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jochym / qe-util

Set of utilities for using Quantum-Espresso with ASE and ipython notebooks.
GNU General Public License v3.0
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Installation of ipython #3

Closed lim520 closed 10 years ago

lim520 commented 10 years ago

Dear Dr. Jochym

We recently got a new computer and was trying to install nipy and we were following the instruction from your website. We are encountering the following problem in installing Scipy.

pip install scipy Downloading/unpacking scipy Downloading scipy-0.14.0.tar.gz (10.2MB): 10.2MB downloaded Running setup.py (path:/home/lim520/nipy/build/scipy/setup.py) egg_info for package scipy

warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src'
no previously-included directories found matching 'scipy/special/tests/data/boost'
no previously-included directories found matching 'scipy/special/tests/data/gsl'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
no previously-included directories found matching '*/__pycache__'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.bak' found anywhere in distribution
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution

Installing collected packages: scipy Running setup.py install for scipy blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

openblas_info:
  libraries  not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
  libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

atlas_blas_info:
  libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  warnings.warn(AtlasNotFoundError.__doc__)
blas_info:
  libraries blas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
  NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
  warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
  NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:
    Blas (http://www.netlib.org/blas/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [blas_src]) or by setting
    the BLAS_SRC environment variable.
  warnings.warn(BlasSrcNotFoundError.__doc__)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/lim520/nipy/build/scipy/setup.py", line 237, in <module>
    setup_package()
  File "/home/lim520/nipy/build/scipy/setup.py", line 234, in setup_package
    setup(**metadata)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
    config = configuration()
  File "/home/lim520/nipy/build/scipy/setup.py", line 173, in configuration
    config.add_subpackage('scipy')
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
    caller_level = 2)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
    caller_level = caller_level + 1)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "scipy/setup.py", line 12, in configuration
    config.add_subpackage('integrate')
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
    caller_level = 2)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
    caller_level = caller_level + 1)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "scipy/integrate/setup.py", line 12, in configuration
    blas_opt = get_info('blas_opt',notfound_action=2)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info
    return cl().get_info(notfound_action)
  File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info
    raise self.notfounderror(self.notfounderror.__doc__)
numpy.distutils.system_info.BlasNotFoundError:
    Blas (http://www.netlib.org/blas/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [blas]) or by setting
    the BLAS environment variable.
Complete output from command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;__file__='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-j0R65A-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7:
blas_opt_info:

blas_mkl_info:

libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

openblas_info:

libraries not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_info:

libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

blas_info:

libraries blas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

warnings.warn(BlasNotFoundError.doc)

blas_src_info:

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:

Blas (http://www.netlib.org/blas/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [blas_src]) or by setting

the BLAS_SRC environment variable.

warnings.warn(BlasSrcNotFoundError.doc)

Traceback (most recent call last):

File "", line 1, in

File "/home/lim520/nipy/build/scipy/setup.py", line 237, in 

setup_package()

File "/home/lim520/nipy/build/scipy/setup.py", line 234, in setup_package

setup(**metadata)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup

config = configuration()

File "/home/lim520/nipy/build/scipy/setup.py", line 173, in configuration

config.add_subpackage('scipy')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/setup.py", line 12, in configuration

config.add_subpackage('integrate')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/integrate/setup.py", line 12, in configuration

blas_opt = get_info('blas_opt',notfound_action=2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info

return cl().get_info(notfound_action)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info

raise self.notfounderror(self.notfounderror.__doc__)

numpy.distutils.system_info.BlasNotFoundError:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

Cleaning up... Command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;file='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-j0R65A-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7 failed with error code 1 in /home/lim520/nipy/build/scipy Storing debug log for failure in /home/lim520/.pip/pip.log

We have installed all the prerequisite you have mentioned in your website.

Kindly please help in this regards

Linu

jochym commented 10 years ago

W dniu 16.05.2014 01:35, lim520 pisze:

Dear Dr. Jochym

We recently got a new computer and was trying to install nipy and we were following the instruction from your website. We are encountering the following problem in installing Scipy.

Command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;file='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-6HHpcX-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7 failed with error code 1 in /home/lim520/nipy/build/scipy Storing debug log for failure in /home/lim520/.pip/pip.log.

We have installed all the prerequisite you have mentioned in your website.

I will be happy to help you but this message contains to little information. I will need the /home/lim520/.pip/pip.log file as well as the information on the version of the operating system and installed components (the os for starters, I will ask more detailed questions later based on this info).

