Disabling logs in IMP
Hello all,
I would like first to say that IMP has been a great help for me and I have been using it extensively in my current project. Thank you!
I just pulled the latest IMP from the git and built it after doing :
cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release
Suddenly when running code using IMP (python bindings) I'm getting tons of logs (for each creation/destruction of a Model object for example)
I thought I was building in release so why do I get all of those logs? Can I disable them?
You can see below the output of the cmake command. I'm using cmake version 2.8.7
Thank you, Dany * * *Example for some logs : * Matched Atom N of residue 525 with [] and 1 end search begin search: Matched Atom CA of residue 525 with [] and 1 end search begin search: Matched Atom C of residue 525 with [] and 1 end search begin search: Matched Atom O of residue 525 with [] and 1 end search begin search: Matched Atom CB of residue 525 with [] and 1 end search begin search: Matched Atom CG of residue 525 with [] and 1 end search begin search: Matched Atom CD of residue 525 with [] and 1 end search Matched PRO with [4365, 4367, 4368, 4369, 4370, 4371, 4372] and 1 end search Matched Chain E with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 end search Matched 1oel_E.pdb: with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 end search * * *The cmake output : *
$ cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- 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 -- Running check_common_problems -- Running setup_cmake -- Wrong doxygen version at /usr/bin/doxygen. Found 1.7.6.1, but needed 1.8.4 -- Will download doxygen from http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.4.linux.bin.tar.gz -- Running setup_doxygen -- Python version is 2.7 -- Found PythonLibs: /usr/lib/libpython2.7.so (found suitable exact version "2.7.3") -- Running setup -- Running setup_containers -- Running setup_all -- Running setup_module_alias for compatibility -- Setting up alias for module base as compatibility -- Running setup_module_alias for kernel -- Setting up alias for module kernel as -- Boost version: 1.46.1 -- Found the following Boost libraries: -- system -- filesystem -- thread -- program_options -- Performing Test IMP_COMPILER_HAS_AUTO -- Performing Test IMP_COMPILER_HAS_AUTO - Failed -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Success -- checking for module 'gperftools' -- package 'gperftools' not found GPerfTools not found -- checking for module 'log4cxx' -- package 'log4cxx' not found -- Found LOG4CXX -- Performing Test Log4CXX_found -- Performing Test Log4CXX_found - Success -- Found Log4CXX -- checking for module 'tcmalloc_heapchecker' -- package 'tcmalloc_heapchecker' not found TCMalloc_HeapChecker not found -- checking for module 'tcmalloc_heapprofiler' -- package 'tcmalloc_heapprofiler' not found TCMalloc_HeapProfiler not found -- Running generate paths.cpp Configuring module base ... yes -- Running setup_swig_wrappers base Configuring module benchmark ... yes -- Running setup_swig_wrappers benchmark -- Build type: Release -- USING CXXFLAGS = ' -O3 -DNDEBUG' -- USING EXEFLAGS = ' ' -- Targetting Unix Makefiles -- Using /usr/bin/c++ compiler. -- Updating CMAKE_CXX_FLAGS Configuring module cgal ... yes -- Running setup_swig_wrappers cgal Configuring module kmeans ... yes -- Running setup_swig_wrappers kmeans -- Found MPI_C: /usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so
-- Found MPI_CXX: /usr/local/lib/openmpi-1.4.1/lib/libmpi_cxx.so;/usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so
-- MPI found Configuring module mpi ... yes -- Running setup_swig_wrappers mpi Configuring module test ... yes -- Running setup_swig_wrappers test -- checking for module 'ann' -- package 'ann' not found ANN not found Configuring module algebra ... yes -- Running setup_swig_wrappers algebra Configuring module kernel ... yes -- Running setup_swig_wrappers kernel Configuring module display ... yes -- Running setup_swig_wrappers display -- checking for module 'gsl' -- found gsl, version 1.15 -- Found GSL -- Performing Test GSL_found -- Performing Test GSL_found - Success -- Found GSL Configuring module gsl ... yes -- Running setup_swig_wrappers gsl Configuring module parallel ... yes -- Running setup_swig_wrappers parallel Configuring module score_functor ... yes -- Running setup_swig_wrappers score_functor Configuring module statistics ... yes -- Running