27/2013 06:27 PM, Ed Pozharski wrote:
> > I am trying to compile refmac from source on a machine running
> > Ubuntu 12.04. In a nutshell, after some troubleshooting I end up
> > with executable that generates a segmentation fault. Log-file
> > states that
> >
> >>>>>>> CCP4 library signal ccp4_parser:Failed to open
> >>>>>>> external command
> > file (Success) raised in ccp4_parser <<<<<<
> >
> > (hardly a success). Potentially relevant details are that I had to
> > compile libccp4 and libmmdb to get to this point. If I don't
> > configure the CCP4, I get this when trying to run refmac
> >
> >>>>>>> CCP4 library signal ccp4_general:Cannot open
> >>>>>>> environ.def (Error)
> > raised in ccp4fyp <<<<<< refmacgfortran: Cannot open environ.def
> > refmacgfortran: Cannot open environ.def
> >
> > So perhaps it's some incompatibility between libccp4/libmmdb that I
> > compiled and those that came with CCP4 installation (by the way,
> > the new update feature rocks indeed). But I tried lifting these
> > libraries from CCP4 installation when compiling refmac and I get
> > the same segmentation fault.
> >
> > Any suggestions for troubleshooting/advice on how to compile
> > refmac from source are appreciated.
> >
> > Refmac version is 5.7.0032.
> >
> > Cheers,
> >
> > Ed.
> >
>
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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