Regards, P. Jochym

Paweł T. Jochym, PhD, Prof. Institute of Nuclear Physics, PAN Cracow, Poland

lim520 commented 10 years ago

pip install scipy Downloading/unpacking scipy Downloading scipy-0.14.0.tar.gz (10.2MB): 10.2MB downloaded Running setup.py (path:/home/lim520/nipy/build/scipy/setup.py) egg_info for package scipy

warning: no previously-included files matching 'subr.f' found under directory 'scipy/linalg/src/iddist/src' no previously-included directories found matching 'scipy/special/tests/data/boost' no previously-included directories found matching 'scipy/special/tests/data/gsl' no previously-included directories found matching 'doc/build' no previously-included directories found matching 'doc/source/generated' no previously-included directories found matching '/pycache' warning: no previously-included files matching '~' found anywhere in distribution warning: no previously-included files matching '.bak' found anywhere in distribution warning: no previously-included files matching '_.swp' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution

Installing collected packages: scipy Running setup.py install for scipy blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

openblas_info: libraries not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.doc) blas_info: libraries blas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.doc) blas_src_info: NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.doc) Traceback (most recent call last): File "", line 1, in File "/home/lim520/nipy/build/scipy/setup.py", line 237, in setup_package() File "/home/lim520/nipy/build/scipy/setup.py", line 234, in setup_package setup(_metadata) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/home/lim520/nipy/build/scipy/setup.py", line 173, in configuration config.add_subpackage('scipy') File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(_args) File "scipy/setup.py", line 12, in configuration config.add_subpackage('integrate') File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(args) File "scipy/integrate/setup.py", line 12, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info return cl().get_info(notfound_action) File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info raise self.notfounderror(self.notfounderror.doc) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. Complete output from command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;file='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-j0R65A-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7: blas_opt_info:

blas_mkl_info:

libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

openblas_info:

libraries not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_info:

libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

blas_info:

libraries blas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

warnings.warn(BlasNotFoundError.doc)

blas_src_info:

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:

Blas (http://www.netlib.org/blas/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [blas_src]) or by setting

the BLAS_SRC environment variable.

warnings.warn(BlasSrcNotFoundError.doc)

Traceback (most recent call last):

File "", line 1, in

File "/home/lim520/nipy/build/scipy/setup.py", line 237, in

setup_package()

File "/home/lim520/nipy/build/scipy/setup.py", line 234, in setup_package

setup(**metadata)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup

config = configuration()

File "/home/lim520/nipy/build/scipy/setup.py", line 173, in configuration

config.add_subpackage('scipy')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/setup.py", line 12, in configuration

config.add_subpackage('integrate')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/integrate/setup.py", line 12, in configuration

blas_opt = get_info('blas_opt',notfound_action=2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info

return cl().get_info(notfound_action)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info

raise self.notfounderror(self.notfounderror.doc)

numpy.distutils.system_info.BlasNotFoundError:

Blas (http://www.netlib.org/blas/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [blas]) or by setting

the BLAS environment variable.

Cleaning up... Command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;file='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-j0R65A-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7 failed with error code 1 in /home/lim520/nipy/build/scipy Storing debug log for failure in /home/lim520/.pip/pip.log

We have installed all the prerequisite you have mentioned in your website.

jochym commented 10 years ago

W dniu 17.05.2014 03:22, lim520 pisze:

pip install scipy Downloading/unpacking scipy Downloading scipy-0.14.0.tar.gz (10.2MB): 10.2MB downloaded Running setup.py (path:/home/lim520/nipy/build/scipy/setup.py) egg_info for package scipy

warning: no previously-included files matching '//subr//.f' found under directory 'scipy/linalg/src/id_dist/src' no previously-included directories found matching 'scipy/special/tests/data/boost' no previously-included directories found matching 'scipy/special/tests/data/gsl' no previously-included directories found matching 'doc/build' no previously-included directories found matching 'doc/source/generated' no previously-included directories found matching '//pycache' warning: no previously-included files matching '/~' found anywhere in distribution warning: no previously-included files matching '/.bak' found anywhere in distribution warning: no previously-included files matching '/.swp' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution

Installing collected packages: scipy Running setup.py install for scipy blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

openblas_info: libraries not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib'] NOT AVAILABLE

I looks like you do not have lapac and blas development libraries installed in your system. You need to install some version of these libraries to compile SciPy

P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland

lim520 commented 10 years ago

Dear Dr.Jochym,

We have the red hat linux version of 6.5. We have installed the blas and lapack development files. But we still get the same error. The error in pip.log is as follows

Downloading/unpacking scipy Getting page https://pypi.python.org/simple/scipy/ URLs to search for versions for scipy:

blas_mkl_info:

libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

openblas_info:

libraries not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

atlas_blas_info:

libraries f77blas,cblas,atlas not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/atlas', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

blas_info:

FOUND:

libraries = ['blas']

library_dirs = ['/usr/lib64']

language = f77

FOUND:

libraries = ['blas']

library_dirs = ['/usr/lib64']
language = f77

FOUND:

libraries = ['blas']

library_dirs = ['/usr/lib64']

define_macros = [('NO_ATLAS_INFO', 1)]

language = f77

lapack_opt_info:

lapack_mkl_info:

mkl_info:

libraries mkl,vml,guide not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info:

Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /home/lim520/nipy/lib

libraries lapack_atlas not found in /home/lim520/nipy/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64

libraries lapack_atlas not found in /usr/local/lib64

libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib

libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/atlas

libraries lapack_atlas not found in /usr/lib64/atlas

libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2

libraries lapack_atlas not found in /usr/lib64/sse2

libraries ptf77blas,ptcblas,atlas not found in /usr/lib64

libraries lapack_atlas not found in /usr/lib64

libraries ptf77blas,ptcblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_threads_info

NOT AVAILABLE

atlas_info:

libraries f77blas,cblas,atlas not found in /home/lim520/nipy/lib

libraries lapack_atlas not found in /home/lim520/nipy/lib

libraries f77blas,cblas,atlas not found in /usr/local/lib64

libraries lapack_atlas not found in /usr/local/lib64

libraries f77blas,cblas,atlas not found in /usr/local/lib

libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib64/atlas

libraries lapack_atlas not found in /usr/lib64/atlas

libraries f77blas,cblas,atlas not found in /usr/lib64/sse2

libraries lapack_atlas not found in /usr/lib64/sse2

libraries f77blas,cblas,atlas not found in /usr/lib64

libraries lapack_atlas not found in /usr/lib64

libraries f77blas,cblas,atlas not found in /usr/lib

libraries lapack_atlas not found in /usr/lib

numpy.distutils.system_info.atlas_info

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1427: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

lapack_info:

libraries lapack not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE /home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1427: UserWarning:

Atlas (http://math-atlas.sourceforge.net/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [atlas]) or by setting

the ATLAS environment variable.

warnings.warn(AtlasNotFoundError.doc)

lapack_info:

libraries lapack not found in ['/home/lim520/nipy/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1438: UserWarning:

Lapack (http://www.netlib.org/lapack/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [lapack]) or by setting

the LAPACK environment variable.

warnings.warn(LapackNotFoundError.doc)

lapack_src_info:

NOT AVAILABLE

/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py:1441: UserWarning:

Lapack (http://www.netlib.org/lapack/) sources not found.

Directories to search for the sources can be specified in the

numpy/distutils/site.cfg file (section [lapack_src]) or by setting

the LAPACK_SRC environment variable.

warnings.warn(LapackSrcNotFoundError.doc)

Traceback (most recent call last): File "", line 1, in

File "/home/lim520/nipy/build/scipy/setup.py", line 237, in 

setup_package()

File "/home/lim520/nipy/build/scipy/setup.py", line 234, in setup_package

setup(**metadata)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup

config = configuration()

File "/home/lim520/nipy/build/scipy/setup.py", line 173, in configuration

config.add_subpackage('scipy')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/setup.py", line 13, in configuration

config.add_subpackage('interpolate')

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

caller_level = 2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

caller_level = caller_level + 1)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

config = setup_module.configuration(*args)

File "scipy/interpolate/setup.py", line 11, in configuration

lapack_opt = get_info('lapack_opt', notfound_action=2)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info

return cl().get_info(notfound_action)

File "/home/lim520/nipy/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info

raise self.notfounderror(self.notfounderror.__doc__)

numpy.distutils.system_info.LapackNotFoundError:

Lapack (http://www.netlib.org/lapack/) libraries not found.

Directories to search for the libraries can be specified in the

numpy/distutils/site.cfg file (section [lapack]) or by setting

the LAPACK environment variable.

Cleaning up... Removing temporary dir /home/lim520/nipy/build... Command /home/lim520/nipy/bin/python2.7 -c "import setuptools, tokenize;file='/home/lim520/nipy/build/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-H9c4ls-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/lim520/nipy/include/site/python2.7 failed with error code 1 in /home/lim520/nipy/build/scipy

jochym commented 10 years ago

W dniu 17.05.2014 22:28, lim520 pisze:

Dear Dr.Jochym,

We have the red hat linux version of 6.5. We have installed the blas and lapack development files. But we still get the same error.

