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The NEST simulator
License: GNU General Public License v2.0
This project forked from nest/nest-simulator
The NEST simulator
License: GNU General Public License v2.0
Building wheel...
+ rm -rf /tmp/cibuildwheel/built_wheel
+ mkdir -p /tmp/cibuildwheel/built_wheel
+ python -m pip wheel /project --wheel-dir=/tmp/cibuildwheel/built_wheel --no-deps
error: subprocess-exited-with-error
× Building wheel for nest-simulator (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [437 lines of output]
Not searching for unused variables given on the command line.
-- The C compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/rh/devtoolset-10/root/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- The CXX compiler identification is GNU 10.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/rh/devtoolset-10/root/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /project/_cmake_test_compile/build
-- The CXX compiler identification is GNU 10.2.1
-- The C compiler identification is GNU 10.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/rh/devtoolset-10/root/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: /opt/rh/devtoolset-10/root/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- 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
-- Host triple: x86_64-pc-linux
-- Target triple: x86_64-pc-linux
-- Found Python: /opt/python/cp38-cp38/bin/python (found suitable version "3.8.13", minimum required is "3.8") found components: Interpreter Development.Module
-- Found Cython: /tmp/pip-build-env-v4w_7q17/overlay/bin/cython (found suitable version "0.29.30", minimum required is "0.28.3")
-- Found LTDL: /usr/local/lib/libltdl.so (found version "2.4.7")
-- Could NOT find Readline (missing: READLINE_LIBRARY NCURSES_LIBRARY READLINE_INCLUDE_DIR)
-- 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 OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found Boost: /boost (found suitable version "1.79.0", minimum required is "1.69.0")
-- Check the abort exitcode.
-- Check the abort exitcode. Permission denied
-- Check the segmentation fault exitcode.
-- Check the segmentation fault exitcode. Permission denied
-- Check whether the compiler ignores cmath makros.
-- Check whether the compiler ignores cmath makros. OFF
-- Check whether the compiler does NOT include <*.h> headers ISO conformant.
-- Check whether the compiler does NOT include <*.h> headers ISO conformant. OFF
-- Check whether the compiler respects symbolic signal names in signal.h.
-- Check whether the compiler respects symbolic signal names in signal.h. OFF
-- Check static template member declaration.
-- Check static template member declaration. OFF
-- Check for STL vector capacity base unity.
-- Check for STL vector capacity base unity. ON
-- Check for STL vector capacity doubling strategy.
-- Check for STL vector capacity doubling strategy. ON
-- Check whether the compiler fails with ICE.
-- Check whether the compiler fails with ICE. OFF
-- Check if ::nan is available from cmath.
-- Check if ::nan is available from cmath. ON
-- Check if ::isnan is available from cmath.
-- Check if ::isnan is available from cmath. ON
-- Check if Random123 generators work.
-- Check if Random123 generators work. ON
-- NEST version: reinvention-of-the-wheel@6880e7c669
-- Found PythonInterp: /opt/python/cp38-cp38/bin/python (found version "3.8.13")
-- Wheel build, installing pynestkernel and nestkernel_api to lib64/nest/
--------------------------------------------------------------------------------
NEST Configuration Summary
--------------------------------------------------------------------------------
Build type : Release
Target System : Linux
Cross Compiling : FALSE
C compiler : GNU 10.2.1 (/opt/rh/devtoolset-10/root/usr/bin/cc)
C compiler flags : -O2 -Wall -fopenmp -fdiagnostics-color=auto -O3 -DNDEBUG
C++ compiler : GNU 10.2.1 (/opt/rh/devtoolset-10/root/usr/bin/c++)
C++ compiler flags : -std=c++11 -O2 -Wall -fopenmp -fdiagnostics-color=auto -O3 -DNDEBUG
Build dynamic : ON
Built-in modules : models
User modules : None
Python bindings : Yes (Python 3.8.13: /opt/python/cp38-cp38/bin/python)
Includes : /opt/_internal/cpython-3.8.13/include/python3.8
Libraries :
Cython bindings : Yes (Cython 0.29.30: /tmp/pip-build-env-v4w_7q17/overlay/bin/cython)
MPI4PY header : NO
Use threading : Yes (OpenMP: -fopenmp)
Use GSL : No
Use Readline : No
Use libltdl : Yes (LTDL 2.4.7)
Includes : /usr/local/include
Libraries : /usr/local/lib/libltdl.so
Use doxygen : No
Use MPI : No
Detailed timers : No
Use MUSIC : No
Use libneurosim : No
Use Boost : Yes (Boost 1.79.0)
Includes : /boost
Libraries :
Use SIONlib : No
--------------------------------------------------------------------------------
The NEST executable will be installed to:
/project/_skbuild/linux-x86_64-3.8/cmake-install/bin/
NEST dynamic libraries and user modules will be installed to:
/project/_skbuild/linux-x86_64-3.8/cmake-install/lib64/nest/
Documentation and examples will be installed to:
/project/_skbuild/linux-x86_64-3.8/cmake-install/share/doc/nest/
PyNEST will be installed to:
/project/_skbuild/linux-x86_64-3.8/cmake-install/lib64/python3.8/site-packages
To set necessary environment variables, add the following line
to your ~/.bashrc :
source /project/_skbuild/linux-x86_64-3.8/cmake-install/bin/nest_vars.sh
--------------------------------------------------------------------------------
ATTENTION!
You are about to compile NEST without the GNU Scientific
Library or your GSL is too old (before v1.11). This means
that conductance-based neuron models and some random number
generators will not be available.
--------------------------------------------------------------------------------
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
CMake Warning:
Manually-specified variables were not used by the project:
PYTHON_INCLUDE_DIR
PYTHON_LIBRARY
Python3_EXECUTABLE
Python3_INCLUDE_DIR
Python3_LIBRARY
SKBUILD
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/project/models/spike_generator.cpp: In member function ‘void nest::spike_generator::Parameters_::get(dictionary&) const’:
/project/models/spike_generator.cpp:69:16: warning: unused variable ‘n_offsets’ [-Wunused-variable]
69 | const size_t n_offsets = spike_offsets_.size();
| ^~~~~~~~~
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/project/sli/filesystem.cc: In member function ‘virtual void FilesystemModule::MoveFileFunction::execute(SLIInterpreter*) const’:
/project/sli/filesystem.cc:173:11: warning: unused variable ‘t’ [-Wunused-variable]
173 | int t = unlink( dst->c_str() );
| ^
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[127/236] Building CXX object sli/CMakeFiles/sli_lib.dir/slistartup.cc.o
FAILED: sli/CMakeFiles/sli_lib.dir/slistartup.cc.o
/opt/rh/devtoolset-10/root/usr/bin/c++ -Dsli_lib_EXPORTS -I/boost -I/project/thirdparty -I/project/libnestutil -I/project/_skbuild/linux-x86_64-3.8/cmake-build/libnestutil -std=c++11 -O2 -Wall -fopenmp -fdiagnostics-color=auto -O3 -DNDEBUG -fPIC -fopenmp -MD -MT sli/CMakeFiles/sli_lib.dir/slistartup.cc.o -MF sli/CMakeFiles/sli_lib.dir/slistartup.cc.o.d -o sli/CMakeFiles/sli_lib.dir/slistartup.cc.o -c /project/sli/slistartup.cc
In file included from /project/sli/slistartup.h:30,
from /project/sli/slistartup.cc:23:
/project/sli/slistartup.cc: In member function ‘virtual void SLIStartup::init(SLIInterpreter*)’:
/project/_skbuild/linux-x86_64-3.8/cmake-build/libnestutil/config.h:48:29: error: ‘Permission’ was not declared in this scope
48 | #define NEST_EXITCODE_ABORT Permission denied
| ^~~~~~~~~~
/project/sli/slistartup.cc:476:68: note: in expansion of macro ‘NEST_EXITCODE_ABORT’
476 | exitcodes->insert( exitcode_abort_name, Token( new IntegerDatum( NEST_EXITCODE_ABORT ) ) );
| ^~~~~~~~~~~~~~~~~~~
/project/sli/slistartup.cc:478:51: error: expected primary-expression before ‘(’ token
478 | exitcodes->insert( exitcode_segfault_name, Token( new IntegerDatum( NEST_EXITCODE_SEGFAULT ) ) );
| ^
In file included from /project/sli/slistartup.h:30,
from /project/sli/slistartup.cc:23:
/project/_skbuild/linux-x86_64-3.8/cmake-build/libnestutil/config.h:49:43: error: expected ‘)’ before ‘denied’
49 | #define NEST_EXITCODE_SEGFAULT Permission denied
| ^~~~~~
/project/sli/slistartup.cc:478:71: note: in expansion of macro ‘NEST_EXITCODE_SEGFAULT’
478 | exitcodes->insert( exitcode_segfault_name, Token( new IntegerDatum( NEST_EXITCODE_SEGFAULT ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~
/project/sli/slistartup.cc:478:69: note: to match this ‘(’
478 | exitcodes->insert( exitcode_segfault_name, Token( new IntegerDatum( NEST_EXITCODE_SEGFAULT ) ) );
| ^
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[131/236] Building CXX object sli/CMakeFiles/sli_lib.dir/slistack.cc.o
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[141/236] Building CXX object sli/CMakeFiles/sli_lib.dir/slicontrol.cc.o
/project/sli/slicontrol.cc: In member function ‘virtual void Forallindexed_aFunction::execute(SLIInterpreter*) const’:
/project/sli/slicontrol.cc:1037:19: warning: unused variable ‘proc’ [-Wunused-variable]
1037 | ProcedureDatum* proc = dynamic_cast< ProcedureDatum* >( i->OStack.top().datum() );
| ^~~~
/project/sli/slicontrol.cc: In member function ‘virtual void Forallindexed_sFunction::execute(SLIInterpreter*) const’:
/project/sli/slicontrol.cc:1064:19: warning: unused variable ‘proc’ [-Wunused-variable]
1064 | ProcedureDatum* proc = dynamic_cast< ProcedureDatum* >( i->OStack.top().datum() );
| ^~~~
/project/sli/slicontrol.cc: In member function ‘virtual void Forall_sFunction::execute(SLIInterpreter*) const’:
/project/sli/slicontrol.cc:1091:19: warning: unused variable ‘proc’ [-Wunused-variable]
1091 | ProcedureDatum* proc = dynamic_cast< ProcedureDatum* >( i->OStack.top().datum() );
| ^~~~
[142/236] Building CXX object sli/CMakeFiles/sli_lib.dir/processes.cc.o
[143/236] Building CXX object sli/CMakeFiles/sli_lib.dir/sliarray.cc.o
[144/236] Building CXX object models/CMakeFiles/models.dir/modelsmodule.cpp.o
ninja: build stopped: subcommand failed.
