Dear Greg, Thanks for your help.
I have this: [root@Pc-Eric-linux build]# python -c 'from rdkit import rdBase' Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: libboost_python.so.1.55.0: cannot open shared object file: No such file or directory [root@Pc-Eric-linux build]# and [root@Pc-Eric-linux build]# ldd $RDBASE/rdkit/rdBase.so linux-vdso.so.1 => (0x00007fffe57ff000) libRDGeneral.so.1 => /opt/RDKit/RDKit_2014_03_1/lib/libRDGeneral.so.1 (0x00007ff4d1392000) libRDBoost.so.1 => /opt/RDKit/RDKit_2014_03_1/lib/libRDBoost.so.1 (0x00007ff4d0fc6000) libboost_python.so.1.55.0 => not found libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007ff4d0cae000) libm.so.6 => /opt/anaconda/lib/libm.so.6 (0x00007ff4d0a2a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007ff4d0814000) libc.so.6 => /lib64/libc.so.6 (0x00007ff4d0480000) /lib64/ld-linux-x86-64.so.2 (0x0000003148e00000) libboost_python.so.1.55.0 => not found [root@Pc-Eric-linux build]# What do you think? Thanks Enrico Greg Landrum <greg.land...@gmail.com> a écrit : > given that the failures are all for python tests, I guess you don't have > your PYTHONPATH set properly or that there's an LD_LIBRARY_PATH problem. > > What do you get when you run these two commands? > > python -c 'from rdkit import rdBase' > > ldd $RDBASE/rdkit/rdBase.so > > > -greg > > > > > > -greg > > > > On Mon, Jul 28, 2014 at 12:13 PM, Enrico Perspicace < > e.perspic...@mx.uni-saarland.de> wrote: > >> Dear Christos, >> >> I'm back... So I upgraded my old Centos with Centos 6.5 and I updated it. >> I installed all packages needed as recommended on RDKit website >> followed by anaconda environment (which include Numpy) as you did. >> Now, I get no errors up to the test of the compilation of RDKit. >> Indeed, compilation of RDKit worked but now, after ctest I have some >> fails... >> >> I did first: >> [root@Pc-Eric-linux build]# cmake -D >> PYTHON_LIBRARY=/opt/anaconda/lib/python2.7/config/libpython2.7.a -D >> PYTHON_INCLUDE_DIR=/opt/anaconda/include/python2.7/ -D >> PYTHON_EXECUTABLE=/opt/anaconda/bin/python2.7 -D >> BOOST_ROOT=/opt/boost/boost_1_55_0 .. >> -- The C compiler identification is GNU 4.4.7 >> -- The CXX compiler identification is GNU 4.4.7 >> -- Check for working C compiler: /usr/bin/cc >> -- Check for working C compiler: /usr/bin/cc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- Check if the system is big endian >> -- Searching 16 bit integer >> -- Looking for sys/types.h >> -- Looking for sys/types.h - found >> -- Looking for stdint.h >> -- Looking for stdint.h - found >> -- Looking for stddef.h >> -- Looking for stddef.h - found >> -- Check size of unsigned short >> -- Check size of unsigned short - done >> -- Using unsigned short >> -- Check if the system is big endian - little endian >> -- Found PythonLibs: /opt/anaconda/lib/python2.7/config/libpython2.7.a >> (found version "2.7.7") >> -- Found PythonInterp: /opt/anaconda/bin/python2.7 (found version "2.7.7") >> -- Boost version: 1.55.0 >> -- Found the following Boost libraries: >> -- python >> -- Looking for include file pthread.h >> -- Looking for include file pthread.h - found >> -- Looking for pthread_create >> -- Looking for pthread_create - not found >> -- Looking for pthread_create in pthreads >> -- Looking for pthread_create in pthreads - not found >> -- Looking for pthread_create in pthread >> -- Looking for pthread_create in pthread - found >> -- Found Threads: TRUE >> -- Boost version: 1.55.0 >> -- Found the following Boost libraries: >> -- regex >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /opt/RDKit/RDKit_2014_03_1/build >> [root@Pc-Eric-linux build]# >> >> Then >> >> [root@Pc-Eric-linux build]# make >> [root@Pc-Eric-linux build]# make install >> >> RDKit is compiling correctly withour errors. I just had sometimes this >> warning: >> >> [ 46%] Building CXX object >> Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o >> Dans le fichier inclus à partir de >> >> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761, >> à partir de >> >> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, >> à partir de >> >> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, >> à partir de >> /opt/RDKit/RDKit_2014_03_1/Code/DataStructs/Wrap/DataStructs.cpp:20: >> /opt/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: >> attention : #warning "Using deprecated NumPy API, disable it by " >> "#defining NPY_NO_DEPRECATED_API >> NPY_1_7_API_VERSION" >> >> Finally, I ran ctest: >> >> [root@Pc-Eric-linux build]# ctest >> >> And I got: >> >> Test project /opt/RDKit/RDKit_2014_03_1/build >> Start 1: testDict >> 1/78 Test #1: testDict ......................... Passed 0.03 sec >> Start 2: testDataStructs >> 2/78 Test #2: testDataStructs .................. Passed 0.01 sec >> Start 3: pyBV >> 3/78 Test #3: pyBV .............................***Failed 0.02 sec >> Start 4: pyDiscreteValueVect >> 4/78 Test #4: pyDiscreteValueVect ..............***Failed 0.03 sec >> Start 5: pySparseIntVect >> 5/78 Test #5: pySparseIntVect ..................***Failed 0.03 sec >> Start 6: testTransforms >> 6/78 Test #6: testTransforms ................... Passed 0.01 sec >> Start 7: testGrid >> 7/78 Test #7: testGrid ......................... Passed 0.03 sec >> Start 8: testPyGeometry >> 8/78 Test #8: testPyGeometry ...................***Failed 0.04 sec >> Start 9: testMatrices >> 9/78 Test #9: testMatrices ..................... Passed 0.00 sec >> Start 10: testAlignment >> 10/78 Test #10: testAlignment .................... Passed 0.00 sec >> Start 11: pyAlignment >> 11/78 Test #11: pyAlignment ......................***Failed 0.02 sec >> Start 12: testOptimizer >> 12/78 Test #12: testOptimizer .................... Passed 0.01 sec >> Start 13: testUFFForceField >> 13/78 Test #13: testUFFForceField ................ Passed 0.05 sec >> Start 14: testMMFFForceField >> 14/78 Test #14: testMMFFForceField ............... Passed 17.79 sec >> Start 15: pyForceFieldConstraints >> 15/78 Test #15: pyForceFieldConstraints ..........***Failed 0.03 sec >> Start 16: testDistGeom >> 16/78 Test #16: testDistGeom ..................... Passed 0.00 sec >> Start 17: pyDistGeom >> 17/78 Test #17: pyDistGeom .......................***Failed 0.10 sec >> Start 18: graphmolTest1 >> 18/78 Test #18: graphmolTest1 .................... Passed 0.14 sec >> Start 19: graphmolcpTest >> 19/78 Test #19: graphmolcpTest ................... Passed 0.02 sec >> Start 20: graphmolqueryTest >> 20/78 Test #20: graphmolqueryTest ................ Passed 0.02 sec >> Start 21: graphmolMolOpsTest >> 21/78 Test #21: graphmolMolOpsTest ............... Passed 1.81 sec >> Start 22: graphmoltestCanon >> 22/78 Test #22: graphmoltestCanon ................ Passed 0.00 sec >> Start 23: graphmoltestChirality >> 23/78 Test #23: graphmoltestChirality ............ Passed 0.04 sec >> Start 24: graphmoltestPickler >> 24/78 Test #24: graphmoltestPickler .............. Passed 0.37 sec >> Start 25: graphmolIterTest >> 25/78 Test #25: graphmolIterTest ................. Passed 0.02 sec >> Start 26: testDepictor >> 26/78 Test #26: testDepictor ..................... Passed 0.41 sec >> Start 27: pyDepictor >> 27/78 Test #27: pyDepictor .......................***Failed 0.02 sec >> Start 28: smiTest1 >> 28/78 Test #28: smiTest1 ......................... Passed 0.27 sec >> Start 29: smaTest1 >> 29/78 Test #29: smaTest1 ......................... Passed 1.39 sec >> Start 30: fileParsersTest1 >> 30/78 Test #30: fileParsersTest1 ................. Passed 7.46 sec >> Start 31: testMolSupplier >> 31/78 Test #31: testMolSupplier .................. Passed 0.18 sec >> Start 32: testMolWriter >> 32/78 Test #32: testMolWriter .................... Passed 0.41 sec >> Start 33: testTplParser >> 33/78 Test #33: testTplParser .................... Passed 0.02 sec >> Start 34: testMol2ToMol >> 34/78 Test #34: testMol2ToMol .................... Passed 0.02 sec >> Start 35: testSubstructMatch >> 35/78 Test #35: testSubstructMatch ............... Passed 0.02 sec >> Start 36: testReaction >> 36/78 Test #36: testReaction ..................... Passed 0.08 sec >> Start 37: pyChemReactions >> 37/78 Test #37: pyChemReactions ..................***Failed 0.02 sec >> Start 38: testChemTransforms >> 38/78 Test #38: testChemTransforms ............... Passed 0.07 sec >> Start 39: testSubgraphs1 >> 39/78 Test #39: testSubgraphs1 ................... Passed 0.37 sec >> Start 40: testSubgraphs2 >> 40/78 Test #40: testSubgraphs2 ................... Passed 0.02 sec >> Start 41: testFragCatalog >> 41/78 Test #41: testFragCatalog .................. Passed 1.19 sec >> Start 42: pyFragCatalog >> 42/78 Test #42: pyFragCatalog ....................***Failed 0.03 sec >> Start 43: testDescriptors >> 43/78 Test #43: testDescriptors .................. Passed 0.24 sec >> Start 44: pyMolDescriptors >> 44/78 Test #44: pyMolDescriptors .................***Failed 0.02 sec >> Start 45: testFingerprints >> 45/78 Test #45: testFingerprints ................. Passed 0.20 sec >> Start 46: pyPartialCharges >> 46/78 Test #46: pyPartialCharges .................***Failed 0.02 sec >> Start 47: testMolTransforms >> 47/78 Test #47: testMolTransforms ................ Passed 0.02 sec >> Start 48: pyMolTransforms >> 48/78 Test #48: pyMolTransforms ..................***Failed 0.02 sec >> Start 49: testMMFFForceFieldHelpers >> 49/78 Test #49: testMMFFForceFieldHelpers ........ Passed 0.65 sec >> Start 50: testUFFForceFieldHelpers >> 50/78 Test #50: testUFFForceFieldHelpers ......... Passed 1.51 sec >> Start 51: pyForceFieldHelpers >> 51/78 Test #51: pyForceFieldHelpers ..............***Failed 0.02 sec >> Start 52: testDistGeomHelpers >> 52/78 Test #52: testDistGeomHelpers .............. Passed 0.89 sec >> Start 53: pyDistGeom >> 53/78 Test #53: pyDistGeom .......................