error compiling PYNE
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Kermit Bunde-google
Jun 4, 2021, 9:25:32 AM6/4/21
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I had some difficulty compiling PYNE and I did not see something similar on GitHub.
kermitnuc@MacBook-Pro pyne-pyne-56eef01 % python setup.py install --clean --slow -DCMAKE_Fortran_COMPILER=/usr/local/bin/x86_64-apple-darwin19-gfortran-9 -DCMAKE_C_COMPILER=/usr/local/bin/x86_64-apple-darwin19-gcc-9 -DCMAKE_CXX_COMPILER=/usr/local/bin/x86_64-apple-darwin19-g++-9 -DCYTHON_EXECUTABLE=/users/kermitnuc/anaconda3/bin/cython -DHDF5_ROOT=/usr/local/
deleting src/decay.h
deleting src/decay.cpp
deleting src/cram.h
deleting src/cram.c
deleting src/decay-apple-gnu.s
deleting src/cram-apple-gnu.s
atomic_data.h generated is the same as existing file, skipping.
atomic_data.cpp generated is the same as existing file, skipping.
/usr/local/bin/cmake
CMake command is
cmake .. -DCMAKE_INSTALL_PREFIX=/System/Library/Frameworks/Python.framework/Versions/2.7 -DCMAKE_Fortran_COMPILER=/usr/local/bin/x86_64-apple-darwin19-gfortran-9 -DCMAKE_C_COMPILER=/usr/local/bin/x86_64-apple-darwin19-gcc-9 -DCMAKE_CXX_COMPILER=/usr/local/bin/x86_64-apple-darwin19-g++-9 -DCYTHON_EXECUTABLE=/users/kermitnuc/anaconda3/bin/cython -DHDF5_ROOT=/usr/local/ -DPYNE_FAST_COMPILE=FALSE -DENABLE_SPATIAL_SOLVERS=ON -DPYTHON_EXECUTABLE=/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/local/bin/x86_64-apple-darwin19-gcc-9
-- Check for working C compiler: /usr/local/bin/x86_64-apple-darwin19-gcc-9 - works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/local/bin/x86_64-apple-darwin19-g++-9
-- Check for working CXX compiler: /usr/local/bin/x86_64-apple-darwin19-g++-9 - works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
/ \
) (( )) (
(@) /|\ ))_(( /|\
|-| / | \ (/\|/\) / | \ (@)
| | -------------------/--|-voV---\`|'/--Vov-|--\---------------------|-|
|-| '^` (o o) '^` | |
| | `\Y/' |-|
|-| | |
| | /\ ___ __ __ /\ |-|
|-| /^~\ / _ \_ _ /\ \ \/__\ /^~\ | |
| | /^~\ / /_)/ | | |/ \/ /_\ /^~\ |-|
|-| /^~\ / ___/| |_| / /\ //__ /^~\ | |
| | ^||` \/ \__, \_\ \/\__/ ^||` |-|
|-| || |____/ || | |
| | ==== ==== |-|
|-| | |
| | |-|
|-|___________________________________________________________________| |
(@) l /\ / ( ( \ /\ l `\|-|
l / V \ \ V \ l (@)
l/ _) )_ \I
`\ /'
`
-- Pyne platform defined as: __APPLE__
-- Checking whether to build spatial solvers
-- -- Checking CMAKE_CXX_COMPILER_ID: GNU
-- -- -- Checking CMAKE_CXX_COMPILER_VERSION: 9.3.0
-- -- -- Checking if APPLE: 1
-- Build spatial solvers: false
-- Build type: Release
-- PyNE Fast Compile: FALSE
-- CMAKE_INSTALL_RPATH: /System/Library/Frameworks/Python.framework/Versions/2.7/lib:/usr/local/lib
-- The ASM compiler identification is GNU
-- Found assembler: /usr/local/bin/x86_64-apple-darwin19-gcc-9
-- CMake Install Prefix: /System/Library/Frameworks/Python.framework/Versions/2.7
-- Dependency Root Dir (DEPS_ROOT_DIR): /usr/local
-- Dependency Hints (DEPS_HINTS): HINTS;/usr/local
-- Dependency Binary Hints (DEPS_BIN_HINTS): HINTS;/usr/local;/usr/local/bin
-- Dependency Library Hints (DEPS_LIB_HINTS): HINTS;/usr/local;/usr/local/lib
-- Dependency Include Hints (DEPS_INCLUDE_HINTS): HINTS;/usr/local/include
-- HDF5 Root: /usr/local/
CMake Warning (dev) at CMakeLists.txt:65 (FIND_PACKAGE):
Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
CMake variable HDF5_ROOT is set to:
/usr/local/
For compatibility, CMake is ignoring the variable.
This warning is for project developers. Use -Wno-dev to suppress it.
