Installing from trunk on Fedora 17 64-bit consistently fails with the following build error (but installation on the 32-bit platform succeeds):

out: error: Command "g++ -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D__STDC_FORMAT_MACROS=1 -I/home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c pyamg/amg_core/amg_core_wrap.cxx -o build/temp.linux-x86_64-2.7/pyamg/amg_core/amg_core_wrap.o" failed with exit status 1

Hi,

Thanks for reporting this issue. I'm not sure yet what is causing the problem, but you could try generating the SWIG .cxx files yourself. Try

$ cd somewhere/pyamg/amg_core $ swig -c++ -python amg_core.i $ cd ../../ $ python setup.py build $ python setup.py install

Let us know how this works,

• Jacob

Comment deleted

Hi Jacob, running "python setup.py build" works fine. Running "python setup.py install" gives the following output:

running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building py_modules sources building extension "pyamg.amg_core._amg_core" sources building data_files sources build_src: building npy-pkg config files running build_py copying pyamg/svn_version.py -> build/lib.linux-x86_64-2.7/pyamg copying build/src.linux-x86_64-2.7/pyamg/config.py -> build/lib.linux-x86_64-2.7/pyamg running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext building 'pyamg.amg_core._amg_core' extension compiling C++ sources C compiler: g++ -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC

compile options: '-D__STDC_FORMAT_MACROS=1 -I/home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c' g++: pyamg/amg_core/amg_core_wrap.cxx In file included from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1722:0, from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15, from pyamg/amg_core/amg_core_wrap.cxx:3061: /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] pyamg/amg_core/amg_core_wrap.cxx: In function ‘void init_amg_core()’: pyamg/amg_core/amg_core_wrap.cxx:30543:21: warning: variable ‘md’ set but not used [-Wunused-but-set-variable] In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void cljp_naive_splitting(I, const I*, const I*, const I*, const I*, I*, I) [with I = int]’: pyamg/amg_core/amg_core_wrap.cxx:5032:125: required from here pyamg/amg_core/ruge_stuben.h:291:5: error: ‘vertex_coloring_mis’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/amg_core_wrap.cxx:3067:0: pyamg/amg_core/graph.h:171:3: note: ‘template T vertex_coloring_mis(I, const I*, const I*, T*)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void classical_strength_of_connection(I, F, const I*, const I*, const T*, I*, I*, T*) [with I = int; T = float; F = float]’: pyamg/amg_core/amg_core_wrap.cxx:9484:141: required from here pyamg/amg_core/ruge_stuben.h:58:17: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h:64:38: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void classical_strength_of_connection(I, F, const I*, const I*, const T*, I*, I*, T*) [with I = int; T = double; F = double]’: pyamg/amg_core/amg_core_wrap.cxx:9610:144: required from here pyamg/amg_core/ruge_stuben.h:58:17: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h:64:38: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1722:0, from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15, from pyamg/amg_core/amg_core_wrap.cxx:3061: /home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] pyamg/amg_core/amg_core_wrap.cxx: In function ‘void init_amg_core()’: pyamg/amg_core/amg_core_wrap.cxx:30543:21: warning: variable ‘md’ set but not used [-Wunused-but-set-variable] In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void cljp_naive_splitting(I, const I*, const I*, const I*, const I*, I*, I) [with I = int]’: pyamg/amg_core/amg_core_wrap.cxx:5032:125: required from here pyamg/amg_core/ruge_stuben.h:291:5: error: ‘vertex_coloring_mis’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/amg_core_wrap.cxx:3067:0: pyamg/amg_core/graph.h:171:3: note: ‘template T vertex_coloring_mis(I, const I*, const I*, T*)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void classical_strength_of_connection(I, F, const I*, const I*, const T*, I*, I*, T*) [with I = int; T = float; F = float]’: pyamg/amg_core/amg_core_wrap.cxx:9484:141: required from here pyamg/amg_core/ruge_stuben.h:58:17: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h:64:38: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h: In instantiation of ‘void classical_strength_of_connection(I, F, const I*, const I*, const T*, I*, I*, T*) [with I = int; T = double; F = double]’: pyamg/amg_core/amg_core_wrap.cxx:9610:144: required from here pyamg/amg_core/ruge_stuben.h:58:17: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit In file included from pyamg/amg_core/amg_core_wrap.cxx:3064:0: pyamg/amg_core/ruge_stuben.h:64:38: error: ‘mynorm’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] In file included from pyamg/amg_core/smoothed_aggregation.h:12:0, from pyamg/amg_core/amg_core_wrap.cxx:3065: pyamg/amg_core/linalg.h:72:15: note: ‘double mynorm(const npy_cdouble_wrapper&)’ declared here, later in the translation unit error: Command "g++ -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -D__STDC_FORMAT_MACROS=1 -I/home/ipython/.virtualenv/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c pyamg/amg_core/amg_core_wrap.cxx -o build/temp.linux-x86_64-2.7/pyamg/amg_core/amg_core_wrap.o" failed with exit status 1

Hi,

I just made a commit to the SVN that hopefully addresses these errors. Try updating to the latest SVN and then running these commands again.

$ cd somewhere/pyamg/amg_core $ swig -c++ -python amg_core.i $ cd ../../ $ python setup.py build $ python setup.py install

Hopefully, this will fix things, but I'm not entirely sure.

• Jacob

Hi Jacob,

I ran the commands you listed and everything was successful!

COOL.

I will restore pyamg which is currently an optional dependency of scikit-learn in https://github.com/invisibleroads/crosscompute-scripts

RHH

I'm glad that everything works now. Let us know if you have any other issues.

• Jacob

moved to github: https://github.com/pyamg/pyamg/issues