[SciPy-Dev] SciPy in conda-forge env on Windows
Mark Alexander Mikofski
mikofski at berkeley.edu
Thu Apr 19 20:14:19 EDT 2018
Thanks for your response. I tested it again, and I still hit the same issue.
Here's my procedure:
(base)> conda create -n forge
(base)> conda activate forge
(forge)> conda config --env --add channels conda-forge
(forge)> conda install python=3 pip setuptools wheel
(forge)> conda install nose pytest
(forge)> conda install numpy
(forge)>python
>>> import numpy
>>> numpy.test()
Ran 6413 tests in 84.363s
OK (KNOWNFAIL=19, SKIP=16)
<nose.result.TextTestResult run=6413 errors=0 failures=0>
>>> exit()
(forge)> pip install scipy
(forge)> python
>>> import scipy
>>> scipy.test(verbose=3, tests=['scipy.linalg.tests.test_basic'])
scipy/linalg/tests/test_basic.py::TestDet::test_random FAILED [ 54%]
scipy/linalg/tests/test_basic.py::TestDet::test_random_complex
I have to kill the process here
---
Note, the same thing happens if I install scipy from conda, which installs
scipy from anaconda channel on win_amd64 b/c scipy-feedstock is currently
disabled on conda-forge
---
But, everything passes fine if I just install both numpy and scipy from pip.
And everything passes fine if I install scipy first, which then installs
numpy from the default "anaconda" channel
---
I posted an issue on the numpy-feedstock, and a comment on the conda-forge
google group:
* https://github.com/conda-forge/numpy-feedstock/issues/82
*
https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/conda-forge/PPLWn4U1ZHA/frHthukWCgAJ
---
I'm really sorry if this is a red-herring or wild goose chase. I didn't
mean to cause any trouble. I think following Chris Barker's advice, I
should have installed scipy first, and then I wouldn't have been in this
mess.
Thanks!
On Thu, Apr 19, 2018 at 1:23 PM, Nathaniel Smith <njs at pobox.com> wrote:
> Mixing wheels and conda packages can cause some problems over time because
> of pip and conda getting confused about what's installed. But if you made a
> conda env, and then did a pip install, and that's all you've done, then
> that should work fine AFAIK.
>
> And the scipy wheels should be self contained and work correctly in any
> environment, including a conda env where numpy is using mkl or a different
> version of openblas.
>
> I don't know what's going wrong in your case, but I can at least say that
> as far as I know, it *should* work and you're hitting a genuine bug.
>
> On Thu, Apr 19, 2018, 10:17 Mark Alexander Mikofski <mikofski at berkeley.edu>
> wrote:
>
>> Hi,
>>
>> Sorry if this question is redundant. I checked the "install" page in the
>> SciPy docs, and couldn't find any mention of conda-forge.
>>
>> Can SciPy from pip (scipy-1.0.1-cp36-none-win_amd64.whl) be used with
>> the numpy-feedstock from conda-forge? When I run the tests for scipy, the
>> fail and hang after "scipy\linalg\tests\test_basic.py".
>>
>> The reason I thought this might work is because they both use a variant
>> of OpenBLAS, but perhaps they are not compatible? I can see that NumPy
>> openblas.dll is in miniconda/envs/<envname>/Library/bin (31,053KB) where
>> as the SciPy openblas.dll is in site-packages/scipy/extra-dll (41,762KB)
>> and the name is vendorized with a long alphanumeric string.
>>
>> Unfortunately if I try to use conda to install SciPy, conda uses the
>> default "anaconda" channel, because win_amd64 conda-forge scipy-feedstock
>> has been disabled, and when I run the tests using this mix of
>> conda-forge:numpy and anaconda:scipy, I get the same failure at
>> "scipy\linalg\tests\test_basic.py", which I would expect because the
>> anaconda:scipy uses Intel-MKL not OpenBLAS, and I think these libraries
>> need to be compatible for scipy to work, right?
>>
>> The test that fails is "TestDet.test_random()"
>>
>> scipy/linalg/tests/test_basic.py::TestDet::test_random FAILED [ 54%]
>>
>> this is the pytest traceback:
>>
>> ------------------------------------------------------------
>> ---------------
>> AssertionError Traceback (most recent call
>> last)
>> <ipython-input-3-ff0509141d7f> in <module>()
>> ----> 1 test_det.test_random()
>>
>> ~\AppData\Local\Continuum\miniconda3\envs\forge\lib\
>> site-packages\scipy\linalg\tests\test_basic.py in test_random(self)
>> 907 d1 = det(a)
>> 908 d2 = basic_det(a)
>> --> 909 assert_almost_equal(d1, d2)
>> 910
>> 911 def test_random_complex(self):
>>
>> ~\AppData\Local\Continuum\miniconda3\envs\forge\lib\
>> site-packages\numpy\testing\nose_tools\utils.py in
>> assert_almost_equal(actual, desired, decimal, err_msg, verbose)
>> 579 pass
>> 580 if abs(desired - actual) >= 1.5 * 10.0**(-decimal):
>> --> 581 raise AssertionError(_build_err_msg())
>> 582
>> 583
>>
>> AssertionError:
>> Arrays are not almost equal to 7 decimals
>> ACTUAL: 0.001303440758814572
>> DESIRED: -0.09307217461347188
>>
>> Then the next test hangs for several minute, and I have to kill the
>> process.
>>
>> scipy/linalg/tests/test_basic.py::TestDet::test_random_complex
>>
>> It also hangs when I call it directly from an interpreter.
>>
>> If I use just pip to install both numpy (numpy-1.14.2-cp36-none-win_amd64.whl)
>> and scipy (scipy-1.0.1-cp36-none-win_amd64.whl) then all of the tests
>> pass. And now I can see the vendorized version of openBLAS for numpy in
>> site-packags/numpy/.libs (41762KB) matches the openBLAS in scipy/extra-dll,
>> the vendor alpha-numeric string is also the same: "
>> BNVRK7633HSX7YVO2TADGR4A5KEKXJAW"
>>
>> Maybe this is very basic, and I shouldn't be asking. But I don't
>> understand how to use conda-forge then with SciPy and NumPy on Windows. It
>> seems like users should only use all pip or only the default "anaconda"
>> channel. Or if using conda-forge on window, then only use NumPy without
>> SciPy, but that also means other packages like statsmodels are out too.
>> Also maybe this is a question for conda-forge and not scipy-dev. Again, so
>> sorry if my question is out of place.
>>
>> I'm also sorry if this is received poorly. I am so happy and very
>> grateful for all of the volunteer work that has gone into making SciPy and
>> NumPy work on Windows. I remember the old days when I had to refer people
>> to cgohlke's website. If there is anything I can do to help, I can try. I
>> will take a look at reactivating the conda-forge build for win_amd64, I
>> believe that would solve the problem. Also I will bring up the issue of
>> dependency clashes with conda-forge as well.
>>
>> Thanks,
>> Mark
>>
>> --
>> Mark Mikofski, PhD (2005)
>> *Fiat Lux*
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>>
>
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--
Mark Mikofski, PhD (2005)
*Fiat Lux*
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