***Failed 0.02 sec >> Start 54: testMolAlign >> 54/78 Test #54: testMolAlign ..................... Passed 3.97 sec >> Start 55: pyMolAlign >> 55/78 Test #55: pyMolAlign .......................***Failed 0.03 sec >> Start 56: testFeatures >> 56/78 Test #56: testFeatures ..................... Passed 0.02 sec >> Start 57: pyChemicalFeatures >> 57/78 Test #57: pyChemicalFeatures ...............***Failed 0.02 sec >> Start 58: testShapeHelpers >> 58/78 Test #58: testShapeHelpers ................. Passed 0.02 sec >> Start 59: pyShapeHelpers >> 59/78 Test #59: pyShapeHelpers ...................***Failed 0.03 sec >> Start 60: testMolCatalog >> 60/78 Test #60: testMolCatalog ................... Passed 0.02 sec >> Start 61: pyMolCatalog >> 61/78 Test #61: pyMolCatalog .....................***Failed 0.03 sec >> Start 62: testSLNParse >> 62/78 Test #62: testSLNParse ..................... Passed 0.03 sec >> Start 63: pySLNParse >> 63/78 Test #63: pySLNParse .......................***Failed 0.01 sec >> Start 64: pyGraphMolWrap >> 64/78 Test #64: pyGraphMolWrap ...................***Failed 0.04 sec >> Start 65: pyTestConformerWrap >> 65/78 Test #65: pyTestConformerWrap ..............***Failed 0.02 sec >> Start 66: testQuery >> 66/78 Test #66: testQuery ........................ Passed 0.00 sec >> Start 67: testMatCalc >> 67/78 Test #67: testMatCalc ...................... Passed 0.00 sec >> Start 68: pyMatCalc >> 68/78 Test #68: pyMatCalc ........................***Failed 0.03 sec >> Start 69: pyRanker >> 69/78 Test #69: pyRanker .........................***Failed 0.03 sec >> Start 70: testChemicalFeatures >> 70/78 Test #70: testChemicalFeatures ............. Passed 0.01 sec >> Start 71: pyFeatures >> 71/78 Test #71: pyFeatures .......................***Failed 0.02 sec >> Start 72: pythonTestDbCLI >> 72/78 Test #72: pythonTestDbCLI ..................***Failed 0.23 sec >> Start 73: pythonTestDirML >> 73/78 Test #73: pythonTestDirML ..................***Failed 3.34 sec >> Start 74: pythonTestDirDataStructs >> 74/78 Test #74: pythonTestDirDataStructs ......... Passed 0.02 sec >> Start 75: pythonTestDirDbase >> 75/78 Test #75: pythonTestDirDbase ............... Passed 0.02 sec >> Start 76: pythonTestDirSimDivFilters >> 76/78 Test #76: pythonTestDirSimDivFilters ....... Passed 0.02 sec >> Start 77: pythonTestDirVLib >> 77/78 Test #77: pythonTestDirVLib ................ Passed 0.01 sec >> Start 78: pythonTestDirChem >> 78/78 Test #78: pythonTestDirChem ................***Failed 2.26 sec >> >> 64% tests passed, 28 tests failed out of 78 >> >> Total Test time (real) = 46.52 sec >> >> The following tests FAILED: >> 3 - pyBV (Failed) >> 4 - pyDiscreteValueVect (Failed) >> 5 - pySparseIntVect (Failed) >> 8 - testPyGeometry (Failed) >> 11 - pyAlignment (Failed) >> 15 - pyForceFieldConstraints (Failed) >> 17 - pyDistGeom (Failed) >> 27 - pyDepictor (Failed) >> 37 - pyChemReactions (Failed) >> 42 - pyFragCatalog (Failed) >> 44 - pyMolDescriptors (Failed) >> 46 - pyPartialCharges (Failed) >> 48 - pyMolTransforms (Failed) >> 51 - pyForceFieldHelpers (Failed) >> 53 - pyDistGeom (Failed) >> 55 - pyMolAlign (Failed) >> 57 - pyChemicalFeatures (Failed) >> 59 - pyShapeHelpers (Failed) >> 61 - pyMolCatalog (Failed) >> 63 - pySLNParse (Failed) >> 64 - pyGraphMolWrap (Failed) >> 65 - pyTestConformerWrap (Failed) >> 68 - pyMatCalc (Failed) >> 69 - pyRanker (Failed) >> 71 - pyFeatures (Failed) >> 72 - pythonTestDbCLI (Failed) >> 73 - pythonTestDirML (Failed) >> 78 - pythonTestDirChem (Failed) >> Errors while running CTest >> [root@Pc-Eric-linux build]# >> >> I set variables environment as follow: >> export RDBASE=/opt/RDKit/RDKit_2013_09_2/ >> export LD_LIBRARY_PATH=$RDBASE/lib >> export PYTHONPATH=$RDBASE >> >> What I did wrong? >> >> Do you have any idea? >> >> Thanks in advance for you reply. >> >> Best regards, >> >> Enrico >> >> >> >> >> Enrico Perspicace <e.perspic...@mx.uni-saarland.de> a écrit : >> >> > Dear Christos, >> > >> > Thanks for your reply. >> > I already tried but it didn't work... >> > I downloaded yesterday Centos 6.5 and I will install it. >> > I hope to get less problem with this version as RDKit is available >> > using rpm package. >> > I will let you know if I will succeed or not ;-) >> > >> > Best regards, >> > >> > Enrico >> > >> > >> > Christos Kannas <chriskan...@gmail.com> a écrit : >> > >> >> Enrico, >> >> >> >> According to Boost web site ( >> >> >> http://www.boost.org/doc/libs/1_55_0/libs/log/doc/html/log/installation.html >> ) >> >> it has been tested and working with gcc 4.5+. >> >> Try to update your gcc and gcc-c++ to the latest versions available... I >> >> know CentOS is not up to date... >> >> At the moment I do not recall if I did any update to gcc. >> >> I will get back to you on Monday for this, except if you are in a hurry >> >> I'll go from the office tomorrow to check my dev machine. >> >> >> >> Best, >> >> >> >> Christos >> >> >> >> Christos Kannas >> >> >> >> Researcher >> >> Ph.D Student >> >> >> >> Mob (UK): +44 (0) 7447700937 >> >> Mob (Cyprus): +357 99530608 >> >> >> >> [image: View Christos Kannas's profile on LinkedIn] >> >> <http://cy.linkedin.com/in/christoskannas> >> >> >> >> >> >> On 24 July 2014 15:02, Enrico Perspicace < >> e.perspic...@mx.uni-saarland.de> >> >> wrote: >> >> >> >>> Hi Christos, >> >>> >> >>> Thanks for your help. >> >>> >> >>> I tried what you said but I got an error with boost. >> >>> >> >>> I think the problem came from here... >> >>> >> >>> I use Canopy environment, it is like Anaconda which include Numpy and >> it >> >>> is detected when I did ./bootstrap.sh >> >>> >> >>> [root@eric-pc boost_1_55_0]# ./bootstrap.sh >> --with-libraries=python,regex >> >>> Building Boost.Build engine with toolset gcc... >> tools/build/v2/engine/bin. >> >>> linuxx86_64/b2 >> >>> Detecting Python version... 2.7 >> >>> Detecting Python root... /root/Enthought/Canopy_64bit/User >> >>> Unicode/ICU support for Boost.Regex?... not found. >> >>> Generating Boost.Build configuration in project-config.jam... >> >>> >> >>> Bootstrapping is done. To build, run: >> >>> >> >>> ./b2 >> >>> >> >>> To adjust configuration, edit 'project-config.jam'. >> >>> Further information: >> >>> >> >>> - Command line help: >> >>> ./b2 --help >> >>> >> >>> - Getting started guide: >> >>> http://www.boost.org/more/getting_started/unix-variants.html >> >>> >> >>> - Boost.Build documentation: >> >>> http://www.boost.org/boost-build2/doc/html/index.html >> >>> >> >>> [root@eric-pc boost_1_55_0]# >> >>> >> >>> But, when I performed ./b2 address-model=64 cflags=-fPIC cxxflags=-fPIC >> >>> Install I got errors of compilation with gcc (I use gcc (GCC) 4.1.2 >> >>> 20080704 (Red Hat 