File "/tmp/pip-build-env-v4w_7q17/overlay/lib/python3.8/site-packages/skbuild/setuptools_wrap.py", line 645, in setup
cmkr.make(make_args, install_target=cmake_install_target, env=env)
File "/tmp/pip-build-env-v4w_7q17/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 680, in make
self.make_impl(clargs=clargs, config=config, source_dir=source_dir, install_target=install_target, env=env)
File "/tmp/pip-build-env-v4w_7q17/overlay/lib/python3.8/site-packages/skbuild/cmaker.py", line 704, in make_impl
raise SKBuildError(
--------------------------------------------------------------------------------
-- Trying "Ninja" generator
--------------------------------
---------------------------
----------------------
-----------------
------------
-------
--
--
-------
------------
-----------------
----------------------
---------------------------
--------------------------------
-- Trying "Ninja" generator - success
--------------------------------------------------------------------------------
Configuring Project
Working directory:
/project/_skbuild/linux-x86_64-3.8/cmake-build
Command:
cmake /project -G Ninja -DCMAKE_INSTALL_PREFIX:PATH=/project/_skbuild/linux-x86_64-3.8/cmake-install -DPYTHON_VERSION_STRING:STRING=3.8.13 -DSKBUILD:INTERNAL=TRUE -DCMAKE_MODULE_PATH:PATH=/tmp/pip-build-env-v4w_7q17/overlay/lib/python3.8/site-packages/skbuild/resources/cmake -DPython3_EXECUTABLE:FILEPATH=/opt/python/cp38-cp38/bin/python -DPython3_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.8.13/include/python3.8 -DPython3_LIBRARY:PATH=libpython3.8.a -DPython_EXECUTABLE:FILEPATH=/opt/python/cp38-cp38/bin/python -DPython_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.8.13/include/python3.8 -DPython_LIBRARY:PATH=libpython3.8.a -DPYTHON_EXECUTABLE:FILEPATH=/opt/python/cp38-cp38/bin/python -DPYTHON_INCLUDE_DIR:PATH=/opt/_internal/cpython-3.8.13/include/python3.8 -DPYTHON_LIBRARY:PATH=libpython3.8.a -DCMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-v4w_7q17/overlay/lib/python3.8/site-packages/ninja/data/bin/ninja -DCMAKE_MODULE_PATH=/project/cmake:/skrepo/skbuild/resources/cmake -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_MODULE_PATH=/project/cmake:/skrepo/skbuild/resources/cmake
Traceback (most recent call last):
An error occurred while building with CMake.
Command:
cmake --build . --target install --config Release --
Install target:
install
Source directory:
/project
Working directory:
/project/_skbuild/linux-x86_64-3.8/cmake-build
Please check the install target is valid and see CMake's output for more information.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for nest-simulator
ERROR: Failed to build one or more wheels
WARNING: There was an error checking the latest version of pip.
Processing /project
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: nest-simulator
Building wheel for nest-simulator (pyproject.toml): started
Building wheel for nest-simulator (pyproject.toml): still running...
Building wheel for nest-simulator (pyproject.toml): finished with status 'error'
Failed to build nest-simulator
✕ 134.86s
Error: Command ['python', '-m', 'pip', 'wheel', PurePosixPath('/project'), '--wheel-dir=/tmp/cibuildwheel/built_wheel', '--no-deps'] failed with code 1.
Checking for common errors...
Wheel build is failing, something about exitcodes?
The latest version available through the package manager on the images is 1.53.0
, while I think it needs to be 1.69.0
+, right? What is required for NEST to pick up Boost. I've seen mentions of a BOOST_ROOT
env var in the boost community?
Followup of nest#2409
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