Re: [Rdkit-discuss] Installation of RDKit 2014 on Centos 5.10 (Final)
Just as Christos said: you're missing boost path in LD_LIBRARY_PATH Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-07-28 15:53 GMT+02:00 Enrico Perspicace e.perspic...@mx.uni-saarland.de: 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 = (0x7fffe57ff000) libRDGeneral.so.1 = /opt/RDKit/RDKit_2014_03_1/lib/libRDGeneral.so.1 (0x7ff4d1392000) libRDBoost.so.1 = /opt/RDKit/RDKit_2014_03_1/lib/libRDBoost.so.1 (0x7ff4d0fc6000) libboost_python.so.1.55.0 = not found libstdc++.so.6 = /usr/lib64/libstdc++.so.6 (0x7ff4d0cae000) libm.so.6 = /opt/anaconda/lib/libm.so.6 (0x7ff4d0a2a000) libgcc_s.so.1 = /lib64/libgcc_s.so.1 (0x7ff4d0814000) libc.so.6 = /lib64/libc.so.6 (0x7ff4d048) /lib64/ld-linux-x86-64.so.2 (0x003148e0) 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:
Re: [Rdkit-discuss] Installation of RDKit 2014 on Centos 5.10 (Final)
Dear all, Finally I got: 99% tests passed, 1 tests failed out of 78 Total Test time (real) = 141.17 sec The following tests FAILED: 78 - pythonTestDirChem (Failed) Errors while running CTest I WOULD LIKE TO THANK ALL OF YOU FOR YOUR HELP!!! It was not so easy for a Linux beginner like me and I spent a couple of hours! I don't why, when I installed boost in /opt/boost folder, some libraries have been pasted into /usr/local/lib... I just copy the missing file (libboost_python.so.1.55.0) from /usr/local/lib to /opt/anaconda/lib where I have the other...and set the LD_LIBRARY_PATH as follow: export LD_LIBRARY_PATH=$RDBASE/lib:/opt/anaconda/lib:$LD_LIBRARY_PATH Now everything is OK. Thanks again. Best regards, Enrico Maciek Wójcikowski mac...@wojcikowski.pl a écrit : Just as Christos said: you're missing boost path in LD_LIBRARY_PATH Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.pl 2014-07-28 15:53 GMT+02:00 Enrico Perspicace e.perspic...@mx.uni-saarland.de: 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 = (0x7fffe57ff000) libRDGeneral.so.1 = /opt/RDKit/RDKit_2014_03_1/lib/libRDGeneral.so.1 (0x7ff4d1392000) libRDBoost.so.1 = /opt/RDKit/RDKit_2014_03_1/lib/libRDBoost.so.1 (0x7ff4d0fc6000) libboost_python.so.1.55.0 = not found libstdc++.so.6 = /usr/lib64/libstdc++.so.6 (0x7ff4d0cae000) libm.so.6 = /opt/anaconda/lib/libm.so.6 (0x7ff4d0a2a000) libgcc_s.so.1 = /lib64/libgcc_s.so.1 (0x7ff4d0814000) libc.so.6 = /lib64/libc.so.6 (0x7ff4d048) /lib64/ld-linux-x86-64.so.2 (0x003148e0) 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
Re: [Rdkit-discuss] Installation of RDKit 2014 on Centos 5.10 (Final)
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? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss RDKit Installation on CentOS 5.10 = first create some directories... mkdir devel cd devel/ mkdir boost mkdir cmake mkdir RDKit Install CMake - cd cmake wget http://www.cmake.org/files/v2.8/cmake-2.8.12.2.tar.gz tar -xzvf cmake-2.8.12.2.tar.gz cd cmake cd cmake-2.8.12.2 ./bootstrap sudo make sudo make install ctest Install Boost - cd boost wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.bz2/download tar -xjvf boost_1_55_0.tar.bz2 cd boost_1_55_0 ./bootstrap.sh --with-libraries=python,regex Note: 64-bit OS ./b2 address-model=64 cflags=-fPIC cxxflags=-fPIC Install RDKit - cd RDKit/ wget wget http://downloads.sourceforge.net/project/rdkit/rdkit/Q1_2014/RDKit_2014_03_1.tgz tar -xzvf RDKit_2014_03_1.tgz cd RDKit_2014_03_1 mkdir build cd build/ Note: I was using Anaconda Python environment export PATH=~/anaconda/bin:$PATH export RDBASE=~/devel/RDKit/RDKit_2014_03_1 export LD_LIBRARY_PATH=/home/christos/devel/RDKit/RDKit_2014_03_1/lib:~/devel/boost/boost_1_55_0/stage/lib:$LD_LIBRARY_PATH export PYTHONPATH=$RDBASE:$PYTHONPATH cmake -D PYTHON_LIBRARY=~/anaconda/lib/python2.7/config/libpython2.7.a -D PYTHON_INCLUDE_DIR=~/anaconda/include/python2.7/ -D PYTHON_EXECUTABLE=~/anaconda/bin/python -D BOOST_ROOT=~/devel/boost/boost_1_55_0 .. make make install ctest -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Installation of RDKit 2014 on Centos 5.10 (Final)
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-multilibboost_python.a(clean) for lack of pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/threading-multinumeric.o... ...skipped pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/threading-multilibboost_python.a for lack of pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/threading-multinumeric.o... ...skipped p/usr/local/liblibboost_python.a for lack of pbin.v2/libs/python/build/gcc-4.1.2/release/address-model-64/link-static/threading-multilibboost_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? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
