[Numpy-tickets] [NumPy] #363: failure to install numpy

NumPy numpy-tickets at scipy.net
Thu Nov 16 20:17:47 CST 2006


#363: failure to install numpy
---------------------+------------------------------------------------------
 Reporter:  mbennun  |        Owner:  somebody
     Type:  defect   |       Status:  closed  
 Priority:  normal   |    Milestone:          
Component:  Other    |      Version:          
 Severity:  normal   |   Resolution:  invalid 
 Keywords:           |  
---------------------+------------------------------------------------------
Changes (by rkern):

  * status:  new => closed
  * resolution:  => invalid

Old description:

> Hello:
>
> We have tried to install numpy and failed.
> We have python2.4 and were able to successfully install f2py and
> scipy_distutils.
> The output of the 'python setup.py install' command is attached below.
>
> Thank you for your help.
> -Michal Ben-Nun
>
> Running from numpy source directory.
> F2PY Version 2_3364
> blas_opt_info:
> blas_mkl_info:
>   libraries mkl,vml,guide not found in
> /usr1/mbennun/work/NSFCyber/python_intel/lib
>   libraries mkl,vml,guide not found in /usr/local/lib
>   libraries mkl,vml,guide not found in /usr/lib
>   NOT AVAILABLE
>
> atlas_blas_threads_info:
> Setting PTATLAS=ATLAS
>   libraries lapack,blas not found in
> /usr1/mbennun/work/NSFCyber/python_intel/lib
> Setting PTATLAS=ATLAS
> Setting PTATLAS=ATLAS
>   FOUND:
>     libraries = ['lapack', 'blas']
>     library_dirs = ['/usr/local/lib']
>     language = c
>     include_dirs = ['/usr/local/include/atlas']
>
> Could not locate executable f95
> customize GnuFCompiler
> customize GnuFCompiler
> customize GnuFCompiler using config
> compiling '_configtest.c':
>
> /* This file is generated from numpy_distutils/system_info.py */
> void ATL_buildinfo(void);
> int main(void) {
>   ATL_buildinfo();
>   return 0;
> }
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
> -Wstrict-prototypes -fPIC
>
> compile options: '-c'
> gcc: _configtest.c
> /tmp/ccSQrFKJ.s: Assembler messages:
> /tmp/ccSQrFKJ.s:20: Error: suffix or operands invalid for `push'
> /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
> /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
> /tmp/ccSQrFKJ.s:31: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> /tmp/ccSQrFKJ.s: Assembler messages:
> /tmp/ccSQrFKJ.s:20: Error: suffix or operands invalid for `push'
> /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
> /tmp/ccSQrFKJ.s:31: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> failure.
> removing: _configtest.c _configtest.o
> Status: 255
> Output:
>   FOUND:
>     libraries = ['lapack', 'blas']
>     library_dirs = ['/usr/local/lib']
>     language = c
>     define_macros = [('NO_ATLAS_INFO', 2)]
>     include_dirs = ['/usr/local/include/atlas']
>
> lapack_opt_info:
> lapack_mkl_info:
> mkl_info:
>   libraries mkl,vml,guide not found in
> /usr1/mbennun/work/NSFCyber/python_intel/lib
>   libraries mkl,vml,guide not found in /usr/local/lib
>   libraries mkl,vml,guide not found in /usr/lib
>   NOT AVAILABLE
>
>   NOT AVAILABLE
>
> atlas_threads_info:
> Setting PTATLAS=ATLAS
>   libraries lapack,blas not found in
> /usr1/mbennun/work/NSFCyber/python_intel/lib
>   libraries lapack_atlas not found in
> /usr1/mbennun/work/NSFCyber/python_intel/lib
>   libraries lapack_atlas not found in /usr/local/lib
> numpy.distutils.system_info.atlas_threads_info
> Setting PTATLAS=ATLAS
> /usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/system_info.py:934:
> UserWarning:
> *********************************************************************
>     Lapack library (from ATLAS) is probably incomplete:
>       size of /usr/local/lib/liblapack.a is 3887k (expected >4000k)
>
>     Follow the instructions in the KNOWN PROBLEMS section of the file
>     numpy/INSTALL.txt.
> *********************************************************************
>
>   warnings.warn(message)
> Setting PTATLAS=ATLAS
>   FOUND:
>     libraries = ['lapack', 'lapack', 'blas']
>     library_dirs = ['/usr/local/lib']
>     language = c
>     include_dirs = ['/usr/local/include/atlas']
>
> customize GnuFCompiler
> customize GnuFCompiler
> customize GnuFCompiler using config
> compiling '_configtest.c':
>
> /* This file is generated from numpy_distutils/system_info.py */
> void ATL_buildinfo(void);
> int main(void) {
>   ATL_buildinfo();
>   return 0;
> }
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
> -Wstrict-prototypes -fPIC
>
> compile options: '-c'
> gcc: _configtest.c