setup_swig_wrappers statistics Configuring module system ... yes -- Running setup_swig_wrappers system Configuring module core ... yes -- Running setup_swig_wrappers core Configuring module container ... yes -- Running setup_swig_wrappers container Configuring module modeller ... yes -- Running setup_swig_wrappers modeller Configuring module symmetry ... yes -- Running setup_swig_wrappers symmetry Configuring module atom ... yes -- Running setup_swig_wrappers atom Configuring module scratch ... yes -- Running setup_swig_wrappers scratch Configuring module em ... yes -- Running setup_swig_wrappers em Configuring module kinematics ... yes -- Running setup_swig_wrappers kinematics Configuring module misc ... yes -- Running setup_swig_wrappers misc -- Performing Test RMF_environment -- Performing Test RMF_environment - Failed -- checking for module 'RMF' -- package 'RMF' not found -- Building internal RMF -- checking for module 'log4cxx' -- package 'log4cxx' not found -- Found Log4CXX -- Logging enabled -- Found HDF5: debug;/usr/lib/libhdf5.so;optimized;/usr/lib/libhdf5.so -- Found SWIG: swig (found version "2.0.4") -- /usr/include/python2.7 -- benchmark_size -- benchmark_rmf -- Found Doxygen: /usr/bin/doxygen -- Updating paths for RMF <> Configuring module rmf ... yes -- Running setup_swig_wrappers rmf Configuring module rotamer ... yes -- Running setup_swig_wrappers rotamer Configuring module saxs ... yes -- Running setup_swig_wrappers saxs -- checking for module 'hdf5' -- package 'hdf5' not found -- Found HDF5 -- Performing Test HDF5_found -- Performing Test HDF5_found - Success -- Found HDF5 Configuring module domino ... yes -- Running setup_swig_wrappers domino -- checking for module 'cholmod' -- package 'cholmod' not found CHOLMOD not found -- checking for module 'eigen3' -- package 'eigen3' not found Eigen3 not found Configuring module isd ... Eigen3 not found Different data/build_info/sorted_modules -isd Module IMP.isd disabled Configuring module restrainer ... yes -- Running setup_swig_wrappers restrainer -- checking for module 'fftw3' -- found fftw3, version 3.3.3 -- Found FFTW3 -- Performing Test FFTW3_found -- Performing Test FFTW3_found - Success -- Found FFTW3 -- checking for module 'opencv21' -- package 'opencv21' not found OpenCV21 not found -- checking for module 'opencv22' -- package 'opencv22' not found OpenCV22 not found em2d is disabled Different data/build_info/sorted_modules -em2d Module IMP.em2d disabled -- checking for module 'exampledependency' -- package 'exampledependency' not found ExampleDependency not found Configuring module example ... yes -- Running setup_swig_wrappers example Configuring module multifit ... yes -- Running setup_swig_wrappers multifit Configuring module pepdock ... yes -- Running setup_swig_wrappers pepdock -- checking for module 'libtau' -- package 'libtau' not found libTau not found Configuring module cnmultifit ... libTau not found Different data/build_info/sorted_modules -cnmultifit Module IMP.cnmultifit disabled -- Running setup_swig_dependencies -- Creating thread pool with 16 Configuring application EMageFit ... no Different data/build_info/applications -EMageFit Application EMageFit disabled Configuring application cnmultifit_tools ... no Different data/build_info/applications -cnmultifit_tools Application cnmultifit_tools disabled Configuring application em_tools ... yes Configuring application example_app ... yes Configuring application foxs ... yes Configuring application integrative_docking ... yes Configuring application ligand_score ... yes Configuring application multifit_tools ... yes Configuring application pdb_tools ... yes Configuring application rmf_tools ... yes Configuring application saxs_merge ... no Different data/build_info/applications -saxs_merge Application saxs_merge disabled Configuring application saxs_tools ... yes -- Running setup_doxygen_config -- Running setup_imppy -- Configuring done
You can control logging at both configure time and at runtime.
To build IMP without logging support (which can make IMP faster than just disabling logging) you can - add -DIMP_MAX_LOG=SILENT - rebuild IMP
to control it at runtime you can - add IMP::base::set_log_level(IMP::base::SILENT) (or replace :: with . for python) - add --log_level=0 as a command line argument to many IMP executables
That said, the logging you see is something that got turned on due to some issues we were debugging with atom::Selection and perhaps should go away.
