scipy.io.loadmat crashing python in version 2.5.0

Question

scipy.io.loadmat crashing python in version 2.5.0

bamboocza opened this issue 9 years ago · 20 comments

As title states, I didn't get the loadmat method to work without causing the interpreter to crash. I reproduced the issue on different system too, although it works fine on 2.4.1 and 3.x versions.

Answer 1 · 2016-02-10T03:29:29.000Z

Can you give more information about the crash. Which version of Scipy are you using? I assume 0.17.0. Is this correct? Which OS and version of Python are you using? What is the exact command that causes Python to crash? Is there a traceback? A segfault? Thanks

Answer 2 · 2016-02-13T15:37:06.000Z

Hello,
the OS is windows 10. Here
http://stackoverflow.com/questions/35238878/python-stops-working-on-loadmat's
my query on stackoverflow which should tell you everything I know.

2016-02-10 4:29 GMT+01:00 Ilan Schnell notifications@github.com:

Can you give more information about the crash. Which version of Scipy are
you using? I assume 0.17.0. Is this correct? Which OS and version of Python
are you using? What is the exact command that causes Python to crash? Is
there a traceback? A segfault? Thanks

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Reply to this email directly or view it on GitHub
#650 (comment)
.

Answer 3 · 2016-02-14T20:45:23.000Z

I have absolutely the same problem. Win 10, Anaconda 2.5.0 and scipy.io.loadmat(...)
I've debugged down to mio5.py line 217:
mdtype, byte_count = self._file_reader.read_full_tag()
I can't event step into this function.
It seems the problems are in memory access by mio_utils lib

Any ideas ?

Update: I reproduced the issue on my Win 7 workstation

Update: I downgraded to anaconda 2.4.1 and the issue was resolved.
Then I updated scipy to the latest version and the issue reproduced.
Finally I downgraded scipy only to version 0.16.0-np110py27_0 and the issue disappeared again.
Thus scipy version matters

Answer 4 · 2016-02-19T02:27:08.000Z

I see this problem on a scipy 0.17.0, 32 bit Python 2.7 build, but not on a 64 bit Python 3.4 build. Here's a link to one of my Appveyor builds with more information. The test that it fails on calls loadmat.

Edit: Also fails on 64 bit Python 2.7.

Answer 5 · 2016-02-23T23:01:55.000Z

The code on SO crashes for me, using Miniconda2 on Win7 (64-bit). Python 2.7.11, scipy 0.17.0.

Python 2.7.11 |Continuum Analytics, Inc.| (default, Jan 29 2016, 14:26:21) [MSC
v.1500 64 bit (AMD64)] on win32

Downgrading to 1.16.0 solved the issue. conda install scipy==0.16.0.
I first assumed this was a Windows issue, but it turns out my Linux install was running 0.16.0.

Answer 6 · 2016-02-24T12:00:51.000Z

Saw this on Windows 7, Python 2.7, scipy 0.17.0. Also an Anaconda install. @roessland 's fix worked for me too.

Answer 7 · 2016-02-27T12:26:06.000Z

same here, downgrading scipy worked. does not depend on Windows version, I have Win10.

Answer 8 · 2016-03-07T19:42:14.000Z

It works, but its workaround, not solution. It would be great to fix the issue, because SciPy 0.17 provides some new features which I need to use.
BTW, WinPython distribution is compatible with the latest version of SciPy, and scipy.io.loadmat works just fine, though I would still prefer Anaconda, due to better quality of matplotlib figures.

Answer 9 · 2016-03-14T02:06:28.000Z

same here. Win 10 doesn't work. Repos in heroku and ubuntu work fine. It should be the issue with scipy 0.17 and windows system.

Answer 10 · 2016-03-17T03:22:26.000Z

Windows 7 , Python 3.5.1, scipy 0.17.0

Same issue, to reproduce the bug the matfile needs

to contain a structure
to have a certain size.

Big arrays are fine, it's only when compounded in a structure that they make python blow up.

