First off, let me apologize for a really long message.
I'm trying to get Coot running on a 64-bit machine running fedora core 9. I
picked fedora core 9 because many of the graphics libraries required for
Coot are already installed. However, the autobuild script fails when
compiling the clipper libraries. After some research I discovered that
fedora 9 use gcc4.3, but the version of clipper downloaded from Paul
Emsley's site need gcc3.4 to compile (-which is perplexing because I
compiled the clipper libraries from the CCP4 distribution with gcc4.3)
Running the build-it-gtk2-simple appears to build all the packages without
an error. The script exits with an error that the script can't create the
$AUTOBUILD_INSTALLED/python2.5 directory. However, when I look at proper
directory, the directory is indeed there and coot and coot-real are in the
appropriate bin directory.
The logs say that the coot-test in the script failed. If I start it up
manually, I see the startup image, some verbiage about proper citations, and
then lines about loading a pdb library. It ends with
There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//g/GD.cif
There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//t/TD.cif
There are 2 data in /usr/local/share/CCP4/ccp4-6.0.2/lib/data/monomers//u/UR.cif
Reading coordinate file:
/usr/local/share/coot_build/coot-gtk2/share/coot/standard-residues.pdb
PDB file
/usr/local/share/coot_build/coot-gtk2/share/coot/standard-residues.pdb has
been read.
Spacegroup: P 1
Cell: 40.631 109.18 93.243 90 90 90
Illegal instruction
If I build it with the python option, Coot hangs when it displays the coot
image.
Have I greated a problem by using two different compilers for the libraries
or is this a totally different issue? I've seen posts that refer to similar
behavior that were cured with updating nvidia drivers or messing with
x-windows. Is there a way to tell which it is?
Thanks
Clare
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My wrapper script
#!/bin/bash
export AUTOBUILD_INSTALLED=/usr/local/share/autobuild5/coot
export AUTOBUILD_BUILD=/usr/local/share/autobuild5
export LOGS=$AUTOBUILD_BUILD/logs
export NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
export STABLE_DEST_DIR=$AUTOBUILD_BUILD
export build_coot_prerelease=1
export LD_LIBRARY_DIR=/usr/local/lib:$LD_LIBRARY_DIR
export CC=gcc34
export CXX=g++34
#
# I obtained build-it-gtk-simple using
# wget
http://www.ysbl.york.ac.uk/~emsley/build-logs/build-it-gtk2-simple
#
bash build-it-gtk2-simple > build.log
#
#
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These are the steps that I used to install gcc3.4
Step 1: Install compatibility libraries for programs compiled with earlier
versions of gcc. This may not be strictly necessary for Coot, but it seemed
like a reasonable precaution since I'm installing other programs
yum -y install compat-libstdc++-33 compat-libstdc++-296
Step2: Install gcc3.4
yum install compat-gcc-34 compat-gcc-34-c++
Step 3: Edit wrapper script so that it uses the gcc3.4 compilers
export CC=gcc34
export CXX=g++32
The wrapper script looks like
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I'm perplexed. I've download and compiled the clipper libraries using the
CCP4 install script and everything went great with gcc4.3. So there appears
to be a difference between the two set of clipper libraries. As far as I can
tell, the CCP4 installation works fine.
Any thoughts?
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