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  • IPython crash after xarray.opendataset : free():invalid next size (fast) · 9 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
422459458 https://github.com/pydata/xarray/issues/2275#issuecomment-422459458 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjQ1OTQ1OA== shoyer 1217238 2018-09-18T16:25:32Z 2018-09-18T16:25:32Z MEMBER

You might need to make a new conda environment. I'm not sure why it's only showing 1.2.4 as the latest release.

On Tue, Sep 18, 2018 at 6:37 AM dkobashi notifications@github.com wrote:

Your suggestion did not work. I got the following. Is there any other way to update netcdf4 without messing up the dependencies of other python tools? Thanks, -DJ

~$ conda update netcdf4 Fetching package metadata ........... Solving package specifications: .

All requested packages already installed.

packages in environment at ~/anaconda2/envs/roms:

netcdf4 1.2.4 np113py27_0

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pydata/xarray/issues/2275#issuecomment-422396141, or mute the thread https://github.com/notifications/unsubscribe-auth/ABKS1leMnGsJ9MqJMP7j2pMDrij6dKv8ks5ucPc0gaJpZM4VJsnq . 

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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
422396141 https://github.com/pydata/xarray/issues/2275#issuecomment-422396141 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjM5NjE0MQ== dkobashi 8714949 2018-09-18T13:36:54Z 2018-09-18T13:36:54Z NONE

Your suggestion did not work. I got the following. Is there any other way to update netcdf4 without messing up the dependencies of other python tools? Thanks, -DJ ``` ~$ conda update netcdf4 Fetching package metadata ........... Solving package specifications: .

All requested packages already installed.

packages in environment at ~/anaconda2/envs/roms:

netcdf4 1.2.4 np113py27_0 

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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
422218389 https://github.com/pydata/xarray/issues/2275#issuecomment-422218389 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjIxODM4OQ== shoyer 1217238 2018-09-18T00:58:25Z 2018-09-18T00:58:25Z MEMBER

@dkobashi conda update netcdf4 should do it for you

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
422152422 https://github.com/pydata/xarray/issues/2275#issuecomment-422152422 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjE1MjQyMg== dkobashi 8714949 2018-09-17T20:07:03Z 2018-09-17T20:07:03Z NONE

I use Anaconda python.

My conda version is as follow platform : linux-64 conda version : 4.3.32 conda is private : False conda-env version : 4.3.32 conda-build version : 3.0.27 python version : 2.7.14.final.0 requests version : 2.18.4

I attach xarray.show_versions() at the bottom. I see it uses the same version as the other on the post. I also attach the error I got below.

*** Error in `/home/dj/anaconda2/envs/roms/bin/python': free(): invalid next size (fast): 0x0000556928b744e0 ***

A funny thing is that I have no problem getting the data using netCDF4-python. The file size of the data is big (50-100GB. netCDF4 format), but again I was able to get the data with netCDF4-python. So I guess I need to update netCDF4-python, but I don't know how.

Thanks,

INSTALLED VERSIONS

commit: None python: 2.7.14.final.0 python-bits: 64 OS: Linux OS-release: 4.15.0-34-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: None.None

xarray: 0.10.8 pandas: 0.21.0 numpy: 1.13.3 scipy: 1.0.0 netCDF4: 1.2.4 h5netcdf: None h5py: 2.7.0 Nio: None zarr: None bottleneck: None cyordereddict: None dask: 0.16.0 distributed: 1.20.0 matplotlib: 2.2.2 cartopy: 0.15.0 seaborn: 0.9.0 setuptools: 36.5.0.post20170921 pip: 18.0 conda: None pytest: None IPython: 5.4.1 sphinx: None

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
422126176 https://github.com/pydata/xarray/issues/2275#issuecomment-422126176 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjEyNjE3Ng== shoyer 1217238 2018-09-17T18:43:35Z 2018-09-17T18:43:35Z MEMBER

@dkobashi how did you install Python?

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
422116613 https://github.com/pydata/xarray/issues/2275#issuecomment-422116613 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQyMjExNjYxMw== dkobashi 8714949 2018-09-17T18:13:25Z 2018-09-17T18:13:25Z NONE

I am having the same problem. How can I update netCDF4 library? Thanks in advance. -DJ

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
404088892 https://github.com/pydata/xarray/issues/2275#issuecomment-404088892 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQwNDA4ODg5Mg== Scheibs 16919188 2018-07-11T08:31:53Z 2018-07-11T08:31:53Z NONE

I updated the netcdf4 librairie and it's works. Thanks

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
404082788 https://github.com/pydata/xarray/issues/2275#issuecomment-404082788 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQwNDA4Mjc4OA== Scheibs 16919188 2018-07-11T08:09:32Z 2018-07-11T08:09:32Z NONE

This error appears immediately when i write xr.open_dataset(f) on Ipython console :

An error ocurred while starting the kernel *** Error in `/local01/appli/anaconda2/bin/python': free(): invalid next size (fast): 0x0000000003086710 ***

xr.show_versions()

``` INSTALLED VERSIONS ------------------ commit: None python: 2.7.13.final.0 python-bits: 64 OS: Linux OS-release: 3.16.0-4-amd64 machine: x86_64 processor: byteorder: little LC_ALL: en_US.iso885915 LANG: fr_FR@euro LOCALE: None.None xarray: 0.10.7 pandas: 0.20.3 numpy: 1.13.1 scipy: 0.19.1 netCDF4: 1.2.4 h5netcdf: 0.6.1 h5py: 2.7.0 Nio: None zarr: None bottleneck: 1.2.1 cyordereddict: 1.0.0 dask: 0.18.1 distributed: 1.22.0 matplotlib: 2.0.2 cartopy: None seaborn: None setuptools: 36.4.0 pip: 9.0.1 conda: 4.5.7 pytest: 3.2.1 IPython: 5.3.0 sphinx: 1.6.3 ``` 

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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651
403954586 https://github.com/pydata/xarray/issues/2275#issuecomment-403954586 https://api.github.com/repos/pydata/xarray/issues/2275 MDEyOklzc3VlQ29tbWVudDQwMzk1NDU4Ng== shoyer 1217238 2018-07-10T20:26:39Z 2018-07-10T20:26:39Z MEMBER

Can you please share the output of xarray.show_versions() and an example of the your code that triggers this error?

My free is that this is a bug in one of the underlying libraries xarray uses for reading netCDF files.

 
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   IPython crash after xarray.opendataset : free():invalid next size (fast) 339909651

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