21 Sep
2023
21 Sep
'23
4:09 p.m.
Dear all,
I installed nest from source according to this instruction (Install NEST from source —
NEST Simulator Documentation) but when I run this code to make a module, I face with
following error. Can you help me to solve it?
import matplotlib as mplimport matplotlib.pyplot as pltimport nestimport numpy as npimport
osfrom pynestml.frontend.pynestml_frontend import generate_nest_target
NEST_SIMULATOR_INSTALL_LOCATION = nest.ll_api.sli_func("statusdict/prefix ::")
generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml",
target_path="/home/atiye/new_neuron2",
module_name="hh_psc_alpha1_module",
suffix="_nestml", logging_level="ERROR", # try
"INFO" for more debug information
codegen_opts={"nest_path":
NEST_SIMULATOR_INSTALL_LOCATION})nest.Install("hh_psc_alpha1_module")
errors:cd /home/atiye/New\ folder ; /usr/bin/env /bin/python3
/home/atiye/.vscode-server/extensions/ms-python.python-2023.16.0/pythonFiles/lib/python/debugpy/adapter/../../debugpy/launcher
52383 -- /home/atiye/New\ folder/hh_motor_neuron.py
-- N E S T -- Copyright (C) 2004 The NEST Initiative
Version: 3.5 Built: Jul 13 2023 04:45:54
This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for
details.
Problems or suggestions? Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
-- N E S T -- Copyright (C) 2004 The NEST Initiative
Version: 3.5 Built: Jul 13 2023 04:45:54
This program is provided AS IS and comes with NO WARRANTY. See the file LICENSE for
details.
Problems or suggestions? Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
-- The CXX compiler identification is GNU 11.3.0-- Detecting CXX compiler ABI info--
Detecting CXX compiler ABI info - done-- Check for working CXX compiler: /usr/bin/g++ -
skipped-- Detecting CXX compile features-- Detecting CXX compile features - done
-------------------------------------------------------hh_psc_alpha1_module Configuration
Summary-------------------------------------------------------
C++ compiler : /usr/bin/g++Build static libs : OFFC++ compiler flags : NEST
compiler flags : -g -O2 -ffile-prefix-map=/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389=.
-flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong
-Wformat -Werror=format-security -std=c++11 -Wall -fopenmp -O2
-fdiagnostics-color=autoNEST include dirs :
-I/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/include/nest
-I/usr/include -I/usr/include -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/includeNEST libraries flags :
-L/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nest -lnest -lsli
-fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libreadline.so
/usr/lib/x86_64-linux-gnu/libncurses.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'hh_psc_alpha1_module' using make make install
The library file libhh_psc_alpha1_module.so will be installed to
/build/nest-gCkf8Z/nest-3.5-0ubuntu1ppa1-1389/debian/nest/usr/lib/nestThe module can be
loaded into NEST using (hh_psc_alpha1_module) Install (in SLI)
nest.Install(hh_psc_alpha1_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt: No cmake_minimum_required command is present. A
line of code such as
cmake_minimum_required(VERSION 3.22)
should be added at the top of the file. The version specified may be lower if you wish
to support older CMake versions for this project. For more information run "cmake
--help-policy CMP0000".This warning is for project developers. Use -Wno-dev to
suppress it.
-- Configuring done-- Generating done-- Build files have been written to:
/home/atiye/new_neuron2[ 66%] Building CXX object
CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o[ 66%] Building CXX
object
CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o/home/atiye/new_neuron2/hh_psc_alpha1_module.cpp:26:10:
fatal error: connection_manager_impl.h: No such file or directory 26 | #include
"connection_manager_impl.h" |
^~~~~~~~~~~~~~~~~~~~~~~~~~~compilation terminated.make[2]: ***
[CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:76:
CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_module.o] Error 1make[2]: ***
Waiting for unfinished jobs..../home/atiye/new_neuron2/hh_psc_alpha1_nestml.cpp:29:10:
fatal error: numerics.h: No such file or directory 29 | #include "numerics.h"
| ^~~~~~~~~~~~compilation terminated.make[2]: ***
[CMakeFiles/hh_psc_alpha1_module_module.dir/build.make:90:
CMakeFiles/hh_psc_alpha1_module_module.dir/hh_psc_alpha1_nestml.o] Error 1make[1]: ***
[CMakeFiles/Makefile2:110: CMakeFiles/hh_psc_alpha1_module_module.dir/all] Error 2make:
*** [Makefile:156: all] Error 2Traceback (most recent call last): File
"/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py",
line 176, in build subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout,
shell=shell, File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
raise CalledProcessError(retcode, cmd)subprocess.CalledProcessError: Command
'['make', '-j8', 'all']' returned non-zero exit status 2.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/atiye/New
folder/hh_motor_neuron.py", line 11, in <module>
generate_nest_target(input_path="/home/atiye/nestml/models/neurons/hh_psc_alpha1.nestml",
File
"/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py",
line 229, in generate_nest_target generate_target(input_path,
target_platform="NEST", target_path=target_path, logging_level=logging_level,
File
"/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py",
line 198, in generate_target if not process() == 0: File
"/home/atiye/.local/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py",
line 351, in process _builder.build() File
"/home/atiye/.local/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py",
line 183, in build raise
GeneratedCodeBuildException(stages_exception[current_stage])pynestml.exceptions.generated_code_build_exception.GeneratedCodeBuildException:
Error occurred during 'make all'! More detailed error messages can be found in
stderr.
Thanks a lotBest, Atiyeh