Hi Aref, in this version of Shogun LaplacianInferenceMethod class was renamed to SingleLaplacianInferenceMethod, but it was not renamed in this script. So you could try to rename this import statement to SingleLaplacianInferenceMethod in the script to use Laplace's approximation method.
Best, Roman On Tue, Jan 26, 2016 at 8:07 PM, Aref Nammari <[email protected]> wrote: > 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 >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>> >>> >> >