> /tmp/ccYe889d.s: Assembler messages:
> /tmp/ccYe889d.s:20: Error: suffix or operands invalid for `push'
> /tmp/ccYe889d.s:22: Error: suffix or operands invalid for `push'
> /tmp/ccYe889d.s:31: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> /tmp/ccYe889d.s: Assembler messages:
> /tmp/ccYe889d.s:20: Error: suffix or operands invalid for `push'
> /tmp/ccYe889d.s:22: Error: suffix or operands invalid for `push'
> /tmp/ccYe889d.s:31: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> failure.
> removing: _configtest.c _configtest.o
> Status: 255
> Output:
>   FOUND:
>     libraries = ['lapack', 'lapack', 'blas']
>     library_dirs = ['/usr/local/lib']
>     language = c
>     define_macros = [('NO_ATLAS_INFO', 2)]
>     include_dirs = ['/usr/local/include/atlas']
>
> running install
> running build
> running config_fc
> running build_src
> building py_modules sources
> building extension "numpy.core.multiarray" sources
> Generating build/src.linux-x86_64-2.4/numpy/core/config.h
> customize GnuFCompiler
> customize GnuFCompiler
> customize GnuFCompiler using config
> C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
> -Wstrict-prototypes -fPIC
>
> compile options:
> '-I/usr1/mbennun/work/NSFCyber/python_intel/include/python2.4
> -Inumpy/core/src -Inum
> py/core/include
> -I/usr1/mbennun/work/NSFCyber/python_intel/include/python2.4 -c'
> gcc: _configtest.c
> /tmp/ccaSumWn.s: Assembler messages:
> /tmp/ccaSumWn.s:59: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:61: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:65: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:67: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:70: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> /tmp/ccaSumWn.s: Assembler messages:
> /tmp/ccaSumWn.s:59: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:61: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:65: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:67: Error: suffix or operands invalid for `push'
> /tmp/ccaSumWn.s:70: Internal error, aborting at
> ../../gas/config/tc-i386.c line 3501 in output_imm
> Please report this bug.
> failure.
> removing: _configtest.c _configtest.o
> Traceback (most recent call last):
>   File "setup.py", line 89, in ?
>     setup_package()
>   File "setup.py", line 82, in setup_package
>     configuration=configuration )
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/core.py", line
> 174, in setup
>     return old_setup(**new_attr)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/core.py",
> line 149, in setup
>     dist.run_commands()
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
> line 946, in run_c
> ommands
>     self.run_command(cmd)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
> line 966, in run_c
> ommand
>     cmd_obj.run()
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/install.py",
> line 16, in run
>     r = old_install.run(self)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/command/install.py",
> line 50
> 6, in run
>     self.run_command('build')
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/cmd.py",
> line 333, in run_co
> mmand
>     self.distribution.run_command(command)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
> line 966, in run_c
> ommand
>     cmd_obj.run()
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/command/build.py",
> line 112,
>  in run
>     self.run_command(cmd_name)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/cmd.py",
> line 333, in run_co
> mmand
>     self.distribution.run_command(command)
>   File
> "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
> line 966, in run_c
> ommand
>     cmd_obj.run()
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
> line 87, in r
> un
>     self.build_sources()
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
> line 106, in
> build_sources
>     self.build_extension_sources(ext)
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
> line 212, in
> build_extension_sources
>     sources = self.generate_sources(sources, ext)
>   File
> "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
> line 270, in
> generate_sources
>     source = func(extension, build_dir)
>   File "numpy/core/setup.py", line 50, in generate_config_h
>     raise "ERROR: Failed to test configuration"
> ERROR: Failed to test configuration

New description:

 Hello:

 We have tried to install numpy and failed.
 We have python2.4 and were able to successfully install f2py and
 scipy_distutils.
 The output of the 'python setup.py install' command is attached below.

