-- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- 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 -- Detecting C compile features -- Detecting C compile features - 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 -- Detecting CXX compile features -- Detecting CXX compile features - done -- Config file: /home/shawn/sourcecode/espresso_trial/espresso/src/core/myconfig-default.hpp -- Performing Test result__PRETTY_FUNCTION__ -- Performing Test result__PRETTY_FUNCTION__ - Success CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "7.0") -- Found PythonInterp: /home/shawn/soft/python3/bin/python3 (found version "3.6.5") -- Found Cython version 0.29.12 -- Found Cython: /home/shawn/soft/python3/bin/cython (Required is at least version "0.23") -- Found NumPy: /home/shawn/.local/lib/python3.6/site-packages/numpy/core/include (found version "1.16.4") -- NumPy ver. 1.16.4 found (include: /home/shawn/.local/lib/python3.6/site-packages/numpy/core/include) -- Could NOT find HDF5: Found unsuitable version "", but required is at least "1.8" (found HDF5_hdf5_LIBRARY-NOTFOUND) -- Found PkgConfig: /usr/bin/pkg-config (found version "0.27.1") -- Could NOT find GSL (missing: GSL_INCLUDE_DIR GSL_LIBRARY GSL_CBLAS_LIBRARY) (found version "") -- Found MPI_C: /home/shawn/soft/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /home/shawn/soft/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) -- Boost version: 1.70.0 -- Found the following Boost libraries: -- mpi -- serialization -- filesystem -- system -- unit_test_framework -- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen missing components: dot -- Found Sphinx: /home/shawn/.local/bin/sphinx-build (found suitable version "2.1.2", minimum required is "1.6.6") -- writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/myconfig-sample.hpp -- The following OPTIONAL packages have been found: * FFTW3 * PkgConfig * Doxygen * Sphinx (required version >= 1.6.6) -- The following REQUIRED packages have been found: * PythonInterp * Cython (required version >= 0.23) * NumPy * MPI * Boost (required version >= 1.53.0) -- The following OPTIONAL packages have not been found: * CUDA (required version >= 7.0) * HDF5 (required version >= 1.8) * GSL -- Configuring done -- Generating done -- Build files have been written to: /home/shawn/sourcecode/espresso_trial/espresso/build-patched Scanning dependencies of target object_in_fluid Scanning dependencies of target myconfig [ 0%] Built target myconfig Scanning dependencies of target check_myconfig [ 0%] Built target object_in_fluid [ 0%] Built target check_myconfig [ 0%] Generating config-features.hpp, config-features.cpp Reading definitions from /home/shawn/sourcecode/espresso_trial/espresso/src/features.def... Done. Writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/src/core/config-features.hpp... Done. Writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/src/core/config-features.cpp... Done. Scanning dependencies of target EspressoConfig [ 1%] Building CXX object src/core/CMakeFiles/EspressoConfig.dir/config-features.cpp.o [ 1%] Linking CXX shared library libEspressoConfig.so [ 1%] Built target EspressoConfig Scanning dependencies of target ImmersedBoundary Scanning dependencies of target Shapes Scanning dependencies of target Observables Scanning dependencies of target VirtualSites [ 2%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Cylinder.cpp.o [ 2%] Building CXX object src/core/virtual_sites/CMakeFiles/VirtualSites.dir/VirtualSitesInertialessTracers.cpp.o [ 2%] Building CXX object src/core/immersed_boundary/CMakeFiles/ImmersedBoundary.dir/ImmersedBoundaries.cpp.o [ 2%] Building CXX object src/core/observables/CMakeFiles/Observables.dir/CylindricalLBFluxDensityProfileAtParticlePositions.cpp.o [ 2%] Building CXX object src/core/virtual_sites/CMakeFiles/VirtualSites.dir/VirtualSitesRelative.cpp.o [ 2%] Building CXX object src/core/immersed_boundary/CMakeFiles/ImmersedBoundary.dir/ibm_tribend.cpp.o Scanning dependencies of target cluster_analysis Scanning dependencies of target ObjectInFluid Scanning dependencies of target Accumulators [ 4%] Building CXX object src/core/immersed_boundary/CMakeFiles/ImmersedBoundary.dir/ibm_triel.cpp.o [ 5%] Building CXX object src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/Cluster.cpp.o [ 6%] Building CXX object src/core/object-in-fluid/CMakeFiles/ObjectInFluid.dir/affinity.cpp.o [ 6%] Linking CXX shared library libImmersedBoundary.so [ 6%] Building CXX object src/core/accumulators/CMakeFiles/Accumulators.dir/Correlator.cpp.o [ 6%] Built target ImmersedBoundary [ 6%] Building CXX object src/core/object-in-fluid/CMakeFiles/ObjectInFluid.dir/membrane_collision.cpp.o Scanning dependencies of target Actor [ 6%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/ActorList.cpp.o [ 6%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Ellipsoid.cpp.o [ 8%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/DipolarBarnesHut.cpp.o [ 8%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/HollowCone.cpp.o [ 8%] Building CXX object src/core/cluster_analysis/CMakeFiles/cluster_analysis.dir/ClusterStructure.cpp.o [ 9%] Building CXX object src/core/virtual_sites/CMakeFiles/VirtualSites.dir/lb_inertialess_tracers.cpp.o [ 9%] Building CXX object src/core/virtual_sites/CMakeFiles/VirtualSites.dir/lb_inertialess_tracers_cuda_interface.cpp.o [ 9%] Building CXX object src/core/virtual_sites/CMakeFiles/VirtualSites.dir/virtual_sites_com.cpp.o [ 9%] Building CXX object src/core/object-in-fluid/CMakeFiles/ObjectInFluid.dir/oif_global_forces.cpp.o [ 9%] Linking CXX shared library libVirtualSites.so [ 9%] Built target VirtualSites [ 9%] Building CXX object src/core/object-in-fluid/CMakeFiles/ObjectInFluid.dir/oif_local_forces.cpp.o [ 9%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Maze.cpp.o [ 9%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/DipolarDirectSum.cpp.o [ 9%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/HarmonicOrientationWell.cpp.o [ 10%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Rhomboid.cpp.o [ 10%] Building CXX object src/core/object-in-fluid/CMakeFiles/ObjectInFluid.dir/out_direction.cpp.o [ 10%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/SimplePore.cpp.o [ 10%] Building CXX object src/core/observables/CMakeFiles/Observables.dir/CylindricalLBVelocityProfile.cpp.o [ 10%] Building CXX object src/core/observables/CMakeFiles/Observables.dir/CylindricalLBVelocityProfileAtParticlePositions.cpp.o [ 10%] Building CXX object src/core/accumulators/CMakeFiles/Accumulators.dir/MeanVarianceCalculator.cpp.o [ 10%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/HarmonicWell.cpp.o [ 10%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Slitpore.cpp.o [ 12%] Linking CXX shared library libObjectInFluid.so [ 12%] Built target ObjectInFluid [ 12%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Sphere.cpp.o [ 12%] Building CXX object src/core/actor/CMakeFiles/Actor.dir/Mmm1dgpuForce.cpp.o [ 12%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/SpheroCylinder.cpp.o Scanning dependencies of target Constraints [ 12%] Building CXX object src/core/constraints/CMakeFiles/Constraints.dir/HomogeneousMagneticField.cpp.o [ 12%] Linking CXX shared library libcluster_analysis.so [ 12%] Building CXX object src/core/constraints/CMakeFiles/Constraints.dir/ShapeBasedConstraint.cpp.o [ 13%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Stomatocyte.cpp.o [ 13%] Built target cluster_analysis [ 13%] Building CXX object src/core/shapes/CMakeFiles/Shapes.dir/Wall.cpp.o Scanning dependencies of target LBBoundaries [ 13%] Building CXX object src/core/lbboundaries/CMakeFiles/LBBoundaries.dir/LBBoundary.cpp.o [ 13%] Generating gen_pxiconfig.cpp Reading definitions from /home/shawn/sourcecode/espresso_trial/espresso/src/features.def... Done. Writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/src/python/espressomd/gen_pxiconfig.cpp... Done. 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src/script_interface/CMakeFiles/EspressoScriptInterface.dir/ScriptInterfaceBase.cpp.o [ 57%] Building CXX object src/script_interface/CMakeFiles/EspressoScriptInterface.dir/shapes/initialize.cpp.o [ 57%] Building CXX object src/script_interface/CMakeFiles/EspressoScriptInterface.dir/Variant.cpp.o [ 57%] Building CXX object src/script_interface/CMakeFiles/EspressoScriptInterface.dir/ParallelScriptInterface.cpp.o [ 57%] Building CXX object src/script_interface/CMakeFiles/EspressoScriptInterface.dir/ParallelScriptInterfaceSlave.cpp.o [ 58%] Linking CXX shared library libEspressoScriptInterface.so [ 58%] Built target EspressoScriptInterface [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 58%] Generating myconfig.pxi [ 60%] Generating visualization_opengl.cpp [ 60%] Generating polymer.cpp [ 60%] Generating code_info.pyx [ 60%] Generating visualization.cpp [ 60%] Generating visualization_mayavi.cpp [ 60%] Generating utils.cpp [ 60%] Generating system.cpp [ 60%] Generating version.cpp Reading definitions from /home/shawn/sourcecode/espresso_trial/espresso/src/features.def... Done. Writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/src/python/espressomd/code_info.pyx... Done. [ 60%] Generating code_info.cpp Scanning dependencies of target version Scanning dependencies of target visualization [ 61%] Building CXX object src/python/espressomd/CMakeFiles/version.dir/version.cpp.o [ 63%] Building CXX object src/python/espressomd/CMakeFiles/visualization.dir/visualization.cpp.o Scanning dependencies of target code_info [ 63%] Building CXX object src/python/espressomd/CMakeFiles/code_info.dir/code_info.cpp.o [ 63%] Linking CXX shared library code_info.so [ 63%] Linking CXX shared library version.so [ 63%] Built target code_info [ 63%] Generating script_interface.cpp [ 63%] Built target version [ 63%] Generating scafacos.cpp [ 63%] Linking CXX shared library visualization.so Scanning dependencies of target utils Scanning dependencies of target polymer [ 63%] Building CXX object src/python/espressomd/CMakeFiles/utils.dir/utils.cpp.o [ 64%] Building CXX object src/python/espressomd/CMakeFiles/polymer.dir/polymer.cpp.o [ 64%] Built target visualization [ 64%] Generating reaction_ensemble.cpp Scanning dependencies of target visualization_mayavi [ 64%] Building CXX object src/python/espressomd/CMakeFiles/visualization_mayavi.dir/visualization_mayavi.cpp.o Scanning dependencies of target system [ 65%] Building CXX object src/python/espressomd/CMakeFiles/system.dir/system.cpp.o Scanning dependencies of target script_interface [ 67%] Building CXX object src/python/espressomd/CMakeFiles/script_interface.dir/script_interface.cpp.o Scanning dependencies of target scafacos [ 67%] Building CXX object src/python/espressomd/CMakeFiles/scafacos.dir/scafacos.cpp.o Scanning dependencies of target visualization_opengl [ 67%] Building CXX object src/python/espressomd/CMakeFiles/visualization_opengl.dir/visualization_opengl.cpp.o Scanning dependencies of target reaction_ensemble [ 67%] Building CXX object src/python/espressomd/CMakeFiles/reaction_ensemble.dir/reaction_ensemble.cpp.o [ 68%] Linking CXX shared library scafacos.so [ 68%] Built target scafacos [ 69%] Generating electrokinetics.cpp [ 69%] Linking CXX shared library polymer.so [ 69%] Built target polymer [ 69%] Generating diamond.cpp Scanning dependencies of target electrokinetics [ 69%] Building CXX object src/python/espressomd/CMakeFiles/electrokinetics.dir/electrokinetics.cpp.o [ 71%] Linking CXX shared library utils.so [ 71%] Built target utils [ 71%] Generating cuda_init.cpp Scanning dependencies of target diamond Scanning dependencies of target cuda_init [ 72%] Building CXX object src/python/espressomd/CMakeFiles/cuda_init.dir/cuda_init.cpp.o [ 73%] Building CXX object src/python/espressomd/CMakeFiles/diamond.dir/diamond.cpp.o [ 73%] Linking CXX shared library electrokinetics.so [ 73%] Built target electrokinetics [ 75%] Linking CXX shared library visualization_mayavi.so [ 75%] Generating collision_detection.cpp [ 75%] Built target visualization_mayavi [ 75%] Generating analyze.cpp Scanning dependencies of target collision_detection [ 75%] Building CXX object src/python/espressomd/CMakeFiles/collision_detection.dir/collision_detection.cpp.o [ 75%] Linking CXX shared library cuda_init.so [ 75%] Built target cuda_init [ 76%] Generating actors.cpp Scanning dependencies of target actors [ 76%] Building CXX object src/python/espressomd/CMakeFiles/actors.dir/actors.cpp.o [ 76%] Linking CXX shared library system.so [ 76%] Linking CXX shared library script_interface.so [ 76%] Built target system [ 76%] Generating galilei.cpp [ 76%] Built target script_interface [ 76%] Generating swimmer_reaction.cpp [ 78%] Linking CXX shared library reaction_ensemble.so Scanning dependencies of target analyze [ 78%] Building CXX object src/python/espressomd/CMakeFiles/analyze.dir/analyze.cpp.o [ 78%] Built target reaction_ensemble [ 78%] Generating electrostatics.cpp Scanning dependencies of target galilei [ 78%] Building CXX object src/python/espressomd/CMakeFiles/galilei.dir/galilei.cpp.o [ 78%] Linking CXX shared library collision_detection.so [ 79%] Built target collision_detection [ 79%] Generating electrostatic_extensions.cpp Scanning dependencies of target swimmer_reaction [ 79%] Linking CXX shared library diamond.so [ 79%] Building CXX object src/python/espressomd/CMakeFiles/swimmer_reaction.dir/swimmer_reaction.cpp.o [ 79%] Built target diamond [ 79%] Generating lb.cpp Scanning dependencies of target electrostatics [ 79%] Building CXX object src/python/espressomd/CMakeFiles/electrostatics.dir/electrostatics.cpp.o [ 79%] Linking CXX shared library actors.so [ 79%] Built target actors [ 79%] Generating minimize_energy.cpp Scanning dependencies of target electrostatic_extensions [ 79%] Building CXX object src/python/espressomd/CMakeFiles/electrostatic_extensions.dir/electrostatic_extensions.cpp.o [ 80%] Linking CXX shared library galilei.so [ 80%] Built target galilei [ 82%] Generating globals.cpp Scanning dependencies of target lb [ 82%] Linking CXX shared library swimmer_reaction.so [ 82%] Building CXX object src/python/espressomd/CMakeFiles/lb.dir/lb.cpp.o [ 83%] Built target swimmer_reaction [ 83%] Generating cellsystem.cpp Scanning dependencies of target minimize_energy [ 83%] Building CXX object src/python/espressomd/CMakeFiles/minimize_energy.dir/minimize_energy.cpp.o Scanning dependencies of target globals [ 83%] Building CXX object src/python/espressomd/CMakeFiles/globals.dir/globals.cpp.o Scanning dependencies of target cellsystem [ 83%] Building CXX object src/python/espressomd/CMakeFiles/cellsystem.dir/cellsystem.cpp.o [ 83%] Linking CXX shared library minimize_energy.so [ 84%] Built target minimize_energy [ 84%] Generating integrate.cpp [ 84%] Linking CXX shared library electrostatic_extensions.so [ 86%] Built target electrostatic_extensions [ 86%] Generating magnetostatic_extensions.cpp [ 86%] Linking CXX shared library globals.so [ 86%] Built target globals [ 86%] Generating _init.cpp Scanning dependencies of target integrate [ 86%] Building CXX object src/python/espressomd/CMakeFiles/integrate.dir/integrate.cpp.o Scanning dependencies of target magnetostatic_extensions Scanning dependencies of target _init [ 87%] Building CXX object src/python/espressomd/CMakeFiles/magnetostatic_extensions.dir/magnetostatic_extensions.cpp.o [ 89%] Building CXX object src/python/espressomd/CMakeFiles/_init.dir/_init.cpp.o [ 90%] Linking CXX shared library lb.so [ 90%] Linking CXX shared library cellsystem.so [ 90%] Built target lb [ 90%] Generating interactions.cpp [ 90%] Built target cellsystem [ 90%] Generating magnetostatics.cpp [ 90%] Linking CXX shared library _init.so [ 90%] Linking CXX shared library magnetostatic_extensions.so [ 90%] Built target _init [ 90%] Generating particle_data.cpp [ 90%] Built target magnetostatic_extensions [ 90%] Generating thermostat.cpp Scanning dependencies of target magnetostatics [ 91%] Building CXX object src/python/espressomd/CMakeFiles/magnetostatics.dir/magnetostatics.cpp.o [ 93%] Linking CXX shared library analyze.so [ 94%] Linking CXX shared library integrate.so [ 94%] Built target analyze [ 94%] Built target integrate Scanning dependencies of target thermostat [ 94%] Building CXX object src/python/espressomd/CMakeFiles/thermostat.dir/thermostat.cpp.o Scanning dependencies of target interactions [ 94%] Building CXX object