Hi Harry,
Recently I successfully compiled rosetta 3.2.1 with gcc 4.5 following these
hints:
***
from http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104
Rosetta 3.2 with Ubuntu 11.04
Rosetta is a very useful program for the prediction of protein structure,
folding and interactions be that docking with proteins or ligands.
However, the current version of Rosetta (3.2.1) uses SCons to compile itself on
your system. This is usually fine except that these use gcc libraries 4.1 and
before.
Ubunutu 11.04 considers anything before gcc v4.4 to be obsolete and you can't
install them (even with apt-get).
As a result, a small amount of hacking is required.
First get SCons. Open a new terminal window.
sudo apt-get install scons
Check that the file tree has been updated
sudo apt-get update
Now you can unzip your Rosetta download to wherever you like. I personally put
new software into /opt
Change your terminal window to the correct path. So in my case
cd /opt/rosetta
Now in a perfect world, and according to the installation instructions you
should be able to type:
scons bin mode=release
And Rosetta will install and compile itself. However, amongst a load of other
errors you'll see the root of the problem
KeyError: Unknown version number 4.5 for compiler 'gcc'
Now, the first thing I tried was to specify a fixed gcc version for SCons to run
scons bin mode=release cxx=gcc cxx_ver=4.4
But this doesn't work as gcc v4.4 is still too new. And any version before 4.4
isnt supported by Ubuntu.
The solution
This isnt a short or elegant solution, but it is a solution that got Rosetta to
install for me. If you have any troubles yourself I recommend you head on over
to the Rosetta forums.
Install zlib
Install zlib (developer version) to ensure all your necessary libraries are
installed
sudo apt-get install zlib1g-dev
sudo apt-get update
basic.settings
In /rosetta_path/tools/build there is the file basic.settings
At line 203, I needed to add
gcc, 4.5 : {
appends : {
version : [ 4, 5 ],
flags : {
compile : [ -param inline-unit-growth=1000,
-param large-function-growth=5 ],
},
},
},
I didnt change line 329 but you can for completeness if you so wish.
options.settings
In /rosetta_path/tools/build there is the file options.settings
Line 11 and 12 now read
cxx : {
gcc : [ 3.3, 3.4, 4.0, 4.1, 4.2, 4.3,4.4,4.5, *
],
So as to include v4.4 and 4.5
util.cc
Finally and most importantly, in /rosetta_path/src/core/conformation/symmetry
open util.cc. At line 357 there is an if statement. What we need to do is
change the else argument so that the reference is correct (I've commented out
the old line)
#ifdef WIN32
pose::PDBInfoOP pdb_info_src (new pose::PDBInfo( pose.pdb_info() ));
#else
/// pose::PDBInfoOP pdb_info_src = new pose::PDBInfo::PDBInfo( pose.pdb_info()
);
pose::PDBInfoOP pdb_info_src = new pose::PDBInfo( pose.pdb_info() );
#endif
Apparently this is required as the new versions of gcc are fussier about their
name references than older versions.
After which we can now go back to the terminal and type:
scons bin mode=release cxx=gcc cxx_ver=4.5
After some amount of processing time (~30mins on my dual core 2.8 GHz), you
should be greeted with the final lines
Install file:
build/src/release/linux/2.6/64/x86/gcc/4.5/super_aln.linuxgccrelease as
bin/super_aln.linuxgccrelease
scons: done building targets.
Credit goes to those on the Rosetta forums for help.
qrsh -cwd ./scons.py bin mode=release cxx=gcc cxx_ver=4.5 extras=static -j16
doesn't work
the working solution:
qlogin
module load gcc/4.5.0
/scons.py bin mode=release cxx=gcc cxx_ver=4.5 -j16
exit
***
Best wishes,
Alex
On 8 Jul 2011, at 15:21, Harry Xu wrote:
Hi, everyone on board.
I want to try mr_rosetta for my project, but I had problem installing rosetta
on my computer. My computer is running ubuntu 11.04 with gcc 4.5. Compiling
of rosetta 3.2 failed with the message: KeyError: Unknown version number 4.5
for compiler 'gcc' .
I want to know whether anybody had any experience install rosetta in ubuntu?
Or do I need to change to a different linux distribution? If so, what linux
distribution is best for running most of the main stream crystallography
software?
thanks in advance.
Harry
--
Alex Batyuk
Lab of Prof. Dr. A. Plueckthun
Biochemistry Institute
University of Zurich
Winterthurerstrasse 190
8057 Zurich, Switzerland
Phone: +41 44 635 5574
