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AMont11
New Contributor I
2,447 Views

Upgrading spicy with anaconda

Hi all,

I am trying to update my spicy module in anaconda(for python2.7) that I installed on my edison but the following error occurs :

Downloading/unpacking scipy from https://pypi.python.org/packages/source/s/scipy/scipy-0.17.0.tar.gz# md5=5ff2971e1ce90e762c59d2cd84837224 https://pypi.python.org/packages/source/s/scipy/scipy-0.17.0.tar.gz# md5=5ff2971e1ce90e762c59d2cd84837224

Downloading scipy-0.17.0.tar.gz (12.4MB): 12.4MB downloaded

Running setup.py (path:/tmp/pip_build_root/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 'benchmarks/env'

no previously-included directories found matching 'benchmarks/results'

no previously-included directories found matching 'benchmarks/html'

no previously-included directories found matching 'benchmarks/scipy'

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

Found existing installation: scipy 0.14.0

Uninstalling scipy:

Successfully uninstalled scipy

Running setup.py install for scipy

lapack_opt_info:

openblas_lapack_info:

libraries openblas not found in ['/home/root/anaconda/lib']

NOT AVAILABLE

lapack_mkl_info:

mkl_info:

libraries mkl,vml,guide not found in ['/home/root/anaconda/lib']

NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info:

Setting PTATLAS=ATLAS

libraries ptf77blas,ptcblas,atlas not found in /home/root/anaconda/lib

libraries lapack_atlas not found in /home/root/anaconda/lib

numpy.distutils.system_info.atlas_threads_info

NOT AVAILABLE

atlas_info:

libraries f77blas,cblas,atlas not found in /home/root/anaconda/lib

libraries lapack_atlas not found in /home/root/anaconda/lib

numpy.distutils.system_info.atlas_info

NOT AVAILABLE

/home/root/anaconda/lib/python2.7/site-packages/numpy/distutils/system_info.py:1432: UserWarning:

Atlas (http://math-atlas.sourceforge.net/ 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/root/anaconda/lib']

NOT AVAILABLE

/home/root/anaconda/lib/python2.7/site-packages/numpy/distutils/system_info.py:1443: UserWarning:

Lapack (http://www.netlib.org/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/root/anaconda/lib/python2.7/site-packages/numpy/distutils/system_info.py:1446: UserWarning:

Lapack (http://www.netlib.org/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__)

NOT AVAILABLE

Running from scipy source directory.

Traceback (most recent call last):

File "", line 1, in

File "/tmp/pip_build_root/scipy/setup.py", line 265, in

setup_package()

File "/tmp/pip_build_root/scipy/setup.py", line 262, in setup_package

setup(**metadata)

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

config = configuration()

File "/tmp/pip_build_root/scipy/setup.py", line 182, in configuration

config.add_subpackage('scipy')

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

caller_level = 2)

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

caller_level = caller_level + 1)

File "/home/root/anaconda/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 15, in configuration

config.add_subpackage('linalg')

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

caller_level = 2)

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

caller_level = caller_level + 1)

File "/home/root/anaconda/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/linalg/setup.py", line 20, in configuration

raise NotFoundError('no lapack/blas resources found')

numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

Complete output from command /home/root/anaconda/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-qr1j6d-record/install-record.txt --single-version-externally-managed --compile:

lapack_opt_info:

openb...

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17 Replies
Carlos_M_Intel
Employee
146 Views

Hi a_Monteiro

Thanks for the logs, I would like to ask you some questions.

Did you install Anaconda before doing this? If you did, how did you do it?

I download the file you are using and check the INSTALL file, the correct command should be python setup.py install, did you try with this one too?

The error log mentions that it can't find resources for blas/lapack, have you tried to install these libraries?

http://netlib.org/blas/ BLAS (Basic Linear Algebra Subprograms)

http://netlib.org/lapack/ LAPACK — Linear Algebra PACKage

Did you check all the requirements for the package? http://www.scipy.org/stackspec.html# stackspec The SciPy Stack specification — SciPy.org

Regards,

Charlie

AMont11
New Contributor I
146 Views

no I tried to do this after installing anaconda which comes with scipy already. I was able to install anaconda from the website : https://www.continuum.io/downloads Download Anaconda now! | Continuum . and then scp the folder to the edison and run the shell script file they made. I have to tried to install BLAS and LAPACK however i don't know how to install them after I upload them to the edison since there are only but .f files in the folders. I also have all of the other components in the anaconda package folder.

Carlos_M_Intel
Employee
146 Views

Hi a_Monteiro

Let's try by installing https://github.com/xianyi/OpenBLAS OpenBlas, this should install BLAS and LAPACK, I also saw in your log the message:

openblas_lapack_info:

libraries openblas not found in ['/home/root/anaconda/lib']

NOT AVAILABLE

This could solve the dependencies for BLAS, LAPACK and OpenBlas.