On Aug 4, 2013, at 2:04 AM, Dan Cohen bojemoi@gmail.com wrote:
> Hello all, > > I would like first to say that IMP has been a great help for me and I have been using > it extensively in my current project. Thank you! > > I just pulled the latest IMP from the git and built it after doing : > > cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release > > Suddenly when running code using IMP (python bindings) I'm getting tons > of logs (for each creation/destruction of a Model object for example) > > I thought I was building in release so why do I get all of those logs? Can I disable them? > > You can see below the output of the cmake command. > I'm using cmake version 2.8.7 > > Thank you, > Dany > > Example for some logs : > > Matched Atom N of residue 525 with [] and 1 > end search > begin search: > Matched Atom CA of residue 525 with [] and 1 > end search > begin search: > Matched Atom C of residue 525 with [] and 1 > end search > begin search: > Matched Atom O of residue 525 with [] and 1 > end search > begin search: > Matched Atom CB of residue 525 with [] and 1 > end search > begin search: > Matched Atom CG of residue 525 with [] and 1 > end search > begin search: > Matched Atom CD of residue 525 with [] and 1 > end search > Matched PRO with [4365, 4367, 4368, 4369, 4370, 4371, 4372] and 1 > end search > Matched Chain E with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 > end search > Matched 1oel_E.pdb: with [0, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, ,...] and 1 > end search > > The cmake output : > > $ cmake ../imp-source/ -DCMAKE_BUILD_TYPE=Release > -- The C compiler identification is GNU > -- The CXX compiler identification is GNU > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- 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 > -- Running check_common_problems > -- Running setup_cmake > -- Wrong doxygen version at /usr/bin/doxygen. Found 1.7.6.1, but needed 1.8.4 > -- Will download doxygen from http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.4.linux.bin.tar.gz > -- Running setup_doxygen > -- Python version is 2.7 > -- Found PythonLibs: /usr/lib/libpython2.7.so (found suitable exact version "2.7.3") > -- Running setup > -- Running setup_containers > -- Running setup_all > -- Running setup_module_alias for compatibility > -- Setting up alias for module base as compatibility > -- Running setup_module_alias for kernel > -- Setting up alias for module kernel as > -- Boost version: 1.46.1 > -- Found the following Boost libraries: > -- system > -- filesystem > -- thread > -- program_options > -- Performing Test IMP_COMPILER_HAS_AUTO > -- Performing Test IMP_COMPILER_HAS_AUTO - Failed > -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR > -- Performing Test IMP_COMPILER_HAS_DEBUG_VECTOR - Success > -- checking for module 'gperftools' > -- package 'gperftools' not found > GPerfTools not found > -- checking for module 'log4cxx' > -- package 'log4cxx' not found > -- Found LOG4CXX > -- Performing Test Log4CXX_found > -- Performing Test Log4CXX_found - Success > -- Found Log4CXX > -- checking for module 'tcmalloc_heapchecker' > -- package 'tcmalloc_heapchecker' not found > TCMalloc_HeapChecker not found > -- checking for module 'tcmalloc_heapprofiler' > -- package 'tcmalloc_heapprofiler' not found > TCMalloc_HeapProfiler not found > -- Running generate paths.cpp > Configuring module base ... yes > -- Running setup_swig_wrappers base > Configuring module benchmark ... yes > -- Running setup_swig_wrappers benchmark > -- Build type: Release > -- USING CXXFLAGS = ' -O3 -DNDEBUG' > -- USING EXEFLAGS = ' ' > -- Targetting Unix Makefiles > -- Using /usr/bin/c++ compiler. > -- Updating CMAKE_CXX_FLAGS > Configuring module cgal ... yes > -- Running setup_swig_wrappers cgal > Configuring module kmeans ... yes > -- Running setup_swig_wrappers kmeans > -- Found MPI_C: /usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so > -- Found MPI_CXX: /usr/local/lib/openmpi-1.4.1/lib/libmpi_cxx.so;/usr/local/lib/openmpi-1.4.1/lib/libmpi.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-rte.so;/usr/local/lib/openmpi-1.4.1/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libnsl.so;/usr/lib/x86_64-linux-gnu/libutil.