 Thank you for your help.
 -Michal Ben-Nun

 {{{

 Running from numpy source directory.
 F2PY Version 2_3364
 blas_opt_info:
 blas_mkl_info:
   libraries mkl,vml,guide not found in
 /usr1/mbennun/work/NSFCyber/python_intel/lib
   libraries mkl,vml,guide not found in /usr/local/lib
   libraries mkl,vml,guide not found in /usr/lib
   NOT AVAILABLE

 atlas_blas_threads_info:
 Setting PTATLAS=ATLAS
   libraries lapack,blas not found in
 /usr1/mbennun/work/NSFCyber/python_intel/lib
 Setting PTATLAS=ATLAS
 Setting PTATLAS=ATLAS
   FOUND:
     libraries = ['lapack', 'blas']
     library_dirs = ['/usr/local/lib']
     language = c
     include_dirs = ['/usr/local/include/atlas']

 Could not locate executable f95
 customize GnuFCompiler
 customize GnuFCompiler
 customize GnuFCompiler using config
 compiling '_configtest.c':

 /* This file is generated from numpy_distutils/system_info.py */
 void ATL_buildinfo(void);
 int main(void) {
   ATL_buildinfo();
   return 0;
 }
 C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
 -Wstrict-prototypes -fPIC

 compile options: '-c'
 gcc: _configtest.c
 /tmp/ccSQrFKJ.s: Assembler messages:
 /tmp/ccSQrFKJ.s:20: Error: suffix or operands invalid for `push'
 /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
 /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
 /tmp/ccSQrFKJ.s:31: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 /tmp/ccSQrFKJ.s: Assembler messages:
 /tmp/ccSQrFKJ.s:20: Error: suffix or operands invalid for `push'
 /tmp/ccSQrFKJ.s:22: Error: suffix or operands invalid for `push'
 /tmp/ccSQrFKJ.s:31: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 failure.
 removing: _configtest.c _configtest.o
 Status: 255
 Output:
   FOUND:
     libraries = ['lapack', 'blas']
     library_dirs = ['/usr/local/lib']
     language = c
     define_macros = [('NO_ATLAS_INFO', 2)]
     include_dirs = ['/usr/local/include/atlas']

 lapack_opt_info:
 lapack_mkl_info:
 mkl_info:
   libraries mkl,vml,guide not found in
 /usr1/mbennun/work/NSFCyber/python_intel/lib
   libraries mkl,vml,guide not found in /usr/local/lib
   libraries mkl,vml,guide not found in /usr/lib
   NOT AVAILABLE

   NOT AVAILABLE

 atlas_threads_info:
 Setting PTATLAS=ATLAS
   libraries lapack,blas not found in
 /usr1/mbennun/work/NSFCyber/python_intel/lib
   libraries lapack_atlas not found in
 /usr1/mbennun/work/NSFCyber/python_intel/lib
   libraries lapack_atlas not found in /usr/local/lib
 numpy.distutils.system_info.atlas_threads_info
 Setting PTATLAS=ATLAS
 /usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/system_info.py:934:
 UserWarning:
 *********************************************************************
     Lapack library (from ATLAS) is probably incomplete:
       size of /usr/local/lib/liblapack.a is 3887k (expected >4000k)

     Follow the instructions in the KNOWN PROBLEMS section of the file
     numpy/INSTALL.txt.
 *********************************************************************

   warnings.warn(message)
 Setting PTATLAS=ATLAS
   FOUND:
     libraries = ['lapack', 'lapack', 'blas']
     library_dirs = ['/usr/local/lib']
     language = c
     include_dirs = ['/usr/local/include/atlas']

 customize GnuFCompiler
 customize GnuFCompiler
 customize GnuFCompiler using config
 compiling '_configtest.c':

 /* This file is generated from numpy_distutils/system_info.py */
 void ATL_buildinfo(void);
 int main(void) {
   ATL_buildinfo();
   return 0;
 }
 C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
 -Wstrict-prototypes -fPIC

 compile options: '-c'
 gcc: _configtest.c
 /tmp/ccYe889d.s: Assembler messages:
 /tmp/ccYe889d.s:20: Error: suffix or operands invalid for `push'
 /tmp/ccYe889d.s:22: Error: suffix or operands invalid for `push'
 /tmp/ccYe889d.s:31: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 /tmp/ccYe889d.s: Assembler messages:
 /tmp/ccYe889d.s:20: Error: suffix or operands invalid for `push'
 /tmp/ccYe889d.s:22: Error: suffix or operands invalid for `push'
 /tmp/ccYe889d.s:31: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 failure.
 removing: _configtest.c _configtest.o
 Status: 255
 Output:
   FOUND:
     libraries = ['lapack', 'lapack', 'blas']
     library_dirs = ['/usr/local/lib']
     language = c
     define_macros = [('NO_ATLAS_INFO', 2)]
     include_dirs = ['/usr/local/include/atlas']

