Quantcast

h5ls weird error when dumping PyTables files

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

h5ls weird error when dumping PyTables files

Francesc Altet-2

Hi,


I am a bit puzzled by an error that the h5ls utility is spitting out when dumping the contents of files created with PyTables.  For example:


$ h5ls -v ~/Downloads/test-pytables.h5/mydata

Opened "/Users/faltet/Downloads/test-pytables.h5" with sec2 driver.

mydata                   Dataset {10/10}

    Attribute: CLASS scalar

        Type:      5-byte null-terminated UTF-8 string

        Data:  "ARRAY"

    Attribute: FLAVOR scalar

        Type:      5-byte null-terminated UTF-8 string

        Data:  "numpy"

    Attribute: TITLE null

        Type:      1-byte null-terminated UTF-8 string


    Attribute: VERSION scalar

        Type:      3-byte null-terminated UTF-8 string

        Data:  "2.4"

    Location:  1:1024

    Links:     1

    Storage:   10 logical bytes, 10 allocated bytes, 100.00% utilization

    Type:      native signed char

H5tools-DIAG: Error detected in HDF5:tools (1.8.17) thread 140736151184320:

  #000: h5tools_dump.c line 1836 in h5tools_dump_mem(): H5Sis_simple failed

    major: Failure in tools library

    minor: error in function


Whereas I am not seeing the error with files created with h5py:


$ h5ls -v ~/Downloads/test-h5py.h5/mydata

Opened "/Users/faltet/Downloads/test-h5py.h5" with sec2 driver.

mydata                   Dataset {10/10}

    Location:  1:800

    Links:     1

    Storage:   10 logical bytes, 10 allocated bytes, 100.00% utilization

    Type:      native signed char


Curiously enough, both files work perfectly well when used inside their own Python libraries, so I suspect that something weird is going on with h5ls.  I am attaching the two files for your inspection.


Thanks,

Francesc Alted


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

test-h5py.h5 (2K) Download Attachment
test-pytables.h5 (2K) Download Attachment
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: h5ls weird error when dumping PyTables files

bljones

Hi Francesc,

 

I can reproduce the problem (with 1.10.1), and entered bug HDFFV-10188 for the issue.

The h5dump utility works correctly with the file, in case you can use that.

 

Thanks!

-Barbara

 

 

 

From: Hdf-forum [mailto:[hidden email]] On Behalf Of Francesc Altet
Sent: Monday, May 08, 2017 5:34 AM
To: [hidden email]
Subject: [Hdf-forum] h5ls weird error when dumping PyTables files

 

Hi,

 

I am a bit puzzled by an error that the h5ls utility is spitting out when dumping the contents of files created with PyTables.  For example:

 

$ h5ls -v ~/Downloads/test-pytables.h5/mydata

Opened "/Users/faltet/Downloads/test-pytables.h5" with sec2 driver.

mydata                   Dataset {10/10}

    Attribute: CLASS scalar

        Type:      5-byte null-terminated UTF-8 string

        Data:  "ARRAY"

    Attribute: FLAVOR scalar

        Type:      5-byte null-terminated UTF-8 string

        Data:  "numpy"

    Attribute: TITLE null

        Type:      1-byte null-terminated UTF-8 string

 

    Attribute: VERSION scalar

        Type:      3-byte null-terminated UTF-8 string

        Data:  "2.4"

    Location:  1:1024

    Links:     1

    Storage:   10 logical bytes, 10 allocated bytes, 100.00% utilization

    Type:      native signed char

H5tools-DIAG: Error detected in HDF5:tools (1.8.17) thread 140736151184320:

  #000: h5tools_dump.c line 1836 in h5tools_dump_mem(): H5Sis_simple failed

    major: Failure in tools library

    minor: error in function

 

Whereas I am not seeing the error with files created with h5py:

 

$ h5ls -v ~/Downloads/test-h5py.h5/mydata

Opened "/Users/faltet/Downloads/test-h5py.h5" with sec2 driver.

mydata                   Dataset {10/10}

    Location:  1:800

    Links:     1

    Storage:   10 logical bytes, 10 allocated bytes, 100.00% utilization

    Type:      native signed char

 

Curiously enough, both files work perfectly well when used inside their own Python libraries, so I suspect that something weird is going on with h5ls.  I am attaching the two files for your inspection.

 

Thanks,

Francesc Alted


_______________________________________________
Hdf-forum is for HDF software users discussion.
[hidden email]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
Loading...