Hi Sergey, Importing modshogun in python works without any errors. I do believe that the issue I was having is not really related to Eigen3 which as you mention is downloaded and used. The error I had was due to not finding LaplacianInferenceMethod in modshogun when I was trying to run an example script was trying to import it. I removed the the import statement and everything works fine (LaplacianInferenceMethod was not even used in the script). At this point I think that this issue could be closed although I am not sure why I was getting the error or why LaplacianInferenceMethod was not found. Thanks for taking the time to look into this issue.
Aref On Tue, Jan 26, 2016 at 9:39 AM, Sergey Lisitsyn <[email protected]> wrote: > Hey Aref, > > it seems that eigen3 is downloaded and used. > > What happens when you just 'import modshogun' within your python? > > Sergey > > On Sun, Jan 24, 2016 at 5:00 PM, Aref Nammari <[email protected]> > wrote: > >> Hi, >> >> Here is the the cmake output and other details. >> >> Below is the cmake command issued. >> >> aref@aref-Inspiron-N5010:~/shogun-develop/release$ cmake >> -DCMAKE_INSTALL_PREFIX="/usr/local" -DPythonModular=ON -DRModular=ON >> -DBUNDLE_EIGEN=ON .. >>cmake_out.txt 2>&1 >> aref@aref-Inspiron-N5010:~/shogun-develop/release$ >> >> >> _______________________________________________________________________________________________________________ >> >> This is the build drectory after cmake >> >> aref@aref-Inspiron-N5010:~/shogun-develop/release$ ls >> CMakeCache.txt cmake_out.txt doc Makefile >> CMakeFiles CPackConfig.cmake Eigen3 src >> cmake_install.cmake CPackSourceConfig.cmake examples >> aref@aref-Inspiron-N5010:~/shogun-develop/release$ >> >> >> ________________________________________________________________________________________________________________ >> >> This is the output of cmake written to file. >> >> >> -- The C compiler identification is GNU 4.8.4 >> -- The CXX compiler identification is GNU 4.8.4 >> -- 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 >> -- Found CCache: /usr/bin/ccache >> -- Found SWIG: /usr/bin/swig2.0 (found suitable version "2.0.11", minimum >> required is "2.0.5") >> -- Performing Test _HAS_CXX11_FLAG >> -- Performing Test _HAS_CXX11_FLAG - Success >> -- Checking C++11 support for "__func__" >> -- Checking C++11 support for "__func__": works >> -- Checking C++11 support for "atomic" >> -- Checking C++11 support for "atomic": works >> -- Checking C++11 support for "auto" >> -- Checking C++11 support for "auto": works >> -- Checking C++11 support for "auto_ret_type" >> -- Checking C++11 support for "auto_ret_type": works >> -- Checking C++11 support for "class_override_final" >> -- Checking C++11 support for "class_override_final": not supported >> -- Checking C++11 support for "constexpr" >> -- Checking C++11 support for "constexpr": works >> -- Checking C++11 support for "cstdint" >> -- Checking C++11 support for "cstdint": works >> -- Checking C++11 support for "decltype" >> -- Checking C++11 support for "decltype": works >> -- Checking C++11 support for "initializer_list" >> -- Checking C++11 support for "initializer_list": works >> -- Checking C++11 support for "lambda" >> -- Checking C++11 support for "lambda": works >> -- Checking C++11 support for "long_long" >> -- Checking C++11 support for "long_long": works >> -- Checking C++11 support for "nullptr" >> -- Checking C++11 support for "nullptr": works >> -- Checking C++11 support for "regex" >> -- Checking C++11 support for "regex": not supported >> -- Checking C++11 support for "rvalue-references" >> -- Checking C++11 support for "rvalue-references": works >> -- Checking C++11 support for "sizeof_member" >> -- Checking C++11 support for "sizeof_member": works >> -- Checking C++11 