search

hakonsbm / nest-simulator

The NEST simulator
GNU General Public License v2.0
0 stars 0 forks source link

Cython errors in `nestkernel_api` #49

Closed Helveg closed 1 year ago

Helveg commented 1 year ago 
(workshop-env) robin@LAPTOP-JF6T3PSU:~/git/nest-simulator/build$ cmake .. -Dwith-mpi=ON
-- The CXX compiler identification is GNU 9.3.0
-- The C compiler identification is GNU 9.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.17") found components: doxygen dot
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file mach-o/dyld.h
-- Looking for include file mach-o/dyld.h - not found
-- Looking for include file mach/mach.h
-- Looking for include file mach/mach.h - not found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for C++ include istream
-- Looking for C++ include istream - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of long long
-- Check size of long long - done
-- Check size of u_int16_t
-- Check size of u_int16_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of u_int64_t
-- Check size of u_int64_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Looking for NAN
-- Looking for NAN - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for M_E
-- Looking for M_E - found
-- Looking for M_PI
-- Looking for M_PI - found
-- Looking for expm1
-- Looking for expm1 - not found
-- Info: Host triple: x86_64-pc-linux
-- Info: Target triple: x86_64-pc-linux
-- Found Python: /home/robin/.pyenv/versions/workshop-env/bin/python3.9 (found suitable version "3.9.9", minimum required is "3.8") found components: Interpreter Development.Module
-- Found Cython: /home/robin/.pyenv/versions/workshop-env/bin/cython (Required is at least version "0.28.3")
-- Looking for libs in install prefix: /home/robin/.pyenv/versions/workshop-env/lib/nest
-- Looking for libs in relfolder: $ORIGIN/../../lib/nest
-- Found LTDL: /usr/lib/x86_64-linux-gnu/libltdl.so (found version "2.4.6")
-- Found Readline: /usr/lib/x86_64-linux-gnu/libreadline.so (found version "8.0")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Found GSL: /usr/include (found version "2.5")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found PY_mpi4py: /home/robin/.pyenv/versions/workshop-env/lib/python3.9/site-packages/mpi4py
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.71.0/BoostConfig.cmake (found suitable version "1.71.0", minimum required is "1.69.0")
-- Info: Check the abort exitcode.
-- Info: Check the abort exitcode. 255
-- Info: Check the segmentation fault exitcode.
-- Info: Check the segmentation fault exitcode. 127
-- Info: Check whether the compiler ignores cmath makros.
-- Info: Check whether the compiler ignores cmath makros. OFF
-- Info: Check whether the compiler does NOT include <*.h> headers ISO conformant.
-- Info: Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF
-- Info: Check whether the compiler respects symbolic signal names in signal.h.
-- Info: Check whether the compiler respects symbolic signal names in signal.h. OFF
-- Info: Check static template member declaration.
-- Info: Check static template member declaration. OFF
-- Info: Check for STL vector capacity base unity.
-- Info: Check for STL vector capacity base unity. ON
-- Info: Check for STL vector capacity doubling strategy.
-- Info: Check for STL vector capacity doubling strategy. ON
-- Info: Check whether the compiler fails with ICE.
-- Info: Check whether the compiler fails with ICE. OFF
-- Info: Check if ::nan is available from cmath.
-- Info: Check if ::nan is available from cmath. ON
-- Info: Check if ::isnan is available from cmath.
-- Info: Check if ::isnan is available from cmath. ON
-- Info: Check if Random123 generators work.
-- Info: Check if Random123 generators work. ON
-- Info: -- NEST version: pynest-publicapi@9bba983fa

--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------

Target System       : Linux
Cross Compiling     : FALSE
C compiler          : GNU 9.3.0 (/usr/bin/cc)
C compiler flags    :  -O2 -Wall -fopenmp   -pthread -fdiagnostics-color=auto
C++ compiler        : GNU 9.3.0 (/usr/bin/c++)
C++ compiler flags  :  -O2 -std=c++11 -Wall -fopenmp -pthread -fdiagnostics-color=auto
Build dynamic       : ON

Built-in modules    : models
User modules        : None

Python bindings     : Yes (Python 3.9.9: /home/robin/.pyenv/versions/workshop-env/bin/python3.9)
    Includes        : /home/robin/.pyenv/versions/3.9.9/include/python3.9
    Libraries       :
    Cython          : Yes (Cython 0.29.32: /home/robin/.pyenv/versions/workshop-env/bin/cython)
    MPI4Py          : Yes (/home/robin/.pyenv/versions/workshop-env/lib/python3.9/site-packages/mpi4py/include)

Use threading       : Yes (OpenMP: -fopenmp)

Use GSL             : Yes (GSL 2.5)
    Includes        : /usr/include
    Libraries       : /usr/lib/x86_64-linux-gnu/libgsl.so;/usr/lib/x86_64-linux-gnu/libgslcblas.so

Use Readline        : Yes (GNU Readline 8.0)
    Includes        : /usr/include
    Libraries       : /usr/lib/x86_64-linux-gnu/libreadline.so;/usr/lib/x86_64-linux-gnu/libncurses.so

Use libltdl         : Yes (LTDL 2.4.6)
    Includes        : /usr/include
    Libraries       : /usr/lib/x86_64-linux-gnu/libltdl.so

Use doxygen         : Yes (/usr/bin/doxygen); make target `doc` is available
    Graphviz        : Yes (/usr/bin/dot); make target `fulldoc` is available

Use MPI             : Yes (MPI: /usr/bin/mpicxx)
    Includes        : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include
    Libraries       : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
    Compile Flags   : -pthread
    Link Flags      : -pthread
    Launcher        : /usr/bin/mpiexec -n <np> <prog> <args>

Detailed timers     : No

Use MUSIC           : No

Use libneurosim     : No

Use Boost           : Yes (Boost 1.71.0)
    Includes        : /usr/include
    Libraries       :

Use SIONlib         : No

For details on setting specific flags for your MPI launcher command, see the
CMake documentation at https://cmake.org/cmake/help/latest/module/FindMPI.html

--------------------------------------------------------------------------------

The NEST executable will be installed to:
  /home/robin/.pyenv/versions/workshop-env/bin/

NEST dynamic libraries and user modules will be installed to:
  /home/robin/.pyenv/versions/workshop-env/lib/nest/

Documentation and examples will be installed to:
  /home/robin/.pyenv/versions/workshop-env/share/doc/nest/

PyNEST will be installed to:
    /home/robin/.pyenv/versions/workshop-env/lib/python3.9/site-packages

To set necessary environment variables, add the following line
to your ~/.bashrc :
  source /home/robin/.pyenv/versions/workshop-env/bin/nest_vars.sh

--------------------------------------------------------------------------------

You can now build and install NEST with
  make
  make install
  make installcheck

If you experience problems with the installation or the use of NEST,
please see https://www.nest-simulator.org/frequently_asked_questions
or go to https://www.nest-simulator.org/community to find out how to
join the user mailing list.

-- Configuring done
-- Generating done
-- Build files have been written to: /home/robin/git/nest-simulator/build
(workshop-env) robin@LAPTOP-JF6T3PSU:~/git/nest-simulator/build$ make install -j8 && python -c "import nest.plot"
[  0%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/allocator.cpp.o
[  1%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/dictionary.cpp.o
[  1%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/dictionary_access_flag_manager.cpp.o
[  2%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o
[  2%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/numerics.cpp.o
[  3%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o
[  3%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o
[  4%] Linking CXX shared library libnestutil.so
[  4%] Built target nestutil
[  5%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/clopath_archiving_node.cpp.o
[  5%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/archiving_node.cpp.o
[  6%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/common_synapse_properties.cpp.o
[  7%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connector_model.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_id.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/deprecation_warning.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/device.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/event.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/exceptions.cpp.o
[  9%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/node_collection.cpp.o
[  9%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/histentry.cpp.o
[ 10%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/model.cpp.o
/home/robin/git/nest-simulator/nestkernel/exceptions.cpp: In member function ‘virtual const char* nest::IOError::what() const’:
/home/robin/git/nest-simulator/nestkernel/exceptions.cpp:349:30: warning: function returns address of local variable [-Wreturn-local-addr]
  349 |   return std::string().c_str();
      |                              ^
/home/robin/git/nest-simulator/nestkernel/exceptions.cpp:349:22: note: declared here
  349 |   return std::string().c_str();
      |                      ^
[ 10%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/model_manager.cpp.o
[ 11%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest_time.cpp.o
[ 11%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest_timeconverter.cpp.o
[ 12%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/modelrange.cpp.o
[ 12%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/modelrange_manager.cpp.o
[ 13%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/node.cpp.o
[ 13%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/parameter.cpp.o
[ 13%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/per_thread_bool_indicator.cpp.o
[ 14%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/proxynode.cpp.o
[ 14%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_device.cpp.o
[ 15%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/ring_buffer.cpp.o
[ 15%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/slice_ring_buffer.cpp.o
[ 16%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/spikecounter.cpp.o
/home/robin/git/nest-simulator/nestkernel/recording_device.cpp: In member function ‘virtual void nest::RecordingDevice::set_status(const dictionary&)’:
/home/robin/git/nest-simulator/nestkernel/recording_device.cpp:145:17: warning: unused variable ‘kv_pair’ [-Wunused-variable]
  145 |     for ( auto& kv_pair : d )
      |                 ^~~~~~~
/home/robin/git/nest-simulator/nestkernel/recording_device.cpp:158:17: warning: unused variable ‘kv_pair’ [-Wunused-variable]
  158 |     for ( auto& kv_pair : backend_params )
      |                 ^~~~~~~
[ 16%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/stimulation_device.cpp.o
[ 17%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/sparse_node_array.cpp.o
[ 17%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/conn_parameter.cpp.o
[ 18%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/conn_builder.cpp.o
[ 18%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/conn_builder_conngen.cpp.o
[ 18%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/music_event_handler.cpp.o
[ 19%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/music_rate_in_handler.cpp.o
[ 19%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/music_manager.cpp.o
[ 20%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest.cpp.o
[ 20%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_psc_alpha.cpp.o
[ 21%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_psc_delta.cpp.o
[ 21%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_psc_exp.cpp.o
[ 22%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_psc_exp_multisynapse.cpp.o
[ 22%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/parrot_neuron.cpp.o
[ 22%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/weight_recorder.cpp.o
[ 23%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/stdp_pl_synapse_hom.cpp.o
[ 23%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/stdp_dopamine_synapse.cpp.o
[ 24%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/stdp_synapse_hom.cpp.o
[ 24%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/volume_transmitter.cpp.o
[ 25%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/tsodyks_synapse_hom.cpp.o
[ 25%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/ac_generator.cpp.o
[ 26%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/dc_generator.cpp.o
[ 26%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/spike_generator.cpp.o
[ 27%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/spike_recorder.cpp.o
[ 27%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/poisson_generator.cpp.o
[ 27%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/poisson_generator_ps.cpp.o
[ 28%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/multimeter.cpp.o
[ 28%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/noise_generator.cpp.o
[ 29%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_cond_alpha.cpp.o
[ 29%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_cond_alpha_multisynapse.cpp.o
[ 30%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_cond_beta_multisynapse.cpp.o
[ 30%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_psc_delta_clopath.cpp.o
[ 31%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/cm_default.cpp.o
[ 31%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/cm_tree.cpp.o
[ 32%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/cm_compartmentcurrents.cpp.o
[ 32%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/erfc_neuron.cpp.o
[ 32%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/glif_cond.cpp.o
[ 33%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/glif_psc.cpp.o
[ 33%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/hh_psc_alpha_gap.cpp.o
[ 34%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/ht_neuron.cpp.o
[ 34%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_cond_alpha_mc.cpp.o
[ 35%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/pp_psc_delta.cpp.o
[ 35%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/lin_rate.cpp.o
[ 36%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/tanh_rate.cpp.o
[ 36%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/threshold_lin_rate.cpp.o
[ 37%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_cond_alpha.cpp.o
[ 37%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/parrot_neuron_ps.cpp.o
[ 37%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/step_rate_generator.cpp.o
[ 38%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/step_current_generator.cpp.o
[ 38%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/hh_psc_alpha_clopath.cpp.o
[ 39%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_cond_exp.cpp.o
[ 39%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_cond_exp.cpp.o
[ 40%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_psc_alpha.cpp.o
[ 40%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_psc_delta.cpp.o
[ 41%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/aeif_psc_exp.cpp.o
[ 41%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/spin_detector.cpp.o
[ 41%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/pp_cond_exp_mc_urbanczik.cpp.o
[ 42%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/synaptic_element.cpp.o
[ 42%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/growth_curve.cpp.o
[ 43%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/kernel_manager.cpp.o
[ 43%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/vp_manager.cpp.o
[ 44%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/io_manager.cpp.o
[ 44%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/mpi_manager.cpp.o
[ 45%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/simulation_manager.cpp.o
[ 45%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_manager.cpp.o
[ 46%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/sp_manager.cpp.o
[ 46%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/delay_checker.cpp.o
[ 46%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/random_manager.cpp.o
[ 47%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/event_delivery_manager.cpp.o
[ 47%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/node_manager.cpp.o
[ 48%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/logging_manager.cpp.o
[ 48%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend.cpp.o
/home/robin/git/nest-simulator/nestkernel/node_manager.cpp: In member function ‘nest::NodeCollectionPTR nest::NodeManager::get_nodes(const dictionary&, bool)’:
/home/robin/git/nest-simulator/nestkernel/node_manager.cpp:389:19: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
  389 |   return std::move( nodecollection );
      |          ~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/robin/git/nest-simulator/nestkernel/node_manager.cpp:389:19: note: remove ‘std::move’ call
[ 49%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_ascii.cpp.o
[ 49%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_memory.cpp.o
[ 50%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_screen.cpp.o
[ 50%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/target_table.cpp.o
[ 51%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/target_table_devices.cpp.o
[ 51%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/source_table.cpp.o
[ 51%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/structural_plasticity_node.cpp.o
[ 52%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_creator.cpp.o
[ 52%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/layer.cpp.o
[ 53%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/mask.cpp.o
[ 53%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/spatial.cpp.o
[ 54%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_backend_mpi.cpp.o
[ 54%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/stimulation_backend_mpi.cpp.o
[ 55%] Linking CXX shared library libnestkernel.so
[ 55%] Built target nestkernel
[ 55%] Building CXX object models/CMakeFiles/models.dir/ac_generator.cpp.o
[ 56%] Building CXX object models/CMakeFiles/models.dir/aeif_cond_alpha.cpp.o
[ 56%] Building CXX object models/CMakeFiles/models.dir/aeif_cond_alpha_multisynapse.cpp.o
[ 57%] Building CXX object models/CMakeFiles/models.dir/aeif_cond_beta_multisynapse.cpp.o
[ 57%] Building CXX object models/CMakeFiles/models.dir/aeif_cond_exp.cpp.o
[ 59%] Building CXX object models/CMakeFiles/models.dir/aeif_psc_alpha.cpp.o
[ 59%] Building CXX object models/CMakeFiles/models.dir/aeif_psc_exp.cpp.o
[ 59%] Building CXX object models/CMakeFiles/models.dir/aeif_psc_delta.cpp.o
[ 59%] Building CXX object models/CMakeFiles/models.dir/aeif_psc_delta_clopath.cpp.o
[ 59%] Building CXX object models/CMakeFiles/models.dir/amat2_psc_exp.cpp.o
[ 60%] Building CXX object models/CMakeFiles/models.dir/cm_default.cpp.o
[ 60%] Building CXX object models/CMakeFiles/models.dir/cm_tree.cpp.o
[ 61%] Building CXX object models/CMakeFiles/models.dir/cm_compartmentcurrents.cpp.o
[ 61%] Building CXX object models/CMakeFiles/models.dir/correlation_detector.cpp.o
[ 62%] Building CXX object models/CMakeFiles/models.dir/correlomatrix_detector.cpp.o
[ 62%] Building CXX object models/CMakeFiles/models.dir/correlospinmatrix_detector.cpp.o
[ 63%] Building CXX object models/CMakeFiles/models.dir/dc_generator.cpp.o
[ 63%] Building CXX object models/CMakeFiles/models.dir/erfc_neuron.cpp.o
[ 64%] Building CXX object models/CMakeFiles/models.dir/gamma_sup_generator.cpp.o
[ 64%] Building CXX object models/CMakeFiles/models.dir/gauss_rate.cpp.o
[ 64%] Building CXX object models/CMakeFiles/models.dir/gif_psc_exp.cpp.o
[ 65%] Building CXX object models/CMakeFiles/models.dir/gif_cond_exp.cpp.o
[ 65%] Building CXX object models/CMakeFiles/models.dir/gif_psc_exp_multisynapse.cpp.o
[ 66%] Building CXX object models/CMakeFiles/models.dir/gif_cond_exp_multisynapse.cpp.o
[ 66%] Building CXX object models/CMakeFiles/models.dir/gif_pop_psc_exp.cpp.o
[ 67%] Building CXX object models/CMakeFiles/models.dir/ginzburg_neuron.cpp.o
[ 67%] Building CXX object models/CMakeFiles/models.dir/glif_cond.cpp.o
[ 68%] Building CXX object models/CMakeFiles/models.dir/glif_psc.cpp.o
[ 68%] Building CXX object models/CMakeFiles/models.dir/hh_cond_exp_traub.cpp.o
[ 69%] Building CXX object models/CMakeFiles/models.dir/hh_cond_beta_gap_traub.cpp.o
[ 69%] Building CXX object models/CMakeFiles/models.dir/hh_psc_alpha.cpp.o
[ 69%] Building CXX object models/CMakeFiles/models.dir/hh_psc_alpha_clopath.cpp.o
[ 70%] Building CXX object models/CMakeFiles/models.dir/hh_psc_alpha_gap.cpp.o
[ 70%] Building CXX object models/CMakeFiles/models.dir/ht_neuron.cpp.o
[ 71%] Building CXX object models/CMakeFiles/models.dir/iaf_chs_2007.cpp.o
[ 71%] Building CXX object models/CMakeFiles/models.dir/iaf_chxk_2008.cpp.o
[ 72%] Building CXX object models/CMakeFiles/models.dir/iaf_cond_alpha.cpp.o
[ 72%] Building CXX object models/CMakeFiles/models.dir/iaf_cond_alpha_mc.cpp.o
[ 73%] Building CXX object models/CMakeFiles/models.dir/iaf_cond_beta.cpp.o
[ 73%] Building CXX object models/CMakeFiles/models.dir/iaf_cond_exp.cpp.o
[ 74%] Building CXX object models/CMakeFiles/models.dir/iaf_cond_exp_sfa_rr.cpp.o
[ 74%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_alpha.cpp.o
[ 74%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_alpha_canon.cpp.o
[ 75%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_alpha_multisynapse.cpp.o
[ 75%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_alpha_ps.cpp.o
[ 76%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_delta.cpp.o
[ 76%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_delta_ps.cpp.o
[ 77%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_exp.cpp.o
[ 77%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_exp_htum.cpp.o
[ 78%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_exp_multisynapse.cpp.o
[ 78%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_exp_ps.cpp.o
[ 78%] Building CXX object models/CMakeFiles/models.dir/iaf_psc_exp_ps_lossless.cpp.o
[ 79%] Building CXX object models/CMakeFiles/models.dir/izhikevich.cpp.o
[ 79%] Building CXX object models/CMakeFiles/models.dir/lin_rate.cpp.o
[ 80%] Building CXX object models/CMakeFiles/models.dir/mat2_psc_exp.cpp.o
[ 80%] Building CXX object models/CMakeFiles/models.dir/mcculloch_pitts_neuron.cpp.o
[ 81%] Building CXX object models/CMakeFiles/models.dir/mip_generator.cpp.o
[ 81%] Building CXX object models/CMakeFiles/models.dir/multimeter.cpp.o
[ 82%] Building CXX object models/CMakeFiles/models.dir/music_cont_in_proxy.cpp.o
[ 82%] Building CXX object models/CMakeFiles/models.dir/music_cont_out_proxy.cpp.o
[ 83%] Building CXX object models/CMakeFiles/models.dir/music_event_in_proxy.cpp.o
[ 83%] Building CXX object models/CMakeFiles/models.dir/music_event_out_proxy.cpp.o
[ 83%] Building CXX object models/CMakeFiles/models.dir/music_rate_in_proxy.cpp.o
[ 84%] Building CXX object models/CMakeFiles/models.dir/music_rate_out_proxy.cpp.o
[ 84%] Building CXX object models/CMakeFiles/models.dir/music_message_in_proxy.cpp.o
[ 85%] Building CXX object models/CMakeFiles/models.dir/noise_generator.cpp.o
[ 85%] Building CXX object models/CMakeFiles/models.dir/parrot_neuron.cpp.o
[ 86%] Building CXX object models/CMakeFiles/models.dir/parrot_neuron_ps.cpp.o
[ 86%] Building CXX object models/CMakeFiles/models.dir/inhomogeneous_poisson_generator.cpp.o
[ 87%] Building CXX object models/CMakeFiles/models.dir/poisson_generator.cpp.o
[ 87%] Building CXX object models/CMakeFiles/models.dir/poisson_generator_ps.cpp.o
[ 88%] Building CXX object models/CMakeFiles/models.dir/pp_psc_delta.cpp.o
[ 88%] Building CXX object models/CMakeFiles/models.dir/pp_pop_psc_delta.cpp.o
[ 88%] Building CXX object models/CMakeFiles/models.dir/pp_cond_exp_mc_urbanczik.cpp.o
[ 89%] Building CXX object models/CMakeFiles/models.dir/ppd_sup_generator.cpp.o
[ 89%] Building CXX object models/CMakeFiles/models.dir/pulsepacket_generator.cpp.o
[ 90%] Building CXX object models/CMakeFiles/models.dir/siegert_neuron.cpp.o
[ 90%] Building CXX object models/CMakeFiles/models.dir/sigmoid_rate.cpp.o
[ 91%] Building CXX object models/CMakeFiles/models.dir/sigmoid_rate_gg_1998.cpp.o
[ 91%] Building CXX object models/CMakeFiles/models.dir/sinusoidal_poisson_generator.cpp.o
[ 92%] Building CXX object models/CMakeFiles/models.dir/sinusoidal_gamma_generator.cpp.o
[ 92%] Building CXX object models/CMakeFiles/models.dir/spike_recorder.cpp.o
[ 93%] Building CXX object models/CMakeFiles/models.dir/spike_generator.cpp.o
[ 93%] Building CXX object models/CMakeFiles/models.dir/spin_detector.cpp.o
[ 93%] Building CXX object models/CMakeFiles/models.dir/stdp_dopamine_synapse.cpp.o
[ 94%] Building CXX object models/CMakeFiles/models.dir/stdp_pl_synapse_hom.cpp.o
[ 94%] Building CXX object models/CMakeFiles/models.dir/stdp_synapse_hom.cpp.o
[ 95%] Building CXX object models/CMakeFiles/models.dir/step_current_generator.cpp.o
[ 95%] Building CXX object models/CMakeFiles/models.dir/step_rate_generator.cpp.o
[ 96%] Building CXX object models/CMakeFiles/models.dir/tanh_rate.cpp.o
[ 96%] Building CXX object models/CMakeFiles/models.dir/threshold_lin_rate.cpp.o
[ 97%] Building CXX object models/CMakeFiles/models.dir/tsodyks_synapse_hom.cpp.o
[ 97%] Building CXX object models/CMakeFiles/models.dir/volume_transmitter.cpp.o
[ 97%] Building CXX object models/CMakeFiles/models.dir/weight_recorder.cpp.o
[ 98%] Building CXX object models/CMakeFiles/models.dir/spike_dilutor.cpp.o
[ 98%] Linking CXX shared library libmodels.so
[ 98%] Built target models
[ 98%] Generating C source pynest/nestkernel_api.c
[ 98%] Building CXX object testsuite/cpptests/CMakeFiles/run_all_cpptests.dir/run_all.cpp.o
/home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /home/robin/git/nest-simulator/pynest/nestkernel_api.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:194:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:195:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:196:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:197:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:198:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:199:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:200:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:201:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:202:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:203:20: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:206:12: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:207:12: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:209:13: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:210:13: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:212:19: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:213:19: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:216:23: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:217:23: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:219:29: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:220:29: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:223:14: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:225:15: Function signature does not match previous declaration
warning: /home/robin/.pyenv/versions/3.9.9/envs/workshop-env/lib/python3.9/site-packages/Cython/Includes/libcpp/string.pxd:227:21: Function signature does not match previous declaration
warning: /home/robin/git/nest-simulator/pynest/nestkernel_api.pxd:90:36: Function signature does not match previous declaration
warning: /home/robin/git/nest-simulator/pynest/nestkernel_api.pxd:125:30: Function signature does not match previous declaration
warning: /home/robin/git/nest-simulator/pynest/nestkernel_api.pxd:135:49: Function signature does not match previous declaration
warning: /home/robin/git/nest-simulator/pynest/nestkernel_api.pxd:138:24: Function signature does not match previous declaration

