error of compilation under python for qutip (linux debian7)

[Stéphane Le Bec]

Hello,

I have a problem with compiling qutip in order to test it.
Here is the message.

Regards,

Stéphane

import qutip.testing as qt
QuTiP warning: old version of scipy detected (0.10.1), requiring 0.11.0.

Error compiling Cython file:
------------------------------------------------------------
...
                        np.ndarray[ITYPE_t, ndim=1, mode="c"] idx,
                        np.ndarray[ITYPE_t, ndim=1, mode="c"] ptr,
                        np.ndarray[CTYPE_t, ndim=1, mode="c"] state,
                        int isherm):

    cdef complex [:] y = spmv_csr(data,idx,ptr,state)
                 ^
------------------------------------------------------------

/usr/local/lib/python2.7/dist-packages/qutip/cy/spmatfuncs.pyx:263:18: Expected an identifier or literal

Traceback (most recent call last):
  File "<pyshell#0>", line 1, in <module>
    import qutip.testing as qt
  File "/usr/local/lib/python2.7/dist-packages/qutip/__init__.py", line 213, in <module>
    from qutip.qobj import *
  File "/usr/local/lib/python2.7/dist-packages/qutip/qobj.py", line 60, in <module>
    from qutip.ptrace import _ptrace
  File "/usr/local/lib/python2.7/dist-packages/qutip/ptrace.py", line 38, in <module>
    from qutip.sparse import sp_reshape
  File "/usr/local/lib/python2.7/dist-packages/qutip/sparse.py", line 49, in <module>
    from qutip.cy.sparse_utils import (_sparse_profile, _sparse_permute,
  File "/usr/local/lib/python2.7/dist-packages/qutip/cy/__init__.py", line 1, in <module>
    from qutip.cy.spmatfuncs import *
  File "/usr/lib/pymodules/python2.7/pyximport/pyximport.py", line 335, in load_module
    self.pyxbuild_dir)
  File "/usr/lib/pymodules/python2.7/pyximport/pyximport.py", line 183, in load_module
    so_path = build_module(name, pyxfilename, pyxbuild_dir)
  File "/usr/lib/pymodules/python2.7/pyximport/pyximport.py", line 167, in build_module
    reload_support=pyxargs.reload_support)
  File "/usr/lib/pymodules/python2.7/pyximport/pyxbuild.py", line 85, in pyx_to_dll
    dist.run_commands()
  File "/usr/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/lib/pymodules/python2.7/Cython/Distutils/build_ext.py", line 135, in run
    _build_ext.build_ext.run(self)
  File "/usr/lib/python2.7/distutils/command/build_ext.py", line 339, in run
    self.build_extensions()
  File "/usr/lib/pymodules/python2.7/Cython/Distutils/build_ext.py", line 143, in build_extensions
    self.build_extension(ext)
  File "/usr/lib/python2.7/distutils/command/build_ext.py", line 498, in build_extension
    depends=ext.depends)
  File "/usr/lib/python2.7/distutils/ccompiler.py", line 572, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/usr/lib/python2.7/distutils/unixccompiler.py", line 180, in _compile
    raise CompileError, msg
ImportError: Building module failed: ["CompileError: command 'gcc' failed with exit status 1\n"]
>>>

[Paul Nation]

It looks like the scipy version on your computer is quite old.  This is probably due to the fact that debian uses only stable packages.  The Cython package may be out of date as well.

Paul

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[jrjoh...@gmail.com]

Indeed, your scipy version is quite old. As Paul points out you will not get around this using Debian's native package manager, but you can easily update python packages using pip. Something along these lines should do it:

sudo apt-get install pip

sudo pip install --upgrade cython

sudo pip install --upgrade scipy

You might need to upgrade numpy and matplotlib too. Try

import qutip

qutip.about()

and see which versions of the packages you have, and compare them to the requirements on this page: http://qutip.org/docs/3.1.0/installation.html

Rob

[Stéphane Le Bec]

Thank you Rob and Paul. I will try and get a feedback. 

Regards,

Stéphane

[benjaminja...@gmail.com]

Hi. I get an identical error except not mention of scipy being an old version... Updating seems not to fix it.

[benjaminja...@gmail.com]

Did you ever get this to work? I'm having an identical issue.

On Sunday, 8 February 2015 15:20:58 UTC-5, Stéphane Le Bec wrote:

[Paul Nation]

It is likely that you have an older version of Cython or the GCC compiler that is causing issues.  Can you specify the versions for each of those items?

[hrmn.a...@gmail.com]

I am getting same error while importing qutip ,ImportError: Building module qutip.cy.spmatfuncs failed: ["CompileError: command 'gcc' failed with exit status 1\n"]
I have latest Cython version "Cython version 0.27.1" and latest gcc version "gcc (GCC) 4.8.5"


Below is copy paste from terminal
harman@harman-SVE15116ENB:~$ cd Desktop/qutip-4.2.0
harman@harman-SVE15116ENB:~/Desktop/qutip-3.0.1$ sudo python setup.py install
[sudo] password for harman:
Installing without the fortran mcsolver.
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 "qutip.cy.spmatfuncs" sources
building extension "qutip.cy.stochastic" sources
building extension "qutip.cy.sparse_utils" sources
building extension "qutip.cy.graph_utils" sources
building data_files sources
build_src: building npy-pkg config files
running build_py
copying qutip/version.py -> build/lib.linux-x86_64-2.7/qutip
copying build/src.linux-x86_64-2.7/qutip/__config__.py -> build/lib.linux-x86_64-2.7/qutip
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
running install_lib
copying build/lib.linux-x86_64-2.7/qutip/version.py -> /usr/local/lib/python2.7/dist-packages/qutip
copying build/lib.linux-x86_64-2.7/qutip/__config__.py -> /usr/local/lib/python2.7/dist-packages/qutip
byte-compiling /usr/local/lib/python2.7/dist-packages/qutip/version.py to version.pyc
byte-compiling /usr/local/lib/python2.7/dist-packages/qutip/__config__.py to __config__.pyc
running install_data
running install_egg_info
Removing /usr/local/lib/python2.7/dist-packages/qutip-3.0.1.egg-info
Writing /usr/local/lib/python2.7/dist-packages/qutip-3.0.1.egg-info
running install_clib
customize UnixCCompiler
harman@harman-SVE15116ENB:~/Desktop/qutip-3.0.1$ python
Python 2.7.13 | packaged by conda-forge | (default, May  2 2017, 12:48:11)
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
Type "help", "copyright", "credits" or "license" for more information.

>>> from qutip import*
/home/harman/.pyxbld/temp.linux-x86_64-2.7/pyrex/qutip/cy/spmatfuncs.c:520:25: fatal error: src/zspmv.hpp: No such file or directory
 #include "src/zspmv.hpp"
                         ^
compilation terminated.

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>
  File "qutip/__init__.py", line 193, in <module>
    from qutip.qobj import *
  File "qutip/qobj.py", line 56, in <module>
    from qutip.ptrace import _ptrace
  File "qutip/ptrace.py", line 37, in <module>
    from qutip.sparse import sp_reshape
  File "qutip/sparse.py", line 44, in <module>
    from qutip.cy.sparse_utils import (
  File "qutip/cy/__init__.py", line 1, in <module>
    from qutip.cy.spmatfuncs import *
  File "/home/harman/miniconda2/lib/python2.7/site-packages/pyximport/pyximport.py", line 458, in load_module
    language_level=self.language_level)
  File "/home/harman/miniconda2/lib/python2.7/site-packages/pyximport/pyximport.py", line 233, in load_module
    exec("raise exc, None, tb", {'exc': exc, 'tb': tb})
  File "/home/harman/miniconda2/lib/python2.7/site-packages/pyximport/pyximport.py", line 215, in load_module
    inplace=build_inplace, language_level=language_level)
  File "/home/harman/miniconda2/lib/python2.7/site-packages/pyximport/pyximport.py", line 191, in build_module
    reload_support=pyxargs.reload_support)
  File "/home/harman/miniconda2/lib/python2.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
    dist.run_commands()
  File "/home/harman/miniconda2/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/home/harman/miniconda2/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/home/harman/miniconda2/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
    _build_ext.build_ext.run(self)
  File "/home/harman/miniconda2/lib/python2.7/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/home/harman/miniconda2/lib/python2.7/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
    self.build_extension(ext)
  File "/home/harman/miniconda2/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension
    depends=ext.depends)
  File "/home/harman/miniconda2/lib/python2.7/distutils/ccompiler.py", line 574, in compile

    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)

  File "/home/harman/miniconda2/lib/python2.7/distutils/unixccompiler.py", line 124, in _compile
    raise CompileError, msg
ImportError: Building module qutip.cy.spmatfuncs failed: ["CompileError: command 'gcc' failed with exit status 1\n"]
>>>

Thanks
Harman

[Paul Nation]

You are running QuTiP from the installation directory.

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[harman singh]

Many Thanks ,Sir . ☺

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