Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos.
[ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2
######## -------------------------------------------------------------------------------- NEST Configuration Summary --------------------------------------------------------------------------------
Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON
Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a
Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) 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 ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so
Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
Use MUSIC : No Use libneurosim : No Use Boost : No
--------------------------------------------------------------------------------
Carlos, Why don’t you just delete everyone and start a build from scratch?
On Fri, Sep 4, 2020 at 20:37 Carlos Gutierrez carlosengutierrez@gmail.com wrote:
Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos.
[ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2
########
NEST Configuration Summary
Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON
Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a
Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) 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 ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so
Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
Use MUSIC : No Use libneurosim : No Use Boost : No
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To unsubscribe send an email to users-leave@nest-simulator.org
Carlos, And show us as to how CMake is executed.
On Sat, Sep 5, 2020 at 9:53 AM Itaru Kitayama itaru.kitayama@gmail.com wrote:
Carlos, Why don’t you just delete everyone and start a build from scratch?
On Fri, Sep 4, 2020 at 20:37 Carlos Gutierrez carlosengutierrez@gmail.com wrote:
Dear All, I get the following error when making NEST 2.20 on my desktop, any idea where is the problem?. Thanks, Carlos.
[ 99%] Building CXX object pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o [100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103: pynest/pynestkernel.so] Error 1 make[1]: *** [CMakeFiles/Makefile2:1030: pynest/CMakeFiles/pynestkernel.dir/all] Error 2 make: *** [Makefile:141: all] Error 2
########
NEST Configuration Summary
Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread -fdiagnostics-color=auto C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread -fdiagnostics-color=auto Build dynamic : ON
Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a
Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) 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 ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so
Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes : /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include Link Flags : -pthread Libraries : /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
Use MUSIC : No Use libneurosim : No Use Boost : No
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To unsubscribe send an email to users-leave@nest-simulator.org
Hi Itaru, I installed python from source and forgot to add the flag --enable-shared
I recompiled Python and the issue is solved, Thanks, C.
On Sat, Sep 5, 2020 at 10:53 AM Itaru Kitayama itaru.kitayama@gmail.com wrote:
Carlos, And show us as to how CMake is executed.
On Sat, Sep 5, 2020 at 9:53 AM Itaru Kitayama itaru.kitayama@gmail.com wrote:
Carlos, Why don’t you just delete everyone and start a build from scratch?
On Fri, Sep 4, 2020 at 20:37 Carlos Gutierrez <
carlosengutierrez@gmail.com> wrote:
Dear All, I get the following error when making NEST 2.20 on my desktop, any
idea where is the problem?. Thanks, Carlos.
[ 99%] Building CXX object
pynest/CMakeFiles/pynestkernel.dir/pynestkernel.cxx.o
[100%] Linking CXX shared module pynestkernel.so /usr/bin/ld: /usr/local/lib/libpython3.8.a(abstract.o): relocation
R_X86_64_PC32 against symbol `_Py_NotImplementedStruct' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status make[2]: *** [pynest/CMakeFiles/pynestkernel.dir/build.make:103:
pynest/pynestkernel.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:1030:
pynest/CMakeFiles/pynestkernel.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
########
NEST Configuration Summary
Build type : Target System : Linux Cross Compiling : FALSE C compiler : GNU 9.3.0 (/usr/bin/cc) C compiler flags : -fPIC -fopenmp -pthread
-fdiagnostics-color=auto
C++ compiler : GNU 9.3.0 (/usr/bin/c++) C++ compiler flags : -std=c++11 -fPIC -fopenmp -pthread
-fdiagnostics-color=auto
Build dynamic : ON
Built-in modules : models;precise;topology User modules : None Python bindings : Yes (Python 3.8: /usr/local/bin/python3) Includes : /usr/local/include/python3.8 Libraries : /usr/local/lib/libpython3.8.a
Cython bindings : Yes (Cython 0.29.21: /usr/local/bin/cython) 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 ) Includes : /usr/include Libraries : /usr/lib/x86_64-linux-gnu/libltdl.so
Use doxygen : No Use MPI : Yes (MPI: /usr/bin/mpicxx) FLAGS : -pthread Includes :
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include
Link Flags : -pthread Libraries :/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
Use MUSIC : No Use libneurosim : No Use Boost : No
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
-
Carlos Gutierrez -
Itaru Kitayama