For installing this you have to run the following commands:

If you have git:

git clone https://github.com/xianyi/OpenBLAS https://github.com/xianyi/OpenBLAS

cd OpenBLAS

Or you can download it with:

wget https://github.com/xianyi/OpenBLAS/archive/develop.zip https://github.com/xianyi/OpenBLAS/archive/develop.zip

unzip develop.zip

cd OpenBLAS-develop

Then, compile the library with: [https://github.com/xianyi/OpenBLAS/wiki/User-Manual User Manual · xianyi/OpenBLAS Wiki · GitHub]

make TARGET=ATOM

[Note: Targets List: https://github.com/xianyi/OpenBLAS/blob/develop/TargetList.txt OpenBLAS/TargetList.txt at develop · xianyi/OpenBLAS · GitHub]

Try this and let me know if it works for you, I'm currently compiling it too.

Regards,

Charlie

AMont11
New Contributor I
146 Views

hi,

have you finished compiling it? If so, what was your result?

AMont11
New Contributor I
146 Views

I have finished compiling and the results of the compile is this but in doing what the instructions says to do further is not working:

OpenBLAS build complete. (BLAS CBLAS)

OS ... Linux

Architecture ... x86

BINARY ... 32bit

C compiler ... GCC (command line : gcc)

Library Name ... libopenblas_atomp-r0.2.16.dev.a (Multi threaded; Max num-threads is 2)

To install the library, you can run "make PREFIX=/path/to/your/installation install".

I tried make PREFIX=/home/root/ .. this does not work. What must I do, I'm not sure .

Admir M.

Carlos_M_Intel
Employee
146 Views

Hi Admir M.

I got the same result as you, I ran make install and tried with a different PREFIX but I got some problems too.

I know you currently have scipy installed, which is the updates you want on your board? Do you want to change the version that you have? If this is the case, which version do you have?

Another thing you need to have in mind is the space available on the board. While trying to install scipy 0.17, Blas and Lapack in different ways I have had problems with this.

I found the way to install BLAS and LAPACK from source.

For BLAS: http://faculty.washington.edu/rjl/uwamath583s11/sphinx/notes/html/lapack_install.html Installing LAPACK and BLAS — AMath 483/583, Spring 2011 v1.0 documentation

wget http://www.netlib.org/blas/blas.tgz http://www.netlib.org/blas/blas.tgz

tar -zxf blas.tgz

cd BLAS

gfortran -O3 -c *.f

ar cr libblas.a *.o

For Lapack (I'm currently working on this): http://www.netlib.org/lapack/lawn41/node10.html Installing LAPACK on a Unix System & https://gcc.gnu.org/wiki/GfortranBuild GfortranBuild - GCC Wiki

wget http://www.netlib.org/lapack/lapack.tgz http://www.netlib.org/lapack/lapack.tgz

We need to change the make.inc and Makefile to make it work

Install Blas and start trying with Lapack, I will work on this too so we (probably) could use different approaches

Regards,

Charlie

AMont11
New Contributor I
146 Views

Hi,

I tried to install gfortran with opkg, it works but for some reason I cannot call it to install Blas.

thanks.

Carlos_M_Intel
Employee
146 Views

Hi Admir M.

What is the output you are getting after gfortran -O3 -c *.f ? If you are receiving an error message, please post it.

Regards,

Charlie

AMont11
New Contributor I
146 Views

hi,

I have fortran installed:

opkg install gfortran

Package gfortran (4.9.1-r0) installed in root is up to date.

but I try to run it ::

root@edison:~# gfortran -O3 -c *.f

-sh: gfortran: command not found

Carlos_M_Intel
Employee
146 Views

Hi,

Run the command opkg install gfortran-symlinks

Regards,

Charlie

AMont11
New Contributor I
146 Views

Hi,

When I run :gfortran -O3 -c *.f

Output :

gfortran: error: *.f: No such file or directory

gfortran: fatal error: no input files

compilation terminated.

Carlos_M_Intel
Employee
146 Views

Hi,

You need to run first the commands:

wget http://www.netlib.org/blas/blas.tgz http://www.netlib.org/blas/blas.tgz

tar -zxf blas.tgz

cd BLAS-3.5.0

Be sure that you are located in that folder to be able to run gfortran, you should be able to see the .f files in that location. If you still have problems, delete the folder and the .tgz file, then download and extract the file again.

Regards,

Charlie

AMont11
New Contributor I
146 Views

Hi,

I ran the gfortran -O3 -c *.f command inside the BLAS folder and nothing for an output came out(No errors messages.)

Admir M.

Carlos_M_Intel
Employee
146 Views

Hi Admir,

That is the expected behavior, after running the command you should be able to see the .o files in the folder.

I would like to know if you have been to update the scipy version you have. Could you tell us the version you have and the features you want to enable?

Regards,

Charlie

AMont11
New Contributor I
146 Views

Hey CMata_Intel,

I had the older version but what i am going to do is delete my current version of anaconda. I then install it again and now it has all of the new module for python. I have done this on my laptop. The same then must be for linux.

Thanks.

Carlos_M_Intel
Employee
146 Views

Hi Admir,

Did you try this? I would like to know if this worked for you

Regards,

Charlie

AMont11
New Contributor I
146 Views

yes I did get a newer version of anaconda and newer version of spicy is on it. thanks !

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