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simphony / simphony-jyulb

SimPhoNy Wrapper for the JYU-LB code.
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install of simphony-jyu-lb fails on Ubuntu 12.04.5 LTS - 32bit #26

Open nathanfranklin opened 9 years ago

nathanfranklin commented 9 years ago 
(simphony)franklin@ubuntu:~/simphony-framework$ uname -a
Linux ubuntu 3.13.0-32-generic #57~precise1-Ubuntu SMP Tue Jul 15 03:50:54 UTC 2014 i686 i686 i386 GNU/Linux

Command and error message:

(simphony)franklin@ubuntu:~/simphony-framework$ make simphony-jyu-lb
pip install --upgrade git+https://github.com/simphony/simphony-jyulb.git@0.1.3
Collecting git+https://github.com/simphony/simphony-jyulb.git@0.1.3
  Cloning https://github.com/simphony/simphony-jyulb.git (to 0.1.3) to /tmp/pip-_VTrNG-build
/home/franklin/simphony/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Requirement already up-to-date: simphony in /home/franklin/simphony/lib/python2.7/site-packages (from jyu-engine==0.1.3)
Requirement already up-to-date: enum34>=1.0.4 in /home/franklin/simphony/lib/python2.7/site-packages (from simphony->jyu-engine==0.1.3)
Requirement already up-to-date: stevedore>=1.2.0 in /home/franklin/simphony/lib/python2.7/site-packages (from simphony->jyu-engine==0.1.3)
Requirement already up-to-date: numpy>=1.4.1 in /home/franklin/simphony/lib/python2.7/site-packages (from simphony->jyu-engine==0.1.3)
Collecting argparse (from stevedore>=1.2.0->simphony->jyu-engine==0.1.3)
  Using cached argparse-1.3.0-py2.py3-none-any.whl
Requirement already up-to-date: six>=1.9.0 in /home/franklin/simphony/lib/python2.7/site-packages (from stevedore>=1.2.0->simphony->jyu-engine==0.1.3)
Requirement already up-to-date: pbr<2.0,>=0.11 in /home/franklin/simphony/lib/python2.7/site-packages (from stevedore>=1.2.0->simphony->jyu-engine==0.1.3)
Installing collected packages: jyu-engine, argparse
  Running setup.py install for jyu-engine
    Complete output from command /home/franklin/simphony/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-_VTrNG-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-5dn3qX-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/franklin/simphony/include/site/python2.7/jyu-engine:
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-i686-2.7
    creating build/lib.linux-i686-2.7/jyulb
    copying jyulb/__init__.py -> build/lib.linux-i686-2.7/jyulb
    copying jyulb/cuba_extension.py -> build/lib.linux-i686-2.7/jyulb
    creating build/lib.linux-i686-2.7/jyulb/internal
    copying jyulb/internal/__init__.py -> build/lib.linux-i686-2.7/jyulb/internal
    creating build/lib.linux-i686-2.7/jyulb/fileio
    copying jyulb/fileio/__init__.py -> build/lib.linux-i686-2.7/jyulb/fileio
    creating build/lib.linux-i686-2.7/jyulb/internal/isothermal
    copying jyulb/internal/isothermal/__init__.py -> build/lib.linux-i686-2.7/jyulb/internal/isothermal
    copying jyulb/internal/isothermal/jyu_engine.py -> build/lib.linux-i686-2.7/jyulb/internal/isothermal
    creating build/lib.linux-i686-2.7/jyulb/internal/common
    copying jyulb/internal/common/__init__.py -> build/lib.linux-i686-2.7/jyulb/internal/common
    copying jyulb/internal/common/proxy_lattice.py -> build/lib.linux-i686-2.7/jyulb/internal/common
    creating build/lib.linux-i686-2.7/jyulb/internal/isothermal/tests
    copying jyulb/internal/isothermal/tests/__init__.py -> build/lib.linux-i686-2.7/jyulb/internal/isothermal/tests
    copying jyulb/internal/isothermal/tests/test_plugin_integration.py -> build/lib.linux-i686-2.7/jyulb/internal/isothermal/tests
    copying jyulb/internal/isothermal/tests/test_jyu_engine.py -> build/lib.linux-i686-2.7/jyulb/internal/isothermal/tests
    creating build/lib.linux-i686-2.7/jyulb/internal/common/tests
    copying jyulb/internal/common/tests/__init__.py -> build/lib.linux-i686-2.7/jyulb/internal/common/tests
    copying jyulb/internal/common/tests/test_proxy_lattice.py -> build/lib.linux-i686-2.7/jyulb/internal/common/tests
    creating build/lib.linux-i686-2.7/jyulb/fileio/isothermal
    copying jyulb/fileio/isothermal/__init__.py -> build/lib.linux-i686-2.7/jyulb/fileio/isothermal
    copying jyulb/fileio/isothermal/jyu_engine.py -> build/lib.linux-i686-2.7/jyulb/fileio/isothermal
    creating build/lib.linux-i686-2.7/jyulb/fileio/common