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found HDF5: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib (found version "1.10.7")
-- HDF5 Include directory: /usr/local/include
-- HDF5 Library directories:
-- HDF5 Libraries: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib
-- HDF5 library version: 1.10.7
-- Found PythonInterp: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python (found version "2.7.16")
-- Found PythonLibs: /usr/lib/libpython2.7.dylib (found version "2.7.16")
-- PYTHON_EXECUTABLE: /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python
-- PYTHON_SITE_PACKAGES: /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python/site-packages
-- NUMPY_VERSION_STRING = 1.8.0rc1
-- Found Numpy: 1.8.0rc1
-- The Fortran compiler identification is GNU 9.3.0
-- Checking whether Fortran compiler has -isysroot
-- Checking whether Fortran compiler has -isysroot - yes
-- Checking whether Fortran compiler supports OSX deployment target flag
-- Checking whether Fortran compiler supports OSX deployment target flag - yes
-- Check for working Fortran compiler: /usr/local/bin/x86_64-apple-darwin19-gfortran-9
-- Check for working Fortran compiler: /usr/local/bin/x86_64-apple-darwin19-gfortran-9 - works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/x86_64-apple-darwin19-gfortran-9 supports Fortran 90
-- Checking whether /usr/local/bin/x86_64-apple-darwin19-gfortran-9 supports Fortran 90 - yes
-- CMAKE_Fortran_IMPLICIT_LINK_DIRECTORIES: /usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9/gcc/x86_64-apple-darwin19/9.3.0;/usr/local/Cellar/gcc@9/9.3.0_1/lib/gcc/9;/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib
-- CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES Before Fix: gfortran;gcc_ext.10.5;gcc;quadmath;m;gcc_ext.10.5;gcc
-- LIBGCC_S_PATH = /usr/lib/libgcc_s.1.dylib.
-- LIBGCC_S = gcc_s.1.
-- CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES: gfortran;gcc_ext.10.5;gcc;quadmath;m;gcc_ext.10.5;gcc;gcc_s.1
-- Found Cython: /users/kermitnuc/anaconda3/bin/cython
-- LIBS: /usr/local/lib/libhdf5.dylib;/usr/local/lib/libz.dylib;/usr/lib/libdl.dylib;/usr/lib/libm.dylib;/usr/lib/libpython2.7.dylib
-- Extracting decay.tar.gz
x decay.h
x decay.cpp
-- Extracting decay-apple-gnu.tar.gz
x decay-apple-gnu.s
-- Extracting cram.tar.gz
x cram.c
x cram.h
-- Extracting cram-apple-gnu.tar.gz
x cram-apple-gnu.s
-- Not fast compiling decay.cpp since PyNE fast compile is disabled.
-- Not fast compiling cram.c since PyNE fast compile is disabled.
-- Include paths for /Users/kermitnuc/pyne/pyne-pyne-56eef01/src: /usr/local/include;/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include;/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne;/Users/kermitnuc/pyne/pyne-pyne-56eef01/src
-- Include paths for /Users/kermitnuc/pyne/pyne-pyne-56eef01/pyne: /usr/local/include;/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include;/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne;/Users/kermitnuc/pyne/pyne-pyne-56eef01/src
-- Modules to Cythonize: ace;bins;data;dtypes;endf;enrichment;extra_types;jsoncpp;material;material_library;nucname;particle;pyne_config;rxname;source;stlcontainers;tally;transmuters;_utils
-- F2PY F90 FLAGS:
-- Include paths for /Users/kermitnuc/pyne/pyne-pyne-56eef01/pyne/xs: /usr/local/include;/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include;/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne;/Users/kermitnuc/pyne/pyne-pyne-56eef01/src
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/kermitnuc/pyne/pyne-pyne-56eef01/build
Scanning dependencies of target ReplicatePythonSourceTree
[ 0%] Built target ReplicatePythonSourceTree
Scanning dependencies of target gtol
[ 1%] Building Fortran object src/CMakeFiles/gtol.dir/ensdf_processing/GTOL/gtol.f.o
[ 2%] Building Fortran object src/CMakeFiles/gtol.dir/ensdf_processing/nsdflib95.f.o
[ 3%] Linking Fortran executable gtol
[ 3%] Built target gtol
Scanning dependencies of target seqhst
[ 4%] Building Fortran object src/CMakeFiles/seqhst.dir/ensdf_processing/HSICC/seqhst.for.o
[ 5%] Building Fortran object src/CMakeFiles/seqhst.dir/ensdf_processing/nsdflib95.f.o
[ 6%] Linking Fortran executable seqhst
[ 6%] Built target seqhst
Scanning dependencies of target hsicc
…
[ 72%] Linking CXX shared module source.so
[ 72%] Built target source
[ 73%] Compiling Cython CXX source for jsoncpp...