support for "static_assert" >> -- Checking C++11 support for "static_assert": works >> -- Checking C++11 support for "variadic_templates" >> -- Checking C++11 support for "variadic_templates": works >> -- Looking for C++ include unordered_map >> -- Looking for C++ include unordered_map - found >> -- Using system's malloc >> -- Looking for isfinite >> -- Looking for isfinite - not found >> -- Looking for isinf >> -- Looking for isinf - found >> -- Looking for isnan >> -- Looking for isnan - found >> -- Looking for signgam >> -- Looking for signgam - found >> -- Looking for fdopen >> -- Looking for fdopen - found >> -- Looking for log2 >> -- Looking for log2 - found >> -- Looking for powl >> -- Looking for powl - found >> -- Looking for lgammal >> -- Looking for lgammal - found >> -- Looking for sqrtl >> -- Looking for sqrtl - found >> -- Looking for finite >> -- Looking for finite - found >> -- Looking for isfinite >> -- Looking for isfinite - not found >> -- Looking for isinf >> -- Looking for isinf - found >> -- Looking for isnan >> -- Looking for isnan - found >> -- Performing Test HAVE_STD_ISINF >> -- Performing Test HAVE_STD_ISINF - Success >> -- Performing Test HAVE_STD_ISFINITE >> -- Performing Test HAVE_STD_ISFINITE - Success >> -- Performing Test HAVE_STD_ISNAN >> -- Performing Test HAVE_STD_ISNAN - Success >> -- Looking for xmmintrin.h >> -- Looking for xmmintrin.h - found >> -- Looking for emmintrin.h >> -- Looking for emmintrin.h - found >> -- Looking for arc4random >> -- Looking for arc4random - not found >> -- Found GDB: /usr/bin/gdb >> -- Could NOT find MOSEK (missing: MOSEK_DIR MOSEK_INCLUDE_DIR >> MOSEK_LIBRARY) >> -- 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 >> -- Try OpenMP C flag = [-fopenmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Try OpenMP CXX flag = [-fopenmp] >> -- Performing Test OpenMP_FLAG_DETECTED >> -- Performing Test OpenMP_FLAG_DETECTED - Success >> -- Found OpenMP: -fopenmp >> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") >> -- Looking for dgemm_ >> -- Looking for dgemm_ - found >> -- A library with BLAS API found. >> -- Looking for cheev_ >> -- Looking for cheev_ - found >> -- A library with LAPACK API found. >> -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 >> -- Looking for clapack_dpotrf in /usr/lib/atlas-base/liblapack_atlas.so.3 >> - found >> -- Could NOT find ATLAS (missing: ATLAS_INCLUDES) >> -- Found CBLAS: /usr/lib/libcblas.so.3 >> -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 >> -- Looking for cblas_dsyrk in /usr/lib/libcblas.so.3 - found >> -- Found GLPK: /usr/lib/x86_64-linux-gnu/libglpk.so >> -- Could NOT find CPLEX (missing: CPLEX_LIBRARY CPLEX_INCLUDE_DIR) >> -- Found Arpack : /usr/lib/libarpack.so >> -- Could NOT find OPENCL (missing: OPENCL_INCLUDE_DIR) >> -- Could NOT find ViennaCL (missing: VIENNACL_INCLUDE_DIR >> OPENCL_INCLUDE_DIRS OPENCL_LIBRARIES) (Required is at least version "1.5.0") >> -- checking for one of the modules 'libColPack>=1.0.9;ColPack>=1.0.9' >> -- Could NOT find NLOPT (missing: NLOPT_LIBRARY NLOPT_INCLUDE_DIR) >> -- Could NOT find LPSOLVE (missing: LPSOLVE_LIBRARIES >> LPSOLVE_INCLUDE_DIR) >> -- Could NOT find ColPack (missing: COLPACK_LIBRARIES >> COLPACK_LIBRARY_DIR COLPACK_INCLUDE_DIR) >> -- Could NOT find ARPREC (missing: ARPREC_LIBRARIES ARPREC_INCLUDE_DIR) >> -- Found Doxygen: /usr/bin/doxygen (found suitable version "1.8.6", >> minimum required is "1.8.6") >> -- Found PythonInterp: /usr/bin/python (found version "2.7.6") >> -- checking for one of the modules 'libjson>=0.11;json>=0.11;json-c>=0.11' >> -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version >> "2.9.1") >> -- Found HDF5: >> /usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so >> >> -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version >> "7.35.0") >> -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") >> -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version >> "1.0.6") >> -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so >> -- Looking for BZ2_bzCompressInit in /usr/lib/x86_64-linux-gnu/libbz2.so >> - found >> -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so >> -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so >> - found >> -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so >> -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so >> - found >> -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so >> -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - >> found >> -- Found LibLZMA: /usr/include (found version "5.1.0") >> -- Could NOT find SNAPPY (missing: SNAPPY_LIBRARIES SNAPPY_INCLUDE_DIR) >> -- Lzo includes and libraries NOT found. >> -- Spinlock support found >> -- Found PROTOBUF: /usr/lib/x86_64-linux-gnu/libprotobuf.so >> -- Supported backend(s) for linear algebra NOT FOUND/NOT ENABLED >> -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found >> version "2.7.6") >> -- Found NumPy: version "1.8.2" >> /usr/lib/python2.7/dist-packages/numpy/core/include >> -- Found R: /usr/bin/R >> -- >> =================================================================================================================== >> -- Summary of Configuration Variables >> -- >> -- The following OPTIONAL packages have been found: >> >> * CCache >> * GDB >> * OpenMP >> * BLAS >> * LAPACK >> * CBLAS >> * GLPK >> * ARPACK >> * Doxygen (required version >= 1.8.6) >> * LibXml2 >> * HDF5 >> * CURL >> * ZLIB >> * BZip2 >> * LibLZMA >> * Spinlock >> * Threads >> * Protobuf >> >> -- The following REQUIRED packages have been found: >> >> * SWIG (required version >= 2.0.5) >> * PythonLibs >> * PythonInterp >> * NumPy >> * R >> >> -- The following OPTIONAL packages have not been found: >> >> * Mosek >> * Atlas >> * CPLEX >> * ViennaCL (required version >= 1.5.0) >> * NLopt >> * LpSolve >> * ColPack >> * ARPREC >> * SNAPPY >> * LZO >> >> -- The following REQUIRED packages have not been found: >> >> * OpenCL >> >> -- >> =================================================================================================================== >> -- Enabled Integration >> -- OpenCV Integration is OFF - enable with -DOpenCV=ON >> -- >> =================================================================================================================== >> -- Enabled Interfaces >> -- libshogun is ON >> -- python modular is ON >> -- octave modular is OFF - enable with -DOctaveModular=ON >> -- java modular is OFF - enable with -DJavaModular=ON >> -- perl modular is OFF - enable with -DPerlModular=ON >> -- ruby modular is OFF - enable with -DRubyModular=ON >> -- csharp modular is OFF - enable with -DCSharpModular=ON >> -- R modular is ON >> -- lua modular is OFF - enable with -DLuaModular=ON >> -- >> -- Enabled legacy interfaces >> -- cmdline static is OFF - enable with -DCmdLineStatic=ON >> -- python static is OFF - enable with -DPythonStatic=ON >> -- octave static is OFF - enable with -DOctaveStatic=ON >> -- matlab static is OFF - enable with -DMatlabStatic=ON >> -- R static is OFF - enable with -DRStatic=ON >> -- >> =================================================================================================================== >> -- To compile shogun type >> -- make >> -- >> -- To install shogun to /usr/local type >> -- make install >> -- >> -- or to install to a custom directory >> -- make install DESTDIR=/my/special/path >> -- (or rerun cmake with -DCMAKE_INSTALL_PREFIX=/my/special/path) to >> just change the prefix >> -- >> =================================================================================================================== >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /home/aref/shogun-develop/release >> >> On Sun, Jan 24, 2016 at 6:07 AM, Aref Nammari <[email protected]> >> wrote: >> >>> I am not sure what do you mean by "cake output". I removed the >>> LaplacianInferenceMethod from the import statement (it wasn't even used in >>> the rest of the script) and everything works. I tried all the examples in >>> the modular_python graphical including eigenfaces.py and everything seems >>> to work--I had to modify some things because some of the examples used >>> functions that were changed or renamed and LaplacianInferenceMethod could >>> be one of those. Am I right to believe that there is not an issue with >>> Eigen but rather the issue us with the examples not following recent >>> changes in shogun 4.0.0? >>> >>> On Sun, Jan 24, 2016 at 3:31 AM, Heiko Strathmann < >>> [email protected]> wrote: >>> >>>> Hi >>>> >>>> Ok, that's one down. Can you post your cake output? Seems like Eigen >>>> wasn't detected >>>> >>>> H >>>> >>>> >>>> On Saturday, 23 January 2016, Aref Nammari <[email protected]> >>>> wrote: >>>> >>>>> Hi Heiko, >>>>> >>>>> I downloaded and built the latest git develop branch and got the same >>>>> results. It is the "from modshogun import LaplacianInferenceMethod " that >>>>> is the source of the error--cannot import error. >>>>> >>>>> Aref >>>>> >>>>> On Fri, Jan 22, 2016 at 8:42 AM, Aref Nammari <[email protected]> >>>>> wrote: >>>>> >>>>>> Hello Heiko, >>>>>> >>>>>> Thank you for the reply. >>>>>> I believe the problem is not related to Eigen3. I took a look at the >>>>>> script I was trying to run and tried to see where the error was. I >>>>>> narrowed >>>>>> it down to an import statement " from modshogun import >>>>>> LaplacianInferenceMethod ". This import causes a not found error. The >>>>>> exception in the script returns 'Eigen3 needed for Gaussian Processes' >>>>>> which led me to believe that there was a problem in the build. I think >>>>>> the >>>>>> build is OK. However, I am not quite sure why the import does not work. >>>>>> The >>>>>> example I was trying to run is in >>>>>> examples/undocumented/python_modular/graphical/classifier_gaussian_process_binary_classification.py >>>>>> I will try the latest version in git and see if the problem persists. >>>>>> >>>>>> >>>>>> Thanks, >>>>>> Aref >>>>>> >>>>>> On Fri, Jan 22, 2016 at 3:52 AM, Heiko Strathmann < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Hi Aref, >>>>>>> >>>>>>> This is weird, can you post a gist with the cmake output somewhere? >>>>>>> >>>>>>> Also, could you try to do the same thing again with the latest git >>>>>>> version of shogun? >>>>>>> >>>>>>> H >>>>>>> >>>>>>> 2016-01-21 20:14 GMT+00:00 Aref Nammari <[email protected]>: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> I have installed shogun-toolbox version 4.0.0 downloaded from >>>>>>>> shogun-toolbox.org. I installed python –modular and RModular. No >>>>>>>> errors were reported during the build process. I tried several >>>>>>>> examples and >>>>>>>> they seem to work with the exception of examples requiring Eigen3. >>>>>>>> During >>>>>>>> the build process I have turned BUNDLE_EIGEN ON and the package >>>>>>>> appears to >>>>>>>> have been downloaded but when I try some of the examples requiring >>>>>>>> Eigen3 >>>>>>>> (such Gaussian_processe examples) I get an error “Gaussian processes >>>>>>>> require Eigen3 be installed). I am not sure what the problem is or how >>>>>>>> to >>>>>>>> solve it. Any help in this area is appreciated. I am running python >>>>>>>> 2.7.6 >>>>>>>> and also have Anaconda installed. The OS is Ubuntu 14.04 LTS. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks, >>>>>>>> >>>>>>>> Aref >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>> >> >