 running install
 running build
 running config_fc
 running build_src
 building py_modules sources
 building extension "numpy.core.multiarray" sources
 Generating build/src.linux-x86_64-2.4/numpy/core/config.h
 customize GnuFCompiler
 customize GnuFCompiler
 customize GnuFCompiler using config
 C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3 -Wall
 -Wstrict-prototypes -fPIC

 compile options:
 '-I/usr1/mbennun/work/NSFCyber/python_intel/include/python2.4
 -Inumpy/core/src -Inum
 py/core/include
 -I/usr1/mbennun/work/NSFCyber/python_intel/include/python2.4 -c'
 gcc: _configtest.c
 /tmp/ccaSumWn.s: Assembler messages:
 /tmp/ccaSumWn.s:59: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:61: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:65: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:67: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:70: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 /tmp/ccaSumWn.s: Assembler messages:
 /tmp/ccaSumWn.s:59: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:61: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:65: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:67: Error: suffix or operands invalid for `push'
 /tmp/ccaSumWn.s:70: Internal error, aborting at ../../gas/config/tc-i386.c
 line 3501 in output_imm
 Please report this bug.
 failure.
 removing: _configtest.c _configtest.o
 Traceback (most recent call last):
   File "setup.py", line 89, in ?
     setup_package()
   File "setup.py", line 82, in setup_package
     configuration=configuration )
   File "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/core.py",
 line 174, in setup
     return old_setup(**new_attr)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/core.py",
 line 149, in setup
     dist.run_commands()
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
 line 946, in run_c
 ommands
     self.run_command(cmd)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
 line 966, in run_c
 ommand
     cmd_obj.run()
   File
 "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/install.py",
 line 16, in run
     r = old_install.run(self)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/command/install.py",
 line 50
 6, in run
     self.run_command('build')
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/cmd.py",
 line 333, in run_co
 mmand
     self.distribution.run_command(command)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
 line 966, in run_c
 ommand
     cmd_obj.run()
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/command/build.py",
 line 112,
  in run
     self.run_command(cmd_name)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/cmd.py",
 line 333, in run_co
 mmand
     self.distribution.run_command(command)
   File
 "/usr1/mbennun/work/NSFCyber/python_intel/lib/python2.4/distutils/dist.py",
 line 966, in run_c
 ommand
     cmd_obj.run()
   File
 "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
 line 87, in r
 un
     self.build_sources()
   File
 "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
 line 106, in
 build_sources
     self.build_extension_sources(ext)
   File
 "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
 line 212, in
 build_extension_sources
     sources = self.generate_sources(sources, ext)
   File
 "/usr1/mbennun/work/NSFCyber/numpy-1.0rc3/numpy/distutils/command/build_src.py",
 line 270, in
 generate_sources
     source = func(extension, build_dir)
   File "numpy/core/setup.py", line 50, in generate_config_h
     raise "ERROR: Failed to test configuration"
 ERROR: Failed to test configuration
 }}}

Comment:

 Note that the standalone version of f2py that you installed does not work
 with numpy; it works with Numeric ([http://www.scipy.org/History_of_SciPy
 see here for a history of the two packages]). It is also no longer
 developed. f2py has been moved into numpy, and all current development and
 support is happening in that version. Similarly, all of the capabilities
 of scipy_distutils have been folded into numpy.distutils.

 It does look like your gcc is misconfigured and is producing bad
 assembler. Can you compile other C programs with similar command line
 options? If it's not a misconfiguration on your part, then it is almost
 certainly a bug in the compiler and should be reported to its developers
 (at least, that's what the error message it generates suggests). The C
 code that we are trying to compile is so small that I can pretty much
 guarantee that it is not the problem.

 Consequently, I am going to close this ticket. If you find that numpy
 actually is causing the problem, go ahead and reopen it with more
 information.

-- 
Ticket URL: <http://projects.scipy.org/scipy/numpy/ticket/363#comment:4>
NumPy <http://projects.scipy.org/scipy/numpy>
The fundamental package needed for scientific computing with Python.


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