Error compiling Cython file:
------------------------------------------------------------
...
        array_bool_ptr = &array_bool_mv[0]
        new_nc_ptr = node_collection_array_index(node_collection.thisptr, array_bool_ptr, len(array))
    elif numpy.issubdtype(array.dtype, numpy.integer):
        array_long_mv = numpy.ascontiguousarray(array, dtype=numpy.long)
        array_long_ptr = &array_long_mv[0]
        new_nc_ptr = node_collection_array_index(node_collection.thisptr, array_long_ptr, len(array))
                                                                         ^
------------------------------------------------------------

/home/robin/git/nest-simulator/pynest/nestkernel_api.pyx:476:74: Cannot assign type 'long *' to 'const bool *'

Error compiling Cython file:
------------------------------------------------------------
...

@catch_cpp_error
def llapi_apply_parameter(ParameterObject parameter, object pos_or_nc):
    if type(pos_or_nc) is nest.NodeCollection:
        return tuple(apply(parameter.thisptr, (<NodeCollectionObject>(pos_or_nc._datum)).thisptr))
                                                                                       ^
------------------------------------------------------------

/home/robin/git/nest-simulator/pynest/nestkernel_api.pyx:504:88: Cannot assign type 'NodeCollectionPTR' to 'const dictionary'

Error compiling Cython file:
------------------------------------------------------------
...
def llapi_dimension_parameter(object list_of_pos_params):
    cdef ParameterPTR dim_parameter
    cdef ParameterObject x, y, z
    if len(list_of_pos_params) == 2:
        x, y = list_of_pos_params
        dim_parameter = dimension_parameter(x.thisptr, y.thisptr)
                                          ^
------------------------------------------------------------

/home/robin/git/nest-simulator/pynest/nestkernel_api.pyx:620:43: Call with wrong number of arguments (expected 3, got 2)

Error compiling Cython file:
------------------------------------------------------------
...
    for conn_object in conns:
        conn_deque.push_back(conn_object.thisobj)

    # params can be a dictionary or a list of dictionaries
    if isinstance(params, dict):
        set_connection_status(conn_deque, pydict_to_dictionary(params))
                                                             ^
------------------------------------------------------------

/home/robin/git/nest-simulator/pynest/nestkernel_api.pyx:669:62: Cannot assign type 'dictionary' to 'const vector[dictionary]'
make[2]: *** [pynest/CMakeFiles/nestkernel_api.dir/build.make:75: pynest/nestkernel_api.c] Error 1
make[2]: *** Deleting file 'pynest/nestkernel_api.c'
make[1]: *** [CMakeFiles/Makefile2:535: pynest/CMakeFiles/nestkernel_api.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 99%] Linking CXX executable run_all_cpptests
[ 99%] Built target run_all_cpptests
make: *** [Makefile:146: all] Error 2
github-actions[bot] commented 1 year ago

Issue automatically marked stale!