Below, only the last matfile fails to load :

A = rand(100,50);
B = rand(101,51);
S = struct('A',A,'B',B);
save('E:\2016\01_HoboAcquisition\WIND\A.mat','A') % OK
save('E:\2016\01_HoboAcquisition\WIND\AB.mat','A','B') % OK
save('E:\2016\01_HoboAcquisition\WIND\S.mat','S') % OK
Big = rand(26499870,2);
save('E:\2016\01_HoboAcquisition\WIND\Big.mat','Big') % OK
A = rand(26499870,1);
B = rand(26499870,1);
save('E:\2016\01_HoboAcquisition\WIND\BigAB.mat','A','B') % OK
BigS = struct('A',rand(26499870,1),'B', rand(26499870,1));
save('E:\2016\01_HoboAcquisition\WIND\BigS.mat','BigS') % fail

Answer 11 · 2016-03-23T19:20:12.000Z

I have the same issue. Windows 10 pro, Anaconda 2.5 64-bit,

conda install scipy=0.17.0
ipython
import scipy.io as sio
sio.test() 
<Python has crashed popup>

conda install scipy=0.16.1
ipython
import scipy.io as sio
sio.test() 
<Python has crashed popup>

conda install scipy=0.16.0
ipython
import scipy.io as sio
sio.test() 
<All Tests Pass>

All the scipy's work on Ubuntu 15 with Anaconda 2.5 64-bit

Answer 12 · 2016-03-24T23:10:06.000Z

Same issue on both Windows 7 and Windows Server 2012 R2. Both 64 bit. Downgrading to scipy 0.16.0 fixes the issue.

Answer 13 · 2016-03-31T04:58:08.000Z

Same issue here. Windows 10(64-bit), Python 2.7.11, Scipy 0.17.0, Miniconda2.
Python crashed when use scipy.io.loadmat().
Downgrading scipy to 0.16.0 solved the issue!conda install scipy==0.16.0

Answer 14 · 2016-04-20T11:21:45.000Z

Same here
Windows 7 (64-bit)
Anaconda distribution 4.0 (Python 2.7.11), Scipy 0.17.0.
I have also downgraded to scipy 0.16.0 to resolve issue.

Answer 15 · 2016-04-26T13:15:33.000Z

I am sorry to report: same...
Windows 7 (64-bit)
Anaconda 2.3.0 (Python 2.7.11); IPython 4.1.2, Scipy 0.17.0
I had to downgrade as well to Scipy 0.16.0, to load a .mat file

Answer 16 · 2016-05-12T17:09:24.000Z

Same here.

Python 2.7.11
Anaconda 4.0.0 (64-bit)
[MSC v.1500 64 bit (AMD64)]
scipy-0.17.0 (build: np110py27_1)

I can confirm, too, that after downgrading to scipy 0.16.0, I can load .mat files.

Answer 17 · 2016-06-14T16:21:59.000Z

I'm still getting this error with the newest scipy release on Anaconda, Windows 7 64-bit, scipy 0.17.1. I was able to downgrade back to scipy 0.16.0 and keep working. Scipy 0.17.x has some features that I would like to be able to take advantage of, but am unable to do so until Anaconda gets their distribution fixed.

from conda info
platform: win-64
conda version: 4.0.8
conda-build version: 1.20.3
python version: 2.7.11.final.0

Answer 18 · 2016-06-14T16:36:16.000Z

You might try nomkl. See this blog post:

https://www.continuum.io/blog/developer-blog/anaconda-25-release-now-mkl-optimizations

On Tue, Jun 14, 2016 at 11:22 AM CompPhysChris notifications@github.com
wrote:

I'm still getting this error with the newest scipy release on Anaconda,
Windows 7 64-bit, scipy 0.17.1. I was able to downgrade back to scipy
0.16.0 and keep working. Scipy 0.17.x has some features that I would like
to be able to take advantage of, but am unable to do so until Anaconda gets
their distribution fixed.

from conda info
platform: win-64
conda version: 4.0.8
conda-build version: 1.20.3
python version: 2.7.11.final.0

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Answer 19 · 2017-03-16T06:11:30.000Z

I also have the same problem.
python version :2.7, scipy :0.17.0.
When I use sio.loadmat(matfn), it'll be crashed. I have searched all the same problem, and we can solve the problem by downgrading the scipy version to 0.16.0 or update the scipy. I succeed using loadmat function when I updated the version to 0.19.0, However, I still have no idea what's wrong with the version 0.17.0 .

Answer 20 · 2017-07-13T12:54:52.000Z

I think it is best to delete the ".local" folder in your home directory instead of playing around with the versions of installed packages. so, rm -r ~/.local should do the trick in Ubuntu.