Scanning dependencies of target jsoncpp
[ 73%] Building CXX object pyne/CMakeFiles/jsoncpp.dir/jsoncpp.cxx.o
[ 74%] Linking CXX shared module jsoncpp.so
[ 74%] Built target jsoncpp
[ 75%] Compiling Cython CXX source for transmuters...
Scanning dependencies of target transmuters
[ 76%] Building CXX object pyne/CMakeFiles/transmuters.dir/transmuters.cxx.o
In file included from /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarraytypes.h:1760,
from /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/ndarrayobject.h:17,
from /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/arrayobject.h:4,
from /Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne/transmuters.cxx:647:
/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
15 | #warning "Using deprecated NumPy API, disable it by " \
| ^~~~~~~
/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne/transmuters.cxx: In function 'PyObject* __pyx_pf_4pyne_11transmuters_cram(PyObject*, PyObject*, PyObject*, int)':
/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne/transmuters.cxx:2952:70: error: '__pyx_builtin_ValueError' was not declared in this scope; did you mean '__pyx_builtin_ImportError'?
2952 | try { throw; } catch(const std::exception& exn) {PyErr_SetString(__pyx_builtin_ValueError, exn.what());} catch(...) { PyErr_SetNone(__pyx_builtin_ValueError); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
| __pyx_builtin_ImportError
/Users/kermitnuc/pyne/pyne-pyne-56eef01/build/pyne/transmuters.cxx:2952:137: error: '__pyx_builtin_ValueError' was not declared in this scope; did you mean '__pyx_builtin_ImportError'?
2952 | try { throw; } catch(const std::exception& exn) {PyErr_SetString(__pyx_builtin_ValueError, exn.what());} catch(...) { PyErr_SetNone(__pyx_builtin_ValueError); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
| __pyx_builtin_ImportError
make[2]: *** [pyne/CMakeFiles/transmuters.dir/build.make:89: pyne/CMakeFiles/transmuters.dir/transmuters.cxx.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:837: pyne/CMakeFiles/transmuters.dir/all] Error 2
make: *** [Makefile:150: all] Error 2
--------------------
If you are having issues building pyne, please report your problem to pyne...@googlegroups.com or look for help at http://pyne.io
--------------------
Traceback (most recent call last):
File "setup.py", line 420, in <module>
main()
File "setup.py", line 404, in main
main_safe(ns)
File "setup.py", line 396, in main_safe
main_body(ns)
File "setup.py", line 379, in main_body
rtn = subprocess.check_call(['make'] + ns.make_args, cwd=ns.build_dir)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 190, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['make']' returned non-zero exit status 2
Paul Wilson
Jun 4, 2021, 9:27:01 AM6/4/21
to pyne...@googlegroups.com, kerm...@gmail.com
Hello Kermit,
This error does ring some bells as something we've encountered in the past - let me see if I can track down the cause/fix.
Paul
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Chair, Department of Engineering Physics
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Paul P.H. Wilson (he/him/his)
Grainger Professor of Nuclear Engineering
Chair, Department of Engineering Physics
o: 608-263-0807, c: 608-469-9615
paul....@wisc.edu
153 Engineering Research Bldg
1500 Engineering Dr, Madison, WI 53706
Zoom Meeting Room: https://uwmadison.zoom.us/j/6082630807
Zoom Phone Access: +1-929-205-6099, Access code: 6082630807
Paul Wilson
Jun 4, 2021, 9:29:03 AM6/4/21
to pyne...@googlegroups.com, kerm...@gmail.com
Hi again,
Alas, I was able to quickly find this closed issue: https://github.com/pyne/pyne/issues/1340r
I am not sure if it is related, but until we can dig a little deeper, let me know if this offers any solution.
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Baptiste MOUGINOT (BaM)
Jun 4, 2021, 10:06:29 AM6/4/21
to pyne...@googlegroups.com, kerm...@gmail.com
Hi Kermit,
So updating you PyNE source might be the solution.
I can’t confirm this is the source of the problem, but I see that you are using python2 on your machine, but your conda installation comes form anaconda3, which uses python 3.8 by default.
This might be conflicting.
The file that cmake is failing to compile seems to have been generated by cython, so is probably built to be compiled against python 3.8 library.
Also I can see the 56eef01 in you folder name which correspond to a 9 months old commit.
A similar issue as what you are experiencing has been fixed last January:
I hope this might help.
Baptiste
To view this discussion on the web visit https://groups.google.com/d/msgid/pyne-dev/79140581-a518-1cde-4da2-bbe076441dc0%40wisc.edu.
Kermit Bunde-google
Jun 6, 2021, 4:31:59 PM6/6/21
to Baptiste MOUGINOT (BaM), pyne...@googlegroups.com
Thanks for the help.
I downloaded the PYNE 0.7.3 tar file and modified the cpp_transmuters.pxd file as listed in the issue list. It complied.
Kermit Bunde
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