Re: [IMP-users] IMP-1.0-Stable Installation Ubuntu 10.04 Help
To: Help and discussion for users of IMP <>
Subject: Re: [IMP-users] IMP-1.0-Stable Installation Ubuntu 10.04 Help
From: Daniel Russel <>
Date: Tue, 11 Oct 2011 13:11:27 -0700
Reply-to: Help and discussion for users of IMP <>
Various things. First, don't use 1.0, use current SVN, it is much better, faster, more stable etc and we can't easily support 1.0 at this point.
I've been using IMP on ubuntu without any problems, so, in general, things should work. In terms of the specific error messages
- graphviz is only used via the executables (namely dot) so just make sure that is in your path. - libpath=/usr/lib:/usr/lib64 path=/usr/bin should be the default values and can be omitted. - once you install IMP, you are responsible for getting your PYTHONPATH and LD_LIBRARY_PATH right so that python works properly. You can, instead, just use IMP out of the build directory with the help of the tools/imppy.sh script.
- I have no idea about the file descriptor message
Anyway, hope that helps you along.
On Tue, Oct 11, 2011 at 12:31 PM, Martin Turk <">> wrote:
Dear imp users and developers,
I need some help with compiling the source code on Ubuntu 10.04
I tried compiling imp with:
Â>scons prefix=/installation/folder build=debug install
and the only imp binaries being generated are foxs and protein_ligand_score.
the only error I get is:
"""
sh: Syntax error: Bad fd number
"""
and the graphviz, gslcblas and modeller dependencies are missing
otherwise the installation finishes without errors.
Since Ubuntu has system libraries in a different place than Fedora I
tried compiling imp by specifying libpath and linking it to python. What
is odd is that graphviz and gslcblas are not found when I specify libpath
/usr/lib/graphviz/
/usr/lib/libgslcblas.so.0
Â>scons -j 16 libpath=/usr/lib:/usr/lib64 path=/usr/bin
pythonpath=/usr/lib64/python2.6 prefix=/home/turk/imp build=debug install
again I assume the installation directory is missing some content
../bin:
protein_ligand_score
foxs
../lib64/python2.6/site-packages:
IMP
_IMP_algebra.so
_IMP_atom.so
_IMP_benchmark.so
_IMP_container.so
_IMP_core.so
_IMP_display.so
_IMP_domino.so
_IMP_em.so
_IMP_example.so
_IMP_gsl.so
_IMP_helper.so
_IMP_misc.so
_IMP_restrainer.so
_IMP_saxs.so
_IMP.so
_IMP_statistics.so
after adding site-packages to the $PYTHONPATH
python import imp gives me:
i>>> import IMP
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/home/turk/imp/lib64/python2.6/site-packages/IMP/__init__.py",
line 25, in <module>
  _IMP = swig_import_helper()
 File "/home/turk/imp/lib64/python2.6/site-packages/IMP/__init__.py",
line 17, in swig_import_helper
  import _IMP
ImportError: libimp.so: cannot open shared object file: No such file or
directory
Now I don't know what to try next and if playing with swig will bring me
any further -> the email :-)
All suggestions are welcome :)