Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

HDF5 error only on Windows #117

Closed
urlicht opened this issue Apr 21, 2019 · 2 comments
Closed

HDF5 error only on Windows #117

urlicht opened this issue Apr 21, 2019 · 2 comments

Comments

@urlicht
Copy link

urlicht commented Apr 21, 2019

The following error (see the stacktrace) occurs for some .mat files, only on Windows (Windows 10, Julia 1.1, latest stable MAT.jl). In Linux (16.04), the package is able to read the file. The HDF5 package itself is functional without any issues.

julia> data=MAT.matread(path);
HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:
  #000: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5A.c line 1302 in H5Aget_type(): unable to register datatype ID
    major: Object atom
    minor: Unable to register new atom
  #001: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5I.c line 895 in H5I_register(): can't insert ID node into skip list
    major: Object atom
    minor: Unable to insert object
  #002: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5SL.c line 995 in H5SL_insert(): can't create new skip list node
    major: Skip Lists
    minor: Unable to insert object
  #003: /home/abuild/rpmbuild/BUILD/hdf5-1.8.13/src/H5SL.c line 687 in H5SL_insert_common(): can't insert duplicate key
    major: Skip Lists
    minor: Unable to insert object
ERROR: Error getting attribute type
Stacktrace:
 [1] error(::String) at .\error.jl:33
 [2] datatype at C:\Users\$USERNAME\.julia\dev\HDF5\src\HDF5.jl:2250 [inlined]
 [3] hdf5_to_julia(::HDF5Attribute) at C:\Users\$USERNAME\.julia\dev\HDF5\src\HDF5.jl:1884
 [4] read(::HDF5Attribute) at C:\Users\$USERNAME\.julia\dev\HDF5\src\HDF5.jl:1299
 [5] a_read(::HDF5Group, ::String) at C:\Users\$USERNAME\.julia\dev\HDF5\src\HDF5.jl:1275
 [6] m_read(::HDF5Group) at C:\Users\$USERNAME\.julia\packages\MAT\UpKPb\src\MAT_HDF5.jl:197
 [7] read(::MAT.MAT_HDF5.MatlabHDF5File, ::String) at C:\Users\$USERNAME\.julia\packages\MAT\UpKPb\src\MAT_HDF5.jl:260
 [8] read(::MAT.MAT_HDF5.MatlabHDF5File) at C:\Users\$USERNAME\.julia\dev\HDF5\src\datafile.jl:45
 [9] matread(::String) at C:\Users\$USERNAME\.julia\packages\MAT\UpKPb\src\MAT.jl:130
 [10] top-level scope at none:0

@urlicht
Copy link
Author

urlicht commented Apr 21, 2019

This seems to be an issue with HDF5 package on Windows. HDF5 on Windows uses 1.8.13. I installed 1.8.21 instead, and now MAT.jl can load the files.

@musm
Copy link
Member

musm commented Sep 4, 2020

Should be fixed?

@musm musm closed this as completed Dec 31, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants