Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Daπid]

On 8 February 2016 at 20:25, Matthew Brett  wrote:

>
> I used the latest release, v0.2.15:
>
> https://github.com/matthew-brett/manylinux-builds/blob/master/build_openblas.sh#L5
>
> Is there a later version that we should try?
>
> Cheers,
>

That is the one in the Fedora repos that is working for me. How are you
compiling it?

Mine is compiled with GCC 5 with the options seen in the source rpm:
http://koji.fedoraproject.org/koji/packageinfo?packageID=15277
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nadav Horesh]

Do not know what happened --- all test passed, even when removed openblas 
(Nathaniel was right).

Manylinux config:

python -c 'import numpy; print(numpy.__config__.show())'
blas_opt_info:
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas']
language = c
library_dirs = ['/usr/local/lib']
lapack_opt_info:
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas']
language = c
library_dirs = ['/usr/local/lib']
blas_mkl_info:
  NOT AVAILABLE
openblas_lapack_info:
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas']
language = c
library_dirs = ['/usr/local/lib']
openblas_info:
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas']
language = c
library_dirs = ['/usr/local/lib']
None


Source installtion:

python -c 'import numpy; print(numpy.__config__.show())'
openblas_info:
library_dirs = ['/usr/local/lib']
libraries = ['openblas', 'openblas']
language = c
runtime_library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
openblas_lapack_info:
library_dirs = ['/usr/local/lib']
libraries = ['openblas', 'openblas']
language = c
runtime_library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
lapack_opt_info:
extra_compile_args = ['-g -ftree-vectorize -mtune=native -march=native -O3']
runtime_library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas', 'openblas', 'atlas', 'f77blas', 'cblas', 'blas']
language = c
library_dirs = ['/usr/local/lib', '/usr/lib']
blas_mkl_info:
  NOT AVAILABLE
blas_opt_info:
extra_compile_args = ['-g -ftree-vectorize -mtune=native -march=native -O3']
runtime_library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas', 'openblas', 'atlas', 'f77blas', 'cblas', 'blas']
language = c
library_dirs = ['/usr/local/lib', '/usr/lib']
None


From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of 
Matthew Brett <matthew.br...@gmail.com>
Sent: 08 February 2016 09:48
To: Discussion of Numerical Python
Subject: Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

Hi Nadav,

On Sun, Feb 7, 2016 at 11:13 PM, Nathaniel Smith <n...@pobox.com> wrote:
> (This is not relevant to the main topic of the thread, but FYI I think the
> recarray issues are fixed in 1.10.4.)
>
> On Feb 7, 2016 11:10 PM, "Nadav Horesh" <nad...@visionsense.com> wrote:
>>
>> I have atlas-lapack-base installed via pacman (required by sagemath).
>> Since the numpy installation insisted on openblas on /usr/local, I got the
>> openblas source-code and installed  it on /usr/local.
>> BTW, I use 1.11b rather then 1.10.x since the 1.10 is very slow in
>> handling recarrays. For the tests I am erasing the 1.11 installation, and
>> installing the 1.10.4 wheel. I do verify that I have the right version
>> before running the tests, but I am not sure if there no unnoticed side
>> effects.
>>
>> Would it help if I put a side the openblas installation and rerun the
>> test?

Would you mind doing something like this, and posting the output?:

virtualenv test-manylinux
source test-manylinux/bin/activate
pip install -f https://nipy.bic.berkeley.edu/manylinux numpy==1.10.4 nose
python -c 'import numpy; numpy.test()'
python -c 'import numpy; print(numpy.__config__.show())'
deactivate

virtualenv test-from-source
source test-from-source/bin/activate
pip install numpy==1.10.4 nose
python -c 'import numpy; numpy.test()'
python -c 'import numpy; print(numpy.__config__.show())'
deactivate

I'm puzzled that the wheel gives a test error when the source install
does not, and my best guess was an openblas problem, but this just to
make sure we have the output from the exact same numpy version, at
least.

Thanks again,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Julian Taylor]

On 02/08/2016 05:23 PM, Daπid wrote:
> 
> On 8 February 2016 at 16:19, Olivier Grisel  > wrote:
> 
> 
> 
> OPENBLAS_CORETYPE=Nehalem python3 -c "import numpy as np; from scipy
> import linalg; linalg.eigh(np.random.randn(200, 200))"
> 
> So this is an issue with the architecture detection of OpenBLAS.
> 
> 
> I am seeing the same problem on a native Linux box, with Ivy Bridge
> processor (i5-3317U). According to your script, both my native openblas
> and the one in the wheel recognises my CPU as Sandybridge, but the wheel
> produces a segmentation fault. Setting the architecture to Nehalem works.
> 

more likely that is a bug the kernel of openblas instead of its cpu
detection.
The cpuinfo of Oliver indicates its at least a sandy bridge, and ivy
bridge is be sandy bridge compatible.
Is an up to date version of openblas used?
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nathaniel Smith]

On Feb 7, 2016 11:49 PM, "Matthew Brett"  wrote:
>
> Hi Nadav,
>
> On Sun, Feb 7, 2016 at 11:13 PM, Nathaniel Smith  wrote:
> > (This is not relevant to the main topic of the thread, but FYI I think
the
> > recarray issues are fixed in 1.10.4.)
> >
> > On Feb 7, 2016 11:10 PM, "Nadav Horesh"  wrote:
> >>
> >> I have atlas-lapack-base installed via pacman (required by sagemath).
> >> Since the numpy installation insisted on openblas on /usr/local, I got
the
> >> openblas source-code and installed  it on /usr/local.
> >> BTW, I use 1.11b rather then 1.10.x since the 1.10 is very slow in
> >> handling recarrays. For the tests I am erasing the 1.11 installation,
and
> >> installing the 1.10.4 wheel. I do verify that I have the right version
> >> before running the tests, but I am not sure if there no unnoticed side
> >> effects.
> >>
> >> Would it help if I put a side the openblas installation and rerun the
> >> test?
>
> Would you mind doing something like this, and posting the output?:
>
> virtualenv test-manylinux
> source test-manylinux/bin/activate
> pip install -f https://nipy.bic.berkeley.edu/manylinux numpy==1.10.4 nose
> python -c 'import numpy; numpy.test()'
> python -c 'import numpy; print(numpy.__config__.show())'
> deactivate
>
> virtualenv test-from-source
> source test-from-source/bin/activate
> pip install numpy==1.10.4 nose
> python -c 'import numpy; numpy.test()'
> python -c 'import numpy; print(numpy.__config__.show())'
> deactivate
>
> I'm puzzled that the wheel gives a test error when the source install
> does not, and my best guess was an openblas problem, but this just to
> make sure we have the output from the exact same numpy version, at
> least.

It's hard to say without seeing the full output, but AFAICT the only
failures mentioned so far are in long double stuff, which shouldn't have
any connection to openblas at all?

-n
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Olivier Grisel]

I used docker to run the numpy tests on base/archlinux. I had to
pacman -Sy python-pip openssl and gcc (required by one of the numpy
tests):

```
Ran 5621 tests in 34.482s
OK (KNOWNFAIL=4, SKIP=9)
```

Everything looks fine.

-- 
Olivier
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Daπid]

On 6 February 2016 at 21:26, Matthew Brett  wrote:

>
> pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy
> python -c 'import numpy; numpy.test()'
> python -c 'import scipy; scipy.test()'
>


All the tests pass on my Fedora 23 with Python 2.7, but it seems to be
linking to the system openblas:

numpy.show_config()
lapack_opt_info:
libraries = ['openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
blas_opt_info:
libraries = ['openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
openblas_info:
libraries = ['openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
openblas_lapack_info:
libraries = ['openblas']
library_dirs = ['/usr/local/lib']
define_macros = [('HAVE_CBLAS', None)]
language = c
blas_mkl_info:
  NOT AVAILABLE

I can also reproduce Ogrisel's segfault.
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Olivier Grisel]

I found another problem by running the tests of scikit-learn:

python3 -c "import numpy as np; from scipy import linalg;
linalg.eigh(np.random.randn(200, 200))"
Segmentation fault

Note that the following works:

python3 -c "import numpy as np; np.linalg.eigh(np.random.randn(200, 200))"

Also note that all scipy tests pass:

Ran 20180 tests in 366.163s
OK (KNOWNFAIL=97, SKIP=1657)

-- 
Olivier Grisel
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Olivier Grisel]

Note that the above segfault was found in a VM (docker-machine
virtualbox guest VM launched on a OSX host). The DYNAMIC_ARCH feature
of OpenBLAS detects an Sandybridge core (using
https://gist.github.com/ogrisel/ad4e547a32d0eb18b4ff).

Here are the flags of the CPU visible from inside the docker container:

cat /proc/cpuinfo  | grep flags
flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx rdtscp lm
constant_tsc rep_good nopl xtopology nonstop_tsc pni pclmulqdq monitor
ssse3 cx16 sse4_1 sse4_2 popcnt aes xsave avx rdrand hypervisor
lahf_lm

If I fix the Nehalem kernel by setting the environment variable the
problem disappears:

OPENBLAS_CORETYPE=Nehalem python3 -c "import numpy as np; from scipy
import linalg; linalg.eigh(np.random.randn(200, 200))"

So this is an issue with the architecture detection of OpenBLAS.

-- 
Olivier
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

Hi Julian,

On Mon, Feb 8, 2016 at 8:40 AM, Julian Taylor
 wrote:
> On 02/08/2016 05:23 PM, Daπid wrote:
>>
>> On 8 February 2016 at 16:19, Olivier Grisel > > wrote:
>>
>>
>>
>> OPENBLAS_CORETYPE=Nehalem python3 -c "import numpy as np; from scipy
>> import linalg; linalg.eigh(np.random.randn(200, 200))"
>>
>> So this is an issue with the architecture detection of OpenBLAS.
>>
>>
>> I am seeing the same problem on a native Linux box, with Ivy Bridge
>> processor (i5-3317U). According to your script, both my native openblas
>> and the one in the wheel recognises my CPU as Sandybridge, but the wheel
>> produces a segmentation fault. Setting the architecture to Nehalem works.
>>
>
> more likely that is a bug the kernel of openblas instead of its cpu
> detection.
> The cpuinfo of Oliver indicates its at least a sandy bridge, and ivy
> bridge is be sandy bridge compatible.
> Is an up to date version of openblas used?

I used the latest release, v0.2.15:
https://github.com/matthew-brett/manylinux-builds/blob/master/build_openblas.sh#L5

Is there a later version that we should try?

Cheers,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

Hi Nadav,

On Sun, Feb 7, 2016 at 11:13 PM, Nathaniel Smith  wrote:
> (This is not relevant to the main topic of the thread, but FYI I think the
> recarray issues are fixed in 1.10.4.)
>
> On Feb 7, 2016 11:10 PM, "Nadav Horesh"  wrote:
>>
>> I have atlas-lapack-base installed via pacman (required by sagemath).
>> Since the numpy installation insisted on openblas on /usr/local, I got the
>> openblas source-code and installed  it on /usr/local.
>> BTW, I use 1.11b rather then 1.10.x since the 1.10 is very slow in
>> handling recarrays. For the tests I am erasing the 1.11 installation, and
>> installing the 1.10.4 wheel. I do verify that I have the right version
>> before running the tests, but I am not sure if there no unnoticed side
>> effects.
>>
>> Would it help if I put a side the openblas installation and rerun the
>> test?

Would you mind doing something like this, and posting the output?:

virtualenv test-manylinux
source test-manylinux/bin/activate
pip install -f https://nipy.bic.berkeley.edu/manylinux numpy==1.10.4 nose
python -c 'import numpy; numpy.test()'
python -c 'import numpy; print(numpy.__config__.show())'
deactivate

virtualenv test-from-source
source test-from-source/bin/activate
pip install numpy==1.10.4 nose
python -c 'import numpy; numpy.test()'
python -c 'import numpy; print(numpy.__config__.show())'
deactivate

I'm puzzled that the wheel gives a test error when the source install
does not, and my best guess was an openblas problem, but this just to
make sure we have the output from the exact same numpy version, at
least.

Thanks again,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nadav Horesh]

The reult tests of numpy 1.10.4 installed from source:

OK (KNOWNFAIL=4, SKIP=6)


I think I use openblas, as it is installed instead the normal blas/cblas.

  Nadav,

From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of Nadav 
Horesh <nad...@visionsense.com>
Sent: 07 February 2016 07:28
To: Discussion of Numerical Python; SciPy Developers List
Subject: Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

Test platform: python 3.4.1 on archlinux x86_64

scipy test: OK

OK (KNOWNFAIL=97, SKIP=1626)


numpy tests: Failed on long double and int128 tests, and got one error:

Traceback (most recent call last):
  File "/usr/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
  File "/usr/lib/python3.5/site-packages/numpy/core/tests/test_longdouble.py", 
line 108, in test_fromstring_missing
np.array([1]))
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 296, in 
assert_equal
return assert_array_equal(actual, desired, err_msg, verbose)
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 787, in 
assert_array_equal
verbose=verbose, header='Arrays are not equal')
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 668, in 
assert_array_compare
raise AssertionError(msg)
AssertionError:
Arrays are not equal

(shapes (6,), (1,) mismatch)
 x: array([ 1., -1.,  3.,  4.,  5.,  6.])
 y: array([1])

--
Ran 6019 tests in 28.029s

FAILED (KNOWNFAIL=13, SKIP=12, errors=1, failures=18




From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of 
Matthew Brett <matthew.br...@gmail.com>
Sent: 06 February 2016 22:26
To: Discussion of Numerical Python; SciPy Developers List
Subject: [Numpy-discussion] Multi-distribution Linux wheels - please test

Hi,

As some of you may have seen, Robert McGibbon and Nathaniel have just
guided a PEP for multi-distribution Linux wheels past the approval
process over on distutils-sig:

https://www.python.org/dev/peps/pep-0513/

The PEP includes a docker image on which y'all can build wheels which
match the PEP:

https://quay.io/repository/manylinux/manylinux

Now we're at the stage where we need stress-testing of the built
wheels to find any problems we hadn't thought of.

I've built numpy and scipy wheels here:

https://nipy.bic.berkeley.edu/manylinux/

So, if you have a Linux distribution handy, we would love to hear from
you about the results of testing these guys, maybe on the lines of:

pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy
python -c 'import numpy; numpy.test()'
python -c 'import scipy; scipy.test()'

These manylinux wheels should soon be available on pypi, and soon
after, installable with latest pip, so we would like to fix as many
problems as possible before going live.

Cheers,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nathaniel Smith]

On Feb 6, 2016 12:27 PM, "Matthew Brett"  wrote:
>
> Hi,
>
> As some of you may have seen, Robert McGibbon and Nathaniel have just
> guided a PEP for multi-distribution Linux wheels past the approval
> process over on distutils-sig:
>
> https://www.python.org/dev/peps/pep-0513/
>
> The PEP includes a docker image on which y'all can build wheels which
> match the PEP:
>
> https://quay.io/repository/manylinux/manylinux

This is the wrong repository :-) It moved, and there are two now:

quay.io/pypa/manylinux1_x86_64
quay.io/pypa/manylinux1_i686

-n
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

Hi,

On Sun, Feb 7, 2016 at 2:06 AM, Nadav Horesh  wrote:
> The reult tests of numpy 1.10.4 installed from source:
>
> OK (KNOWNFAIL=4, SKIP=6)
>
>
> I think I use openblas, as it is installed instead the normal blas/cblas.

Thanks again for the further tests.

What do you get for:

python -c 'import numpy; print(numpy.__config__.show())'

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

On Sun, Feb 7, 2016 at 10:09 PM, Nadav Horesh  wrote:
> Thank you fo reminding me, it is OK now:
> $ python -c 'import numpy; print(numpy.__config__.show())'
>
> lapack_opt_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> blas_mkl_info:
>   NOT AVAILABLE
> openblas_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> openblas_lapack_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> blas_opt_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> None
>
> I updated openblas to the latest version (0.2.15) and it pass the tests

Oh dear - now I'm confused.  So you installed the wheel, and tested
it, and it gave a test failure.  Then you updated openblas using
pacman, and then reran the tests against the wheel numpy, and they
passed?  That's a bit frightening - the wheel should only see its own
copy of openblas...

Thans for persisting,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nathaniel Smith]

On Sat, Feb 6, 2016 at 9:28 PM, Nadav Horesh  wrote:
> Test platform: python 3.4.1 on archlinux x86_64
>
> scipy test: OK
>
> OK (KNOWNFAIL=97, SKIP=1626)
>
>
> numpy tests: Failed on long double and int128 tests, and got one error:

Could you post the complete output from the test suite somewhere?
(Maybe gist.github.com)

-n

-- 
Nathaniel J. Smith -- https://vorpus.org
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nadav Horesh]

I have atlas-lapack-base installed via pacman (required by sagemath). Since the 
numpy installation insisted on openblas on /usr/local, I got the openblas 
source-code and installed  it on /usr/local.
BTW, I use 1.11b rather then 1.10.x since the 1.10 is very slow in handling 
recarrays. For the tests I am erasing the 1.11 installation, and installing the 
1.10.4 wheel. I do verify that I have the right version before running the 
tests, but I am not sure if there no unnoticed side effects.

Would it help if I put a side the openblas installation and rerun the test?

  Nadav

From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of 
Matthew Brett <matthew.br...@gmail.com>
Sent: 08 February 2016 08:13
To: Discussion of Numerical Python
Subject: Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

On Sun, Feb 7, 2016 at 10:09 PM, Nadav Horesh <nad...@visionsense.com> wrote:
> Thank you fo reminding me, it is OK now:
> $ python -c 'import numpy; print(numpy.__config__.show())'
>
> lapack_opt_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> blas_mkl_info:
>   NOT AVAILABLE
> openblas_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> openblas_lapack_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> blas_opt_info:
> library_dirs = ['/usr/local/lib']
> language = c
> libraries = ['openblas']
> define_macros = [('HAVE_CBLAS', None)]
> None
>
> I updated openblas to the latest version (0.2.15) and it pass the tests

Oh dear - now I'm confused.  So you installed the wheel, and tested
it, and it gave a test failure.  Then you updated openblas using
pacman, and then reran the tests against the wheel numpy, and they
passed?  That's a bit frightening - the wheel should only see its own
copy of openblas...

Thans for persisting,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nadav Horesh]

Thank you fo reminding me, it is OK now: 
$ python -c 'import numpy; print(numpy.__config__.show())'

lapack_opt_info:
library_dirs = ['/usr/local/lib']
language = c
libraries = ['openblas']
define_macros = [('HAVE_CBLAS', None)]
blas_mkl_info:
  NOT AVAILABLE
openblas_info:
library_dirs = ['/usr/local/lib']
language = c
libraries = ['openblas']
define_macros = [('HAVE_CBLAS', None)]
openblas_lapack_info:
library_dirs = ['/usr/local/lib']
language = c
libraries = ['openblas']
define_macros = [('HAVE_CBLAS', None)]
blas_opt_info:
library_dirs = ['/usr/local/lib']
language = c
libraries = ['openblas']
define_macros = [('HAVE_CBLAS', None)]
None

I updated openblas to the latest version (0.2.15) and it pass the tests

  Nadav.

From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of 
Matthew Brett <matthew.br...@gmail.com>
Sent: 08 February 2016 01:33
To: Discussion of Numerical Python
Subject: Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

Hi,

On Sun, Feb 7, 2016 at 2:06 AM, Nadav Horesh <nad...@visionsense.com> wrote:
> The reult tests of numpy 1.10.4 installed from source:
>
> OK (KNOWNFAIL=4, SKIP=6)
>
>
> I think I use openblas, as it is installed instead the normal blas/cblas.

Thanks again for the further tests.

What do you get for:

python -c 'import numpy; print(numpy.__config__.show())'

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nathaniel Smith]

(This is not relevant to the main topic of the thread, but FYI I think the
recarray issues are fixed in 1.10.4.)
On Feb 7, 2016 11:10 PM, "Nadav Horesh" <nad...@visionsense.com> wrote:

> I have atlas-lapack-base installed via pacman (required by sagemath).
> Since the numpy installation insisted on openblas on /usr/local, I got the
> openblas source-code and installed  it on /usr/local.
> BTW, I use 1.11b rather then 1.10.x since the 1.10 is very slow in
> handling recarrays. For the tests I am erasing the 1.11 installation, and
> installing the 1.10.4 wheel. I do verify that I have the right version
> before running the tests, but I am not sure if there no unnoticed side
> effects.
>
> Would it help if I put a side the openblas installation and rerun the test?
>
>   Nadav
> 
> From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of
> Matthew Brett <matthew.br...@gmail.com>
> Sent: 08 February 2016 08:13
> To: Discussion of Numerical Python
> Subject: Re: [Numpy-discussion] Multi-distribution Linux wheels - please
> test
>
> On Sun, Feb 7, 2016 at 10:09 PM, Nadav Horesh <nad...@visionsense.com>
> wrote:
> > Thank you fo reminding me, it is OK now:
> > $ python -c 'import numpy; print(numpy.__config__.show())'
> >
> > lapack_opt_info:
> > library_dirs = ['/usr/local/lib']
> > language = c
> > libraries = ['openblas']
> > define_macros = [('HAVE_CBLAS', None)]
> > blas_mkl_info:
> >   NOT AVAILABLE
> > openblas_info:
> > library_dirs = ['/usr/local/lib']
> > language = c
> > libraries = ['openblas']
> > define_macros = [('HAVE_CBLAS', None)]
> > openblas_lapack_info:
> > library_dirs = ['/usr/local/lib']
> > language = c
> > libraries = ['openblas']
> > define_macros = [('HAVE_CBLAS', None)]
> > blas_opt_info:
> > library_dirs = ['/usr/local/lib']
> > language = c
> > libraries = ['openblas']
> > define_macros = [('HAVE_CBLAS', None)]
> > None
> >
> > I updated openblas to the latest version (0.2.15) and it pass the tests
>
> Oh dear - now I'm confused.  So you installed the wheel, and tested
> it, and it gave a test failure.  Then you updated openblas using
> pacman, and then reran the tests against the wheel numpy, and they
> passed?  That's a bit frightening - the wheel should only see its own
> copy of openblas...
>
> Thans for persisting,
>
> Matthew
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[Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

Hi,

As some of you may have seen, Robert McGibbon and Nathaniel have just
guided a PEP for multi-distribution Linux wheels past the approval
process over on distutils-sig:

https://www.python.org/dev/peps/pep-0513/

The PEP includes a docker image on which y'all can build wheels which
match the PEP:

https://quay.io/repository/manylinux/manylinux

Now we're at the stage where we need stress-testing of the built
wheels to find any problems we hadn't thought of.

I've built numpy and scipy wheels here:

https://nipy.bic.berkeley.edu/manylinux/

So, if you have a Linux distribution handy, we would love to hear from
you about the results of testing these guys, maybe on the lines of:

pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy
python -c 'import numpy; numpy.test()'
python -c 'import scipy; scipy.test()'

These manylinux wheels should soon be available on pypi, and soon
after, installable with latest pip, so we would like to fix as many
problems as possible before going live.

Cheers,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Matthew Brett]

On Sat, Feb 6, 2016 at 9:28 PM, Nadav Horesh  wrote:
> Test platform: python 3.4.1 on archlinux x86_64
>
> scipy test: OK
>
> OK (KNOWNFAIL=97, SKIP=1626)
>
>
> numpy tests: Failed on long double and int128 tests, and got one error:
>
> Traceback (most recent call last):
>   File "/usr/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
> self.test(*self.arg)
>   File 
> "/usr/lib/python3.5/site-packages/numpy/core/tests/test_longdouble.py", line 
> 108, in test_fromstring_missing
> np.array([1]))
>   File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 296, 
> in assert_equal
> return assert_array_equal(actual, desired, err_msg, verbose)
>   File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 787, 
> in assert_array_equal
> verbose=verbose, header='Arrays are not equal')
>   File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 668, 
> in assert_array_compare
> raise AssertionError(msg)
> AssertionError:
> Arrays are not equal
>
> (shapes (6,), (1,) mismatch)
>  x: array([ 1., -1.,  3.,  4.,  5.,  6.])
>  y: array([1])
>
> --
> Ran 6019 tests in 28.029s
>
> FAILED (KNOWNFAIL=13, SKIP=12, errors=1, failures=18

Great - thanks so much for doing this.

Do you get a different error if you compile from source?

If you compile from source, do you link to OpenBLAS?

Thanks again,

Matthew
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Re: [Numpy-discussion] Multi-distribution Linux wheels - please test

[Nadav Horesh]

Test platform: python 3.4.1 on archlinux x86_64

scipy test: OK

OK (KNOWNFAIL=97, SKIP=1626)


numpy tests: Failed on long double and int128 tests, and got one error:

Traceback (most recent call last):
  File "/usr/lib/python3.5/site-packages/nose/case.py", line 198, in runTest
self.test(*self.arg)
  File "/usr/lib/python3.5/site-packages/numpy/core/tests/test_longdouble.py", 
line 108, in test_fromstring_missing
np.array([1]))
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 296, in 
assert_equal
return assert_array_equal(actual, desired, err_msg, verbose)
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 787, in 
assert_array_equal
verbose=verbose, header='Arrays are not equal')
  File "/usr/lib/python3.5/site-packages/numpy/testing/utils.py", line 668, in 
assert_array_compare
raise AssertionError(msg)
AssertionError: 
Arrays are not equal

(shapes (6,), (1,) mismatch)
 x: array([ 1., -1.,  3.,  4.,  5.,  6.])
 y: array([1])

--
Ran 6019 tests in 28.029s

FAILED (KNOWNFAIL=13, SKIP=12, errors=1, failures=18




From: NumPy-Discussion <numpy-discussion-boun...@scipy.org> on behalf of 
Matthew Brett <matthew.br...@gmail.com>
Sent: 06 February 2016 22:26
To: Discussion of Numerical Python; SciPy Developers List
Subject: [Numpy-discussion] Multi-distribution Linux wheels - please test

Hi,

As some of you may have seen, Robert McGibbon and Nathaniel have just
guided a PEP for multi-distribution Linux wheels past the approval
process over on distutils-sig:

https://www.python.org/dev/peps/pep-0513/

The PEP includes a docker image on which y'all can build wheels which
match the PEP:

https://quay.io/repository/manylinux/manylinux

Now we're at the stage where we need stress-testing of the built
wheels to find any problems we hadn't thought of.

I've built numpy and scipy wheels here:

https://nipy.bic.berkeley.edu/manylinux/

So, if you have a Linux distribution handy, we would love to hear from
you about the results of testing these guys, maybe on the lines of:

pip install -f https://nipy.bic.berkeley.edu/manylinux numpy scipy
python -c 'import numpy; numpy.test()'
python -c 'import scipy; scipy.test()'

These manylinux wheels should soon be available on pypi, and soon
after, installable with latest pip, so we would like to fix as many
problems as possible before going live.

Cheers,

Matthew
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