src/python/espressomd/CMakeFiles/interactions.dir/interactions.cpp.o [ 94%] Linking CXX shared library electrostatics.so Scanning dependencies of target particle_data [ 95%] Built target electrostatics [ 95%] Building CXX object src/python/espressomd/CMakeFiles/particle_data.dir/particle_data.cpp.o [ 95%] Linking CXX shared library magnetostatics.so [ 95%] Built target magnetostatics [ 95%] Linking CXX shared library thermostat.so [ 97%] Built target thermostat [ 97%] Linking CXX shared library particle_data.so [ 98%] Built target particle_data [ 98%] Linking CXX shared library interactions.so [ 98%] Built target interactions [100%] Linking CXX shared library visualization_opengl.so [100%] Built target visualization_opengl Scanning dependencies of target espressomd [100%] Built target espressomd Scanning dependencies of target pypresso [100%] Built target pypresso -- Config file: /home/shawn/sourcecode/espresso_trial/espresso/src/core/myconfig-default.hpp CUDA_TOOLKIT_ROOT_DIR not found or specified -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "7.0") -- Found Cython version 0.29.12 -- NumPy ver. 1.16.4 found (include: /home/shawn/.local/lib/python3.6/site-packages/numpy/core/include) -- Could NOT find HDF5: Found unsuitable version "", but required is at least "1.8" (found HDF5_hdf5_LIBRARY-NOTFOUND) -- Could NOT find GSL (missing: GSL_INCLUDE_DIR GSL_LIBRARY GSL_CBLAS_LIBRARY) (found version "") CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) CMake Warning at /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:880 (message): New Boost version may have incorrect or missing dependencies and imported targets Call Stack (most recent call first): /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1002 (_Boost_COMPONENT_DEPENDENCIES) /home/shawn/soft/cmake/share/cmake-3.13/Modules/FindBoost.cmake:1670 (_Boost_MISSING_DEPENDENCIES) CMakeLists.txt:337 (find_package) -- Boost version: 1.70.0 -- Found the following Boost libraries: -- mpi -- serialization -- filesystem -- system -- unit_test_framework -- writing /home/shawn/sourcecode/espresso_trial/espresso/build-patched/myconfig-sample.hpp -- The following OPTIONAL packages have been found: * FFTW3 * PkgConfig * Doxygen * Sphinx (required version >= 1.6.6) -- The following REQUIRED packages have been found: * PythonInterp * Cython (required version >= 0.23) * NumPy * MPI * Boost (required version >= 1.53.0) -- The following OPTIONAL packages have not been found: * CUDA (required version >= 7.0) * HDF5 (required version >= 1.8) * GSL -- Configuring done -- Generating done -- Build files have been written to: /home/shawn/sourcecode/espresso_trial/espresso/build-patched Scanning dependencies of target python_test_data [ 0%] Built target myconfig [ 0%] Built target object_in_fluid [ 0%] Built target python_test_data [ 0%] Built target check_myconfig [ 1%] Built target EspressoConfig [ 2%] Built target gen_pxiconfig [ 4%] Built target cluster_analysis [ 5%] Built target ImmersedBoundary [ 5%] Built target Accumulators [ 9%] Built target Shapes [ 12%] Built target ObjectInFluid [ 16%] Built target Observables [ 16%] Built target VirtualSites [ 17%] Built target Actor [ 17%] Built target Constraints [ 53%] Built target EspressoCore [ 58%] Built target EspressoScriptInterface [ 60%] Built target visualization [ 61%] Built target code_info [ 63%] Built target visualization_opengl [ 64%] Built target version [ 65%] Built target utils [ 67%] Built target electrokinetics [ 68%] Built target visualization_mayavi [ 69%] Built target polymer [ 71%] Built target system [ 73%] Built target cuda_init [ 73%] Built target scafacos [ 75%] Built target script_interface [ 76%] Built target reaction_ensemble [ 78%] Built target actors [ 79%] Built target diamond [ 80%] Built target collision_detection [ 82%] Built target galilei [ 83%] Built target analyze [ 84%] Built target swimmer_reaction [ 86%] Built target electrostatic_extensions [ 87%] Built target lb [ 89%] Built target minimize_energy [ 90%] Built target globals [ 91%] Built target integrate [ 93%] Built target electrostatics [ 93%] Built target cellsystem [ 94%] Built