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libdl.so > -- MPI found > Configuring module mpi ... yes > -- Running setup_swig_wrappers mpi > Configuring module test ... yes > -- Running setup_swig_wrappers test > -- checking for module 'ann' > -- package 'ann' not found > ANN not found > Configuring module algebra ... yes > -- Running setup_swig_wrappers algebra > Configuring module kernel ... yes > -- Running setup_swig_wrappers kernel > Configuring module display ... yes > -- Running setup_swig_wrappers display > -- checking for module 'gsl' > -- found gsl, version 1.15 > -- Found GSL > -- Performing Test GSL_found > -- Performing Test GSL_found - Success > -- Found GSL > Configuring module gsl ... yes > -- Running setup_swig_wrappers gsl > Configuring module parallel ... yes > -- Running setup_swig_wrappers parallel > Configuring module score_functor ... yes > -- Running setup_swig_wrappers score_functor > Configuring module statistics ... yes > -- Running setup_swig_wrappers statistics > Configuring module system ... yes > -- Running setup_swig_wrappers system > Configuring module core ... yes > -- Running setup_swig_wrappers core > Configuring module container ... yes > -- Running setup_swig_wrappers container > Configuring module modeller ... yes > -- Running setup_swig_wrappers modeller > Configuring module symmetry ... yes > -- Running setup_swig_wrappers symmetry > Configuring module atom ... yes > -- Running setup_swig_wrappers atom > Configuring module scratch ... yes > -- Running setup_swig_wrappers scratch > Configuring module em ... yes > -- Running setup_swig_wrappers em > Configuring module kinematics ... yes > -- Running setup_swig_wrappers kinematics > Configuring module misc ... yes > -- Running setup_swig_wrappers misc > -- Performing Test RMF_environment > -- Performing Test RMF_environment - Failed > -- checking for module 'RMF' > -- package 'RMF' not found > -- Building internal RMF > -- checking for module 'log4cxx' > -- package 'log4cxx' not found > -- Found Log4CXX > -- Logging enabled > -- Found HDF5: debug;/usr/lib/libhdf5.so;optimized;/usr/lib/libhdf5.so > -- Found SWIG: swig (found version "2.0.4") > -- /usr/include/python2.7 > -- benchmark_size > -- benchmark_rmf > -- Found Doxygen: /usr/bin/doxygen > -- Updating paths for RMF <> > Configuring module rmf ... yes > -- Running setup_swig_wrappers rmf > Configuring module rotamer ... yes > -- Running setup_swig_wrappers rotamer > Configuring module saxs ... yes > -- Running setup_swig_wrappers saxs > -- checking for module 'hdf5' > -- package 'hdf5' not found > -- Found HDF5 > -- Performing Test HDF5_found > -- Performing Test HDF5_found - Success > -- Found HDF5 > Configuring module domino ... yes > -- Running setup_swig_wrappers domino > -- checking for module 'cholmod' > -- package 'cholmod' not found > CHOLMOD not found > -- checking for module 'eigen3' > -- package 'eigen3' not found > Eigen3 not found > Configuring module isd ... Eigen3 not found > Different data/build_info/sorted_modules > -isd > Module IMP.isd disabled > Configuring module restrainer ... yes > -- Running setup_swig_wrappers restrainer > -- checking for module 'fftw3' > -- found fftw3, version 3.3.3 > -- Found FFTW3 > -- Performing Test FFTW3_found > -- Performing Test FFTW3_found - Success > -- Found FFTW3 > -- checking for module 'opencv21' > -- package 'opencv21' not found > OpenCV21 not found > -- checking for module 'opencv22' > -- package 'opencv22' not found > OpenCV22 not found > em2d is disabled > Different data/build_info/sorted_modules > -em2d > Module IMP.em2d disabled > -- checking for module 'exampledependency' > -- package 'exampledependency' not found > ExampleDependency not found > Configuring module example ... yes > -- Running setup_swig_wrappers example > Configuring module multifit ... yes > -- Running setup_swig_wrappers multifit > Configuring module pepdock ... yes > -- Running setup_swig_wrappers pepdock > -- checking for module 'libtau' > -- package 'libtau' not found > libTau not found > Configuring module cnmultifit ... libTau not found > Different data/build_info/sorted_modules > -cnmultifit > Module IMP.cnmultifit disabled > -- Running setup_swig_dependencies > -- Creating thread pool with 16 > Configuring application EMageFit ... no > Different data/build_info/applications > -EMageFit > Application EMageFit disabled > Configuring application cnmultifit_tools ... no > Different data/build_info/applications > -cnmultifit_tools > Application cnmultifit_tools disabled > Configuring application em_tools ... yes > Configuring application example_app ... yes > Configuring application foxs ... yes > Configuring application integrative_docking ... yes > Configuring application ligand_score ... yes > Configuring application multifit_tools ... yes > Configuring application pdb_tools ... yes > Configuring application rmf_tools ... yes > Configuring application saxs_merge ... no > Different data/build_info/applications > -saxs_merge > Application saxs_merge disabled > Configuring application saxs_tools ... yes > -- Running setup_doxygen_config > -- Running setup_imppy > -- Configuring done > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users
participants (2)
-
Dan Cohen -
Daniel Russel