    copying jyulb/fileio/common/__init__.py -> build/lib.linux-i686-2.7/jyulb/fileio/common
    copying jyulb/fileio/common/jyu_lattice_proxy.py -> build/lib.linux-i686-2.7/jyulb/fileio/common
    creating build/lib.linux-i686-2.7/jyulb/fileio/isothermal/tests
    copying jyulb/fileio/isothermal/tests/__init__.py -> build/lib.linux-i686-2.7/jyulb/fileio/isothermal/tests
    copying jyulb/fileio/isothermal/tests/test_plugin_integration.py -> build/lib.linux-i686-2.7/jyulb/fileio/isothermal/tests
    copying jyulb/fileio/isothermal/tests/test_jyu_engine.py -> build/lib.linux-i686-2.7/jyulb/fileio/isothermal/tests
    creating build/lib.linux-i686-2.7/jyulb/fileio/common/tests
    copying jyulb/fileio/common/tests/__init__.py -> build/lib.linux-i686-2.7/jyulb/fileio/common/tests
    copying jyulb/fileio/common/tests/test_jyu_lattice_proxy.py -> build/lib.linux-i686-2.7/jyulb/fileio/common/tests
    running build_ext
    building 'jyulb.internal.isothermal.solver' extension
    creating build/temp.linux-i686-2.7
    creating build/temp.linux-i686-2.7/jyulb
    creating build/temp.linux-i686-2.7/jyulb/internal
    creating build/temp.linux-i686-2.7/jyulb/internal/isothermal
    creating build/temp.linux-i686-2.7/JYU-LB
    creating build/temp.linux-i686-2.7/JYU-LB/include
    creating build/temp.linux-i686-2.7/JYU-LB/include/common
    creating build/temp.linux-i686-2.7/JYU-LB/include/collision
    creating build/temp.linux-i686-2.7/JYU-LB/include/kernel
    creating build/temp.linux-i686-2.7/JYU-LB/include/solver
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c jyulb/internal/isothermal/solver.cpp -o build/temp.linux-i686-2.7/jyulb/internal/isothermal/solver.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    In file included from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                     from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                     from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from jyulb/internal/isothermal/solver.cpp:281:
    /home/franklin/simphony/local/lib/python2.7/site-packages/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]
    In file included from JYU-LB/include/common/node.h:10:0,
                     from jyulb/internal/isothermal/solver.cpp:284:
    /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
    /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘int _import_umath()’ defined but not used [-Wunused-function]
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c JYU-LB/include/common/node.cpp -o build/temp.linux-i686-2.7/JYU-LB/include/common/node.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c JYU-LB/include/common/filter.cpp -o build/temp.linux-i686-2.7/JYU-LB/include/common/filter.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c JYU-LB/include/collision/collision.cpp -o build/temp.linux-i686-2.7/JYU-LB/include/collision/collision.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c JYU-LB/include/kernel/kernel.cpp -o build/temp.linux-i686-2.7/JYU-LB/include/kernel/kernel.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    JYU-LB/include/kernel/kernel.cpp:48:1: warning: this decimal constant is unsigned only in ISO C90 [enabled by default]
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -IJYU-LB/include/dvs/ -IJYU-LB/include/collision/ -IJYU-LB/include/kernel/ -IJYU-LB/include/solver/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c JYU-LB/include/solver/solver.cpp -o build/temp.linux-i686-2.7/JYU-LB/include/solver/solver.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/jyulb/internal/isothermal/solver.o build/temp.linux-i686-2.7/JYU-LB/include/common/node.o build/temp.linux-i686-2.7/JYU-LB/include/common/filter.o build/temp.linux-i686-2.7/JYU-LB/include/collision/collision.o build/temp.linux-i686-2.7/JYU-LB/include/kernel/kernel.o build/temp.linux-i686-2.7/JYU-LB/include/solver/solver.o -o build/lib.linux-i686-2.7/jyulb/internal/isothermal/solver.so -fopenmp -O3
    building 'jyulb.internal.common.domain' extension
    creating build/temp.linux-i686-2.7/jyulb/internal/common
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -IJYU-LB/include/common/ -I/home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c jyulb/internal/common/domain.cpp -o build/temp.linux-i686-2.7/jyulb/internal/common/domain.o -fopenmp -O3
    cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for Ada/C/ObjC but not for C++ [enabled by default]
    In file included from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                     from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                     from /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from jyulb/internal/common/domain.cpp:275:
    /home/franklin/simphony/local/lib/python2.7/site-packages/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]
    jyulb/internal/common/domain.cpp: In function ‘PyObject* __pyx_pf_5jyulb_8internal_6common_6domain_9PyNodeSet_get_n(__pyx_obj_5jyulb_8internal_6common_6domain_PyNodeSet*, PyArrayObject*)’:
    jyulb/internal/common/domain.cpp:1588:197: error: invalid conversion from ‘__pyx_t_5numpy_uint32_t* {aka long unsigned int*}’ to ‘const UINT* {aka const unsigned int*}’ [-fpermissive]
    JYU-LB/include/common/node.h:20:18: error:   initializing argument 1 of ‘virtual UINT NodeSet::get_n(const UINT*) const’ [-fpermissive]
    jyulb/internal/common/domain.cpp: In function ‘PyObject* __pyx_pf_5jyulb_8internal_6common_6domain_9PyNodeSet_2get_ijk(__pyx_obj_5jyulb_8internal_6common_6domain_PyNodeSet*, unsigned int, PyArrayObject*)’:
    jyulb/internal/common/domain.cpp:1826:198: error: invalid conversion from ‘__pyx_t_5numpy_uint32_t* {aka long unsigned int*}’ to ‘UINT* {aka unsigned int*}’ [-fpermissive]
    JYU-LB/include/common/node.h:21:18: error:   initializing argument 2 of ‘virtual void NodeSet::get_ijk(UINT, UINT*) const’ [-fpermissive]
    jyulb/internal/common/domain.cpp: In function ‘int __pyx_pf_5jyulb_8internal_6common_6domain_9PyLattice___cinit__(__pyx_obj_5jyulb_8internal_6common_6domain_PyLattice*, PyArrayObject*, PyArrayObject*)’:
    jyulb/internal/common/domain.cpp:2184:325: error: invalid conversion from ‘__pyx_t_5numpy_uint32_t* {aka long unsigned int*}’ to ‘const UINT* {aka const unsigned int*}’ [-fpermissive]
    JYU-LB/include/common/node.h:36:14: error:   initializing argument 1 of ‘Lattice::Lattice(const UINT*, const double*)’ [-fpermissive]
    jyulb/internal/common/domain.cpp: In function ‘PyObject* __pyx_pf_5jyulb_8internal_6common_6domain_24PyAbstractIsothermalData_24get_n(__pyx_obj_5jyulb_8internal_6common_6domain_PyAbstractIsothermalData*, PyArrayObject*)’:
    jyulb/internal/common/domain.cpp:5741:212: error: invalid conversion from ‘__pyx_t_5numpy_uint32_t* {aka long unsigned int*}’ to ‘const UINT* {aka const unsigned int*}’ [-fpermissive]
    JYU-LB/include/common/node.h:20:18: error:   initializing argument 1 of ‘virtual UINT NodeSet::get_n(const UINT*) const’ [-fpermissive]
    jyulb/internal/common/domain.cpp: In function ‘PyObject* __pyx_pf_5jyulb_8internal_6common_6domain_24PyAbstractIsothermalData_26get_ijk(__pyx_obj_5jyulb_8internal_6common_6domain_PyAbstractIsothermalData*, unsigned int, PyArrayObject*)’:
    jyulb/internal/common/domain.cpp:5891:213: error: invalid conversion from ‘__pyx_t_5numpy_uint32_t* {aka long unsigned int*}’ to ‘UINT* {aka unsigned int*}’ [-fpermissive]
    JYU-LB/include/common/node.h:21:18: error:   initializing argument 2 of ‘virtual void NodeSet::get_ijk(UINT, UINT*) const’ [-fpermissive]
    In file included from JYU-LB/include/common/node.h:10:0,
                     from jyulb/internal/common/domain.cpp:278:
    /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
    /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
    /home/franklin/simphony/local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘int _import_umath()’ defined but not used [-Wunused-function]
    error: command 'gcc' failed with exit status 1

    ----------------------------------------
Command "/home/franklin/simphony/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-_VTrNG-build/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-5dn3qX-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/franklin/simphony/include/site/python2.7/jyu-engine" failed with error code 1 in /tmp/pip-_VTrNG-build
make: *** [simphony-jyu-lb] Error 1
tuopuu commented 8 years ago

Just an update that JyuLB 0.2.0 has been tested and found working in the following systems: Ubuntu 14.04 LTS 64-bit Cygwin 2.2.1 on Windows 8.1 Pro 64-bit

I don't know right away why compiling fails on Ubuntu 12.02 32bit.