Just my $0.02. You may realize and have tried all of this already, but...
I've spent a lot of time getting RDKit built on CentOS since version 5.4. The newer versions make this much easier with updated CMake, GCC, etc. One problem that I've had is trying to build while still having CentOS' standard (i.e., old) Boost libraries still installed. I know that CMake has some flags with which to set the Boost library location, but I could never get them to work and the build to see the newly built Boost library when the system standard was present. The only thing that worked for me was to remove the system boost and build my own. The make system then finds the custom build without a problem. -Kirk On Fri, Jun 22, 2012 at 9:46 AM, Leonardo Trabuco <ltrab...@gmail.com> wrote: > Hi Greg, > > Thanks for following up. Below is the output you asked for. Looks like an > import error in the boost library. Any ideas? > > Thanks again, > Leo > > UpdateCTestConfiguration from > :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl > Start processing tests > UpdateCTestConfiguration from > :/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/DartConfiguration.tcl > Test project > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build > Constructing a list of tests > Done constructing a list of tests > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/RDGeneral > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataStructs/Wrap > 3/ 76 Testing pyBV > Test command: /usr/bin/python2.6 > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py > Test timeout computed to be: 9.99988e+06 > Traceback (most recent call last): > File > "/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/Code/DataStructs/Wrap/testBV.py", > line 1, in <module> > from rdkit import DataStructs > File > "/net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/rdkit/DataStructs/__init__.py", > line 11, in <module> > from rdkit import rdBase > ImportError: > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/boost/lib/libboost_python.so.1.49.0: > undefined symbol: Py_InitModule4 > -- Process completed > ***Failed > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Geometry/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Alignment/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Numerics/Optimizer > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ForceField > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DistGeom/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Depictor/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SmilesParse > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FileParsers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Substruct > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemReactions/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ChemTransforms > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Subgraphs > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FragCatalog > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/FragCatalog/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Descriptors > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Descriptors/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Fingerprints > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/PartialCharges/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolTransforms > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolTransforms/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ForceFieldHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ForceFieldHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/DistGeomHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/DistGeomHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolAlign > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolAlign/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolChemicalFeatures > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolChemicalFeatures/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ShapeHelpers > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/ShapeHelpers/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolCatalog > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/MolCatalog/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SLNParse > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/SLNParse/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/GraphMol/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/Query > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataManip/MetricMatrixCalc > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/DataManip/MetricMatrixCalc/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ML/FeatureSelect/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ML/InfoTheory/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ChemicalFeatures > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Code/ChemicalFeatures/Wrap > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/Projects > Changing directory into > /net/netfile2/ag-russell/install/CentOS-5.8-x86_64/RDKit_2012_03_1/build/rdkit > > 0% tests passed, 1 tests failed out of 1 > 3 - pyBV (Failed) > > > > On Fri, Jun 22, 2012 at 4:53 PM, Greg Landrum <greg.land...@gmail.com> > wrote: >> >> Hi Leo, >> >> >> On Fri, Jun 22, 2012 at 4:45 PM, Leonardo Trabuco <ltrab...@gmail.com> >> wrote: >> > >> > I'm trying to build RDKit_2012_03_1 on a machine running CentOS 5.8. >> > After >> > finally getting the build to complete, almost all Python-related tests >> > fail. >> >> <snip> >> >> > >> > Finally: >> > $ cd $RDBASE >> > $ mkdir build >> > $ cd build >> > $ cmake -DBOOST_ROOT=$installbase/boost -D >> > PYTHON_EXECUTABLE=/usr/bin/python2.6 .. >> > $ make >> > $ make install >> > $ ctest >> > >> > All python-related tests fail (py*, except for the last ones: >> > pythonTest*). Any suggestions for what to try are highly appreciated! >> >> can you please run: >> ctest -V -R pyBV >> and send the output? >> >> Thanks, >> -greg > > > > > -- > Leonardo Trabuco, Postdoctoral fellow (Russell group) > CellNetworks, University of Heidelberg, Germany > http://www.russelllab.org/people/leo/ > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