4.1.2-54)) and should be ok (miminum required gcc >> 3.3: >> >>> >> >>> ...failed gcc.compile.c++ bin.v2/libs/python/build/gcc- >> >>> 4.1.2/release/address-model-64/link-static/threading- >> >>> multi/object/function_doc_signature.o... >> >>> ...skipped <pbin.v2/libs/python/build/gcc-4.1.2/release/address- >> >>> model-64/link-static/threading-multi>libboost_python.a(clean) for lack >> of >> >>> >> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/ >> >>> threading-multi>numeric.o... >> >>> ...skipped <pbin.v2/libs/python/build/gcc-4.1.2/release/address- >> >>> model-64/link-static/threading-multi>libboost_python.a for lack of >> >>> >> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/ >> >>> threading-multi>numeric.o... >> >>> ...skipped <p/usr/local/lib>libboost_python.a for lack of >> >>> >> <pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/ >> >>> threading-multi>libboost_python.a... >> >>> common.copy /usr/local/lib/libboost_regex.a >> >>> ...failed updating 56 targets... >> >>> ...skipped 6 targets... >> >>> ...updated 3 targets... >> >>> >> >>> >> >>> Regards, >> >>> >> >>> Enrico >> >>> >> >>> >> >>> >> >>> Quoting Christos Kannas <chriskan...@gmail.com>: >> >>> >> >>> Hi Enrico, >> >>>> >> >>>> The latest version of RDKit does not require flex or bison, >> thankfully. >> >>>> >> >>>> In the attached file I list the commands that I used to build CMake >> >>>> (2.8.12.2), Boost libraries (1.55) and RDKit (2014_03_1) on a CentOS >> 5.10 >> >>>> VM. >> >>>> In my case I was using an Anaconda Python environment so I didn't >> have to >> >>>> install NumPy, since it is bundled to it. >> >>>> >> >>>> Best, >> >>>> >> >>>> Christos >> >>>> >> >>>> Christos Kannas >> >>>> >> >>>> Researcher >> >>>> Ph.D Student >> >>>> >> >>>> Mob (UK): +44 (0) 7447700937 >> >>>> Mob (Cyprus): +357 99530608 >> >>>> >> >>>> [image: View Christos Kannas's profile on LinkedIn] >> >>>> <http://cy.linkedin.com/in/christoskannas> >> >>>> >> >>>> >> >>>> >> >>>> On 24 July 2014 10:05, Enrico Perspicace < >> e.perspic...@mx.uni-saarland.de >> >>>> > >> >>>> wrote: >> >>>> >> >>>> >> >>>>> Dear all, >> >>>>> >> >>>>> I would like to install RDKit 2014 on Centos 5.10 (Final) but I did >> not >> >>>>> succeed! >> >>>>> >> >>>>> I follow Instructions for Installation on RDKIT website but I got an >> >>>>> error >> >>>>> when I used cmake command line... >> >>>>> >> >>>>> Indeed, cmake is not able to find boost_python library. >> >>>>> >> >>>>> I installed: Python 2.7, atlas, lapack, blas, fftw3, numpy 1.8 via >> canopy >> >>>>> 1.4.1 (and is working with python import numpy), boost 1.55, flex >> 2.5.35 >> >>>>> and bison 3.0.2 before performing the RDKit installation. >> >>>>> >> >>>>> I followed the procedure described here: >> https://www.mail-archive.com/ >> >>>>> rdkit-discuss@lists.sourceforge.net/msg01376.html >> >>>>> >> >>>>> Please find in attached document related files which describe my >> problem. >> >>>>> >> >>>>> Thanks a lot for you help. >> >>>>> >> >>>>> Best regards, >> >>>>> >> >>>>> Enrico Perspicace >> >>>>> >> >>>>> >> >>>>> ------------------------------------------------------------ >> >>>>> ------------------ >> >>>>> Want fast and easy access to all the code in your enterprise? 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