I have no access to RHEL 6.5 so I cannot reproduce this but:

The blas library is found and used but not the lapack. Please check if you have all required parts. You need either ATLAS package (free, with devel parts) or standard lapack (free, not optimized) or mkl libraries (non-free but not expensive, actually recommended).

The messages are clear - the setup procedure could not find the lapack libraries. If you installed the libraries by non-standard means (eg. by hand compilation from source) or in non-standard place you need to point to them by the environment variable.

P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland

jochym commented 10 years ago

W dniu 17.05.2014 22:28, lim520 pisze:

Dear Dr.Jochym,

We have the red hat linux version of 6.5. We have installed the blas and lapack development files. But we still get the same error. The error in pip.log is as follows

I hope you succeed in installing. If not do not bother to fight. I have found an alternative and much better method of installing the environment and packages. I will update the docs soon (I hope today or tomorrow). I am currently testing the method on CetnOS 6.5 (practically identical to RHEL 6.5). Just wait for a new version of the install docs. You will be glad you did. Otherwise you will just waste few hours of your time.

P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland

jochym commented 10 years ago

W dniu 17.05.2014 22:28, lim520 pisze:

Dear Dr.Jochym,

We have the red hat linux version of 6.5. We have installed the blas and lapack development files. But we still get the same error. The error in pip.log is as follows

As I have promised ( ;) the new instructions are on line on my page. Check the installation document at:

http://nbviewer.ipython.org/github/jochym/qe-doc/blob/master/Installation.ipynb

I have verified the procedure on CentOS 6.5. It should work on RHEL 6.5 without any problems. Note a slight difference in activation/deactivation commands. The whole procedure is much cleaner, simpler and faster. Please let me know how it went!

Good luck!

P. Jochym

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland

lim520 commented 10 years ago

Dear Dr.Jochym,

Thank you. we are able to install and run ipython scripts. We are encountering a problem with 'Lattice Dynamics ' and QHA calculation. We are using plato to submit our scripts and it is giving us the following error. we have verified the calc directory and found that it has the following directories "tmp, matdyn.in ph.in phdos.in pw.in pw.out q2r.in run-pw.pbs SiC-QHA.exxx SiCQHA.exx SicQHA.oxx SicQHA.oxx. Please let me know if you need any other information?

Thanks

PDOS

figsize(9,6)

plot(qe.results['phdos'][0],qe.results['phdos'][1],label='SiC PDOS');

xlim(0,max(qe.results['phdos'][0])) # Limit the x-axis

xlabel('Frequency (cm$^{-1}$)'); # Put proper description on axis

ylabel('PDOS (a.u.)')

legend();

KeyError Traceback (most recent call last)

in () 1 # PDOS 2 figsize(9,6) ----> 3 plot(qe.results['phdos'][0],qe.results['phdos'][1],label='SiC PDOS'); 4 xlim(0,max(qe.results['phdos'][0])) # Limit the x-axis 5 xlabel('Frequency (cm$^{-1}$)'); # Put proper description on axis KeyError: 'phdos' c
jochym commented 10 years ago

W dniu 20.05.2014 23:39, lim520 pisze:

Dear Dr.Jochym,

Thank you. we are able to install and run ipython scripts.

Did you use the new procedure ? Any problems with it? I would really appreciate a short report about how it went.

We are encountering a problem with 'Lattice Dynamics ' and QHA calculation. We are using plato to submit our scripts and it is giving us the following error. we have verified the calc directory and found that it has the following directories "tmp, matdyn.in ph.in phdos.in pw.in pw.out q2r.in run-pw.pbs SiC-QHA.exxx SiCQHA.exx SicQHA.oxx SicQHA.oxx. Please let me know if you need any other information?

It looks like unfinished calculation on plato. Check all the output files and *.exx files for signs of errors.

P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland

lim520 commented 10 years ago

Dear Dr. Jochym We have used the new installation procedure. And it took us only around 10 minutes to complete the whole installation procedure.We didn't encounter any trouble while installing. It is really an easy procedure than the previous one.

Thanking you for making the installation process so easy.

With regards

Linu

jochym commented 10 years ago

W dniu 21.05.2014 19:15, lim520 pisze:

Dear Dr. Jochym We have used the new installation procedure. And it took us only around 10 minutes to complete the whole installation procedure.We didn't encounter any trouble while installing. It is really an easy procedure than the previous one.

Thanking you for making the installation process so easy.

Thanks for the report. I am glad it worked well. Furthermore the new procedure gives you an easy access to a huge repository of other data analysis python packages.

Regards, P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland