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hakonsbm / nest-simulator

The NEST simulator
GNU General Public License v2.0
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Building without MPI flag leads to MPI manager error #48

Closed Helveg closed 1 year ago

Helveg commented 1 year ago 
(workshop-env) robin@LAPTOP-JF6T3PSU:~/git/nest-simulator/build$ cmake ..
-- 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 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 -fdiagnostics-color=auto
C++ compiler        : GNU 9.3.0 (/usr/bin/c++)
C++ compiler flags  :  -O2 -std=c++11 -Wall -fopenmp -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          : No

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             : No

Detailed timers     : No

Use MUSIC           : No

Use libneurosim     : No

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

Use SIONlib         : No

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

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/numerics.cpp.o
[  2%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/logging_event.cpp.o
[  3%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/stopwatch.cpp.o
[  3%] Building CXX object libnestutil/CMakeFiles/nestutil.dir/propagator_stability.cpp.o
[  4%] Linking CXX shared library libnestutil.so
[  4%] Built target nestutil
[  4%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/archiving_node.cpp.o
[  5%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/clopath_archiving_node.cpp.o
[  5%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/common_synapse_properties.cpp.o
[  6%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connector_model.cpp.o
[  7%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_id.cpp.o
[  7%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/deprecation_warning.cpp.o
[  7%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/device.cpp.o
[  7%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/event.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/exceptions.cpp.o
[  8%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/node_collection.cpp.o
[  9%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/histentry.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();
      |                      ^
[  9%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/model.cpp.o
[ 10%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/model_manager.cpp.o
[ 10%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest_time.cpp.o
[ 11%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest_timeconverter.cpp.o
[ 11%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/modelrange.cpp.o
[ 12%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/modelrange_manager.cpp.o
[ 12%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/node.cpp.o
[ 12%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/parameter.cpp.o
[ 13%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/per_thread_bool_indicator.cpp.o
[ 13%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/proxynode.cpp.o
[ 14%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/recording_device.cpp.o
[ 14%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/ring_buffer.cpp.o
[ 15%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/slice_ring_buffer.cpp.o
[ 15%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/spikecounter.cpp.o
[ 16%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/stimulation_device.cpp.o
[ 16%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/sparse_node_array.cpp.o
[ 17%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/conn_parameter.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 )
      |                 ^~~~~~~
[ 17%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/conn_builder.cpp.o
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[ 19%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/music_manager.cpp.o
[ 19%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/nest.cpp.o
[ 20%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/__/models/iaf_psc_alpha.cpp.o
[ 20%] 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
[ 21%] 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
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[ 44%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/io_manager.cpp.o
[ 44%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/mpi_manager.cpp.o
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/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1059:1: error: no declaration matches ‘void nest::MPIManager::communicate(std::vector<long int>&, std::vector<long int>&)’
 1059 | nest::MPIManager::communicate( std::vector< long >&, std::vector< long >& )
      | ^~~~
In file included from /home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:23:
/home/robin/git/nest-simulator/nestkernel/mpi_manager.h:702:1: note: candidates are: ‘void nest::MPIManager::communicate(std::vector<long int>&)’
  702 | MPIManager::communicate( std::vector< long >& )
      | ^~~~~~~~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.h:697:1: note:                 ‘void nest::MPIManager::communicate(std::vector<int>&)’
  697 | MPIManager::communicate( std::vector< int >& )
      | ^~~~~~~~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1052:1: note:                 ‘void nest::MPIManager::communicate(double, std::vector<double>&)’
 1052 | nest::MPIManager::communicate( double send_val, std::vector< double >& recv_buffer )
      | ^~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1042:1: note:                 ‘void nest::MPIManager::communicate(std::vector<int>&, std::vector<int>&, std::vector<int>&)’
 1042 | nest::MPIManager::communicate( std::vector< int >& send_buffer,
      | ^~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1032:1: note:                 ‘void nest::MPIManager::communicate(std::vector<long unsigned int>&, std::vector<long unsigned int>&, std::vector<int>&)’
 1032 | nest::MPIManager::communicate( std::vector< unsigned long >& send_buffer,
      | ^~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1022:1: note:                 ‘void nest::MPIManager::communicate(std::vector<double>&, std::vector<double>&, std::vector<int>&)’
 1022 | nest::MPIManager::communicate( std::vector< double >& send_buffer,
      | ^~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:1007:1: note:                 ‘void nest::MPIManager::communicate(std::vector<nest::MPIManager::OffGridSpike>&, std::vector<nest::MPIManager::OffGridSpike>&, std::vector<int>&)’
 1007 | nest::MPIManager::communicate( std::vector< OffGridSpike >& send_buffer,
      | ^~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:989:1: note:                 ‘void nest::MPIManager::communicate(std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<int>&)’
  989 | nest::MPIManager::communicate( std::vector< unsigned int >& send_buffer,
      | ^~~~
In file included from /home/robin/git/nest-simulator/nestkernel/mpi_manager.cpp:23:
/home/robin/git/nest-simulator/nestkernel/mpi_manager.h:129:8: note:                 ‘void nest::MPIManager::communicate(std::vector<long unsigned int>&, std::vector<long unsigned int>&)’
  129 |   void communicate( std::vector< size_t >& send_buffer, std::vector< size_t >& recv_buffer );
      |        ^~~~~~~~~~~
/home/robin/git/nest-simulator/nestkernel/mpi_manager.h:55:7: note: ‘class nest::MPIManager’ defined here
   55 | class MPIManager : public ManagerInterface
      |       ^~~~~~~~~~
make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/build.make:1294: nestkernel/CMakeFiles/nestkernel.dir/mpi_manager.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:480: nestkernel/CMakeFiles/nestkernel.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
github-actions[bot] commented 1 year ago

Issue automatically marked stale!

Helveg commented 1 year ago

Correctly marked as stale, probably N/A anymore.