(The previous email was sent accidentally while I was still composing)
Dear Open Babel developers and community,
I'm currently trying to build a pre-compiled Python wheel for Open Babel
2.4.1
that is to be installed on Compute Canada's HPC clusters so that users can
quickly install tested python packages into their home directory.
I have already installed Open Babel 2.4.1, which works just fine, but once I
want to use the pybel installed with "pip install ..." - either from a wheel
that I have created with "pip wheel openbabel" - or like demonstrated below
by compiling on installation, I get the error following error when testing:
"ValueError: smi is not a recognised Open Babel format"
The environment variables BABEL_LIBDIR and BABEL_DATADIR are set correctly
and when I run ldd on the `_openbabel.so`, it can find all dependencies,
as our compilers set RUNPATHs for all executables and libraries.
I have confirm with `readelf -d _openbabel.so` that the RPATH is correctly
set.
The curious thing is, that before when I installed the Python bindings
with CMake, it
worked just fine. The disadvantage with that however is that I can only
install either
the Python 2.x or 3.y bindings and that I need to set a PYTHON path in the
environment module, which can make problems when someone wants to use
a different Python version.
Having pre-compiled wheels in a wheelhouse that can swiftly be installed
in a virtual env is a much cleaner solution.
Below I demonstrate how I load my modules, show that obabel works,
create a python virtualenv in which the python bindings are installed.
When running readstring("smi", "CCCC") python will throw the error.
Does anyone have an idea where could be the problem?
Oliver
$ *module load openbabel python/2.7.13*
$ *module list*
Currently Loaded Modules:
1) nixpkgs/16.09 (S) 7) openmpi/2.1.1 (m)
2) icc/.2016.4.258 (H) 8) StdEnv/2016.4 (S)
3) gcccore/.5.4.0 (H) 9) eigen/3.3.2 (math)
4) ifort/.2016.4.258 (H) 10) boost/1.60.0 (t)
5) intel/2016.4 (t) 11) openbabel/2.4.1
6) imkl/11.3.4.258 (math) 12) python/2.7.13 (t)
$ *echo CCCC | obabel -i smi -o cml -*
<?xml version="1.0"?>
<molecule xmlns="http://www.xml-cml.org/schema";>
<atomArray>
<atom id="a1" elementType="C"/>
<atom id="a2" elementType="C"/>
<atom id="a3" elementType="C"/>
<atom id="a4" elementType="C"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="1"/>
<bond atomRefs2="a3 a4" order="1"/>
</bondArray>
</molecule>
1 molecule converted
$ *virtualenv babel*
New python executable in /home/stuekero/openbabel_test/babel/bin/python2.7
Also creating executable in /home/stuekero/openbabel_test/babel/bin/python
Installing setuptools, pip, wheel...done.
$ *source babel/bin/activate*
(babel)$ *pip --no-cache-dir install openbabel*
Collecting openbabel
Downloading openbabel-2.4.1.tar.gz (74kB)
100% |####################| 81kB 6.5MB/s
Installing collected packages: openbabel
Running setup.py install for openbabel ... done
Successfully installed openbabel-2.4.1
(babel)$ *python test_openbabel.py*
Traceback (most recent call last):
File "test_openbabel.py", line 4, in <module>
mymol = readstring("smi", "CCCC")
File
"/home/stuekero/openbabel_test/babel/lib/python2.7/site-packages/pybel.py",
line 199, in readstring
raise ValueError("%s is not a recognised Open Babel format" % format)
ValueError: smi is not a recognised Open Babel format
(babel)$ *echo $BABEL_LIBDIR *
/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/
Compiler/intel2016.4/openbabel/2.4.1/lib/openbabel/2.4.1
(babel)$ *echo $BABEL_DATADIR *
/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/
Compiler/intel2016.4/openbabel/2.4.1/share/openbabel/2.4.1
(babel)$ *python -c "from pybel import * ; print 'smi' in informats "*
True
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