target _init [ 95%] Built target magnetostatic_extensions [ 95%] Built target interactions [ 97%] Built target magnetostatics [ 98%] Built target particle_data [100%] Built target thermostat [100%] Built target espressomd [100%] Built target pypresso Scanning dependencies of target check_python_serial Test project /home/shawn/sourcecode/espresso_trial/espresso/build-patched/testsuite/python Start 1: save_checkpoint 1/115 Test #1: save_checkpoint ......................... Passed 0.50 sec Start 2: test_checkpoint 2/115 Test #2: test_checkpoint ......................... Passed 0.85 sec Start 3: cellsystem 3/115 Test #3: cellsystem .............................. Passed 0.46 sec Start 4: constraint_homogeneous_magnetic_field 4/115 Test #4: constraint_homogeneous_magnetic_field ... Passed 0.52 sec Start 5: constraint_shape_based 5/115 Test #5: constraint_shape_based .................. Passed 0.74 sec Start 6: coulomb_cloud_wall 6/115 Test #6: coulomb_cloud_wall ...................... Passed 1.17 sec Start 7: coulomb_tuning 7/115 Test #7: coulomb_tuning .......................... Passed 8.35 sec Start 8: correlation 8/115 Test #8: correlation ............................. Passed 1.01 sec Start 9: dawaanr-and-dds-gpu 9/115 Test #9: dawaanr-and-dds-gpu ..................... Passed 0.52 sec Start 10: dawaanr-and-bh-gpu 10/115 Test #10: dawaanr-and-bh-gpu ...................... Passed 0.51 sec Start 11: dds-and-bh-gpu 11/115 Test #11: dds-and-bh-gpu .......................... Passed 0.77 sec Start 12: electrostaticInteractions 12/115 Test #12: electrostaticInteractions ............... Passed 0.75 sec Start 13: engine_langevin 13/115 Test #13: engine_langevin ......................... Passed 0.45 sec Start 14: engine_lb 14/115 Test #14: engine_lb ............................... Passed 0.50 sec Start 15: engine_lbgpu 15/115 Test #15: engine_lbgpu ............................ Passed 0.44 sec Start 16: icc 16/115 Test #16: icc ..................................... Passed 0.83 sec Start 17: magnetostaticInteractions 17/115 Test #17: magnetostaticInteractions ............... Passed 0.52 sec Start 18: mass-and-rinertia_per_particle 18/115 Test #18: mass-and-rinertia_per_particle .......... Passed 0.30 sec Start 19: integrate 19/115 Test #19: integrate ............................... Passed 0.47 sec Start 20: interactions_bond_angle 20/115 Test #20: interactions_bond_angle ................. Passed 0.61 sec Start 21: interactions_bonded_interface 21/115 Test #21: interactions_bonded_interface ........... Passed 0.82 sec Start 22: interactions_bonded 22/115 Test #22: interactions_bonded ..................... Passed 0.84 sec Start 23: interactions_non-bonded_interface 23/115 Test #23: interactions_non-bonded_interface ....... Passed 0.46 sec Start 24: interactions_non-bonded 24/115 Test #24: interactions_non-bonded ................. Passed 1.11 sec Start 25: observables 25/115 Test #25: observables ............................. Passed 0.56 sec Start 26: p3m_gpu 26/115 Test #26: p3m_gpu ................................. Passed 0.95 sec Start 27: particle 27/115 Test #27: particle ................................ Passed 0.56 sec Start 28: stress 28/115 Test #28: stress .................................. Passed 0.86 sec Start 29: scafacos_dipoles_1d_2d 29/115 Test #29: scafacos_dipoles_1d_2d .................. Passed 0.76 sec Start 30: tabulated 30/115 Test #30: tabulated ............................... Passed 0.49 sec Start 31: particle_slice 31/115 Test #31: particle_slice .......................... Passed 0.46 sec Start 32: rigid_bond 32/115 Test #32: rigid_bond .............................. Passed 0.54 sec Start 33: rotation_per_particle 33/115 Test #33: rotation_per_particle ................... Passed 0.84 sec Start 34: rotational_inertia 34/115 Test #34: rotational_inertia ...................... Passed 0.51 sec Start 35: script_interface_object_params 35/115 Test #35: script_interface_object_params .......... Passed 0.52 sec Start 36: lbgpu_remove_total_momentum 36/115 Test #36: lbgpu_remove_total_momentum ............. Passed 0.57 sec Start 37: reaction_ensemble 37/115 Test #37: reaction_ensemble ....................... Passed 0.91 sec Start 38: constant_pH 38/115 Test #38: constant_pH ............................. Passed 0.84 sec Start 39: swimmer_reaction 39/115 Test #39: swimmer_reaction ........................ Passed 0.30 sec Start 40: writevtf 40/115 Test #40: writevtf ................................ Passed 0.46 sec Start 41: lb_stokes_sphere 41/115 Test #41: lb_stokes_sphere ........................ Passed 4.58 sec Start 42: ek_eof_one_species_x 42/115 Test #42: ek_eof_one_species_x .................... Passed 0.30 sec Start 43: ek_eof_one_species_y 43/115 Test #43: ek_eof_one_species_y .................... Passed 0.33 sec Start 44: ek_eof_one_species_z 44/115 Test #44: ek_eof_one_species_z .................... Passed 0.33 sec Start 45: ek_eof_one_species_x_nonlinear 45/115 Test #45: ek_eof_one_species_x_nonlinear .......... Passed 0.33 sec Start 46: ek_eof_one_species_y_nonlinear 46/115 Test #46: ek_eof_one_species_y_nonlinear .......... Passed 0.30 sec Start 47: ek_eof_one_species_z_nonlinear 47/115 Test #47: ek_eof_one_species_z_nonlinear .......... Passed 0.32 sec Start 48: exclusions 48/115 Test #48: exclusions .............................. Passed 0.56 sec Start 49: langevin_thermostat 49/115 Test #49: langevin_thermostat ..................... Passed 2.54 sec Start 50: nsquare 50/115 Test #50: nsquare ................................. Passed 0.46 sec Start 51: virtual_sites_relative 51/115 Test #51: virtual_sites_relative .................. Passed 0.63 sec Start 52: virtual_sites_tracers 52/115 Test #52: virtual_sites_tracers ................... Passed 0.58 sec Start 53: virtual_sites_tracers_gpu 53/115 Test #53: virtual_sites_tracers_gpu ............... Passed 0.58 sec Start 54: domain_decomposition 54/115 Test #54: domain_decomposition .................... Passed 0.47 sec Start 55: layered 55/115 Test #55: layered ................................. Passed 0.59 sec Start 56: minimize_energy 56/115 Test #56: minimize_energy ......................... Passed 0.57 sec Start 57: mmm1d 57/115 Test #57: mmm1d ................................... Passed 0.50 sec Start 58: variant_conversion 58/115 Test #58: variant_conversion ...................... Passed 0.37 sec Start 59: dipolar_mdlc_p3m_scafacos_p2nfft 59/115 Test #59: dipolar_mdlc_p3m_scafacos_p2nfft ........ Passed 0.55 sec Start 60: lb 60/115 Test #60: lb ...................................... Passed 5.42 sec Start 61: lb_gpu_viscous 61/115 Test #61: lb_gpu_viscous .......................... Passed 0.37 sec Start 62: force_cap 62/115 Test #62: force_cap ............................... Passed 0.40 sec Start 63: dpd 63/115 Test #63: dpd ..................................... Passed 0.62 sec Start 64: hat 64/115 Test #64: hat ..................................... Passed 0.51 sec Start 65: analyze_energy 65/115 Test #65: analyze_energy .......................... Passed 0.50 sec Start 66: analyze_itensor 66/115 Test #66: analyze_itensor ......................... Passed 0.41 sec Start 67: rdf 67/115 Test #67: rdf ..................................... Passed 0.35 sec Start 68: coulomb_mixed_periodicity 68/115 Test #68: coulomb_mixed_periodicity ............... Passed 2.42 sec Start 69: coulomb_cloud_wall_duplicated 69/115 Test #69: coulomb_cloud_wall_duplicated ........... Passed 2.39 sec Start 70: collision_detection 70/115 Test #70: collision_detection ..................... Passed 0.50 sec Start 71: lb_get_u_at_pos 71/115 Test #71: lb_get_u_at_pos ......................... Passed 0.51 sec Start 72: lj 72/115 Test #72: lj ...................................... Passed 0.92 sec Start 73: pairs 73/115 Test #73: pairs ................................... Passed 0.48 sec Start 74: polymer 74/115 Test #74: polymer ................................. Passed 0.57 sec Start 75: auto_exclusions 75/115 Test #75: auto_exclusions ......................... Passed 0.34 sec Start 76: subt_lj 76/115 Test #76: subt_lj ................................. Passed 0.36 sec Start 77: observable_cylindrical 77/115 Test #77: observable_cylindrical .................. Passed 0.79 sec Start 78: unravel_index 78/115 Test #78: unravel_index ........................... Passed 0.46 sec Start 79: observable_cylindricalLB 79/115 Test #79: observable_cylindricalLB ................ Passed 0.79 sec Start 80: analyze_chains 80/115 Test #80: analyze_chains .......................... Passed 0.31 sec Start 81: analyze_distance 81/115 Test #81: analyze_distance ........................ Passed 0.33 sec Start 82: comfixed 82/115 Test #82: comfixed ................................ Passed 0.39 sec Start 83: rescale 83/115 Test #83: rescale ................................. Passed 0.38 sec Start 84: npt 84/115 Test #84: npt ..................................... Passed 5.99 sec Start 85: elc_vs_mmm2d_neutral 85/115 Test #85: elc_vs_mmm2d_neutral .................... Passed 2.00 sec Start 86: elc_vs_mmm2d_nonneutral 86/115 Test #86: elc_vs_mmm2d_nonneutral ................. Passed 1.72 sec Start 87: accumulator 87/115 Test #87: accumulator ............................. Passed 0.44 sec Start 88: wang_landau_reaction_ensemble 88/115 Test #88: wang_landau_reaction_ensemble ........... Passed 7.67 sec Start 89: array_properties 89/115 Test #89: array_properties ........................ Passed 0.45 sec Start 90: analyze_distribution 90/115 Test #90: analyze_distribution .................... Passed 0.34 sec Start 91: observable_profile 91/115 Test #91: observable_profile ...................... Passed 0.45 sec Start 92: observable_profileLB 92/115 Test #92: observable_profileLB .................... Passed 0.45 sec Start 93: rotate_system 93/115 Test #93: rotate_system ........................... Passed 0.45 sec Start 94: random_pairs 94/115 Test #94: random_pairs ............................ Passed 2.30 sec Start 95: lb_electrohydrodynamics 95/115 Test #95: lb_electrohydrodynamics ................. Passed 0.44 sec Start 96: cluster_analysis 96/115 Test #96: cluster_analysis ........................ Passed 0.52 sec Start 97: pair_criteria 97/115 Test #97: pair_criteria ........................... Passed 0.55 sec Start 98: actor 98/115 Test #98: actor ................................... Passed 0.35 sec Start 99: drude 99/115 Test #99: drude ................................... Passed 0.38 sec Start 100: thermalized_bond 100/115 Test #100: thermalized_bond ........................ Passed 1.56 sec Start 101: thole 101/115 Test #101: thole ................................... Passed 0.40 sec Start 102: lb_switch 102/115 Test #102: lb_switch ............................... Passed 0.57 sec Start 103: lb_boundary_velocity 103/115 Test #103: lb_boundary_velocity .................... Passed 0.48 sec Start 104: lb_thermo_virtual 104/115 Test #104: lb_thermo_virtual ....................... Passed 0.38 sec Start 105: lb_poiseuille 105/115 Test #105: lb_poiseuille ........................... Passed 0.93 sec Start 106: lb_interpolation 106/115 Test #106: lb_interpolation ........................ Passed 0.71 sec Start 107: analyze_gyration_tensor 107/115 Test #107: analyze_gyration_tensor ................. Passed 0.36 sec Start 108: oif_volume_conservation 108/115 Test #108: oif_volume_conservation ................. Passed 0.60 sec Start 109: simple_pore 109/115 Test #109: simple_pore ............................. Passed 0.37 sec Start 110: field_test 110/115 Test #110: field_test .............................. Passed 9.94 sec Start 111: lb_boundary 111/115 Test #111: lb_boundary ............................. Passed 0.44 sec Start 112: lb_streaming 112/115 Test #112: lb_streaming ............................ Passed 0.78 sec Start 113: lb_shear 113/115 Test #113: lb_shear ................................ Passed 0.79 sec Start 114: lb_thermostat 114/115 Test #114: lb_thermostat ........................... Passed 1.55 sec Start 115: p3m_electrostatic_pressure 115/115 Test #115: p3m_electrostatic_pressure .............. Passed 0.37 sec 100% tests passed, 0 tests failed out of 115 Total Test time (real) = 113.82 sec [100%] Built target check_python_serial Scanning dependencies of target check_python [100%] Built target check_python build was successful and the tests passed