Issues reading an HDF5 file

Hdf-forum archives
1

I'm trying to read some small slabs from a database and am getting invalid data returned.
Opening the dataset in HDFView also shows incorrect values.

Trying it via the utilities, this command shows a similar failure:
h5dump -p -d "/Regions/Region1/Dataset" -s "175,0,0" -c "1,5,5" bad.h5
Output:
                HDF5 "bad.h5" {
                DATASET "/Regions/Region1/Dataset" {
                   DATATYPE H5T_IEEE_F32LE
                   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }
   STORAGE_LAYOUT {
      CHUNKED ( 1, 1, 1786 )
      SIZE 219264490 (1.699:1 COMPRESSION)
   }
   FILTERS {
      COMPRESSION DEFLATE { LEVEL 6 }
   }
   FILLVALUE {
      FILL_TIME H5D_FILL_TIME_IFSET
      VALUE 0
   }
   ALLOCATION_TIME {
      H5D_ALLOC_TIME_INCR
   }
                   SUBSET {
                      START ( 175, 0, 0 );
                      STRIDE ( 1, 1, 1 );
                      COUNT ( 1, 5, 5 );
                      BLOCK ( 1, 1, 1 );
                      DATA {
                      (175,0,0): 5.00226e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,1,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,2,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,3,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,4,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022
                      }
                   }
                }
                }

Expanding the selection slight gives the correct data:
h5dump -p -d "/Regions/Region1/Dataset" -s "174,0,0" -c "2,5,5" bad.h5
Output:
HDF5 "bad.h5" {
DATASET "/Regions/Region1/Dataset" {
   DATATYPE H5T_IEEE_F32LE
   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }
   STORAGE_LAYOUT {
      CHUNKED ( 1, 1, 1786 )
      SIZE 219264490 (1.699:1 COMPRESSION)
   }
   FILTERS {
      COMPRESSION DEFLATE { LEVEL 6 }
   }
   FILLVALUE {
      FILL_TIME H5D_FILL_TIME_IFSET
      VALUE 0
   }
   ALLOCATION_TIME {
      H5D_ALLOC_TIME_INCR
   }
   SUBSET {
      START ( 174, 0, 0 );
      STRIDE ( 1, 1, 1 );
      COUNT ( 2, 5, 5 );
      BLOCK ( 1, 1, 1 );
      DATA {
      (174,0,0): 5596.14, 5155, 7550.53, 8183.16, 6550.84,
      (174,1,0): 4673.81, 6764.91, 2571.05, 424.237, 3440.45,
      (174,2,0): 1976.77, 2333.76, 5337.73, 5999.94, 3304.85,
      (174,3,0): 1500.24, 2544.14, 5753.82, 5693.52, 3100.93,
      (174,4,0): 2546.38, 2239.06, 5786.03, 2432.32, 447.349
      (175,0,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,1,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,2,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,3,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,4,0): 2560, 2239.06, 5786.03, 2432.32, 447.349
      }
   }
}
}

Any idea on when I'm doing wrong or how to get the proper data?

Thanks,
  Peter Steinberg

2

Hi Peter,

Thank you for reporting the problem.

Could you send "bad.h5" to our help desk (help@hdfgroup.org) so that
we can debug it?

Thanks
--pc

···

On 6/10/2013 3:01 PM, Steinberg, Peter wrote:

I'm trying to read some small slabs from a database and am getting invalid data returned.

Opening the dataset in HDFView also shows incorrect values.

Trying it via the utilities, this command shows a similar failure:

h5dump -p -d "/Regions/Region1/Dataset" -s "175,0,0" -c "1,5,5" bad.h5

Output:

                HDF5 "bad.h5" {

                DATASET "/Regions/Region1/Dataset" {

                   DATATYPE H5T_IEEE_F32LE

                   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }

   STORAGE_LAYOUT {

      CHUNKED ( 1, 1, 1786 )

      SIZE 219264490 (1.699:1 COMPRESSION)

   }

   FILTERS {

      COMPRESSION DEFLATE { LEVEL 6 }

   }

   FILLVALUE {

      FILL_TIME H5D_FILL_TIME_IFSET

      VALUE 0

   }

   ALLOCATION_TIME {

H5D_ALLOC_TIME_INCR

   }

                   SUBSET {

                      START ( 175, 0, 0 );

                      STRIDE ( 1, 1, 1 );

                      COUNT ( 1, 5, 5 );

                      BLOCK ( 1, 1, 1 );

                      DATA {

                      (175,0,0): 5.00226e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,

                      (175,1,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,

                      (175,2,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,

                      (175,3,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,

                      (175,4,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022

                      }

                   }

                }

                }

Expanding the selection slight gives the correct data:

h5dump -p -d "/Regions/Region1/Dataset" -s "174,0,0" -c "2,5,5" bad.h5

Output:

HDF5 "bad.h5" {

DATASET "/Regions/Region1/Dataset" {

   DATATYPE H5T_IEEE_F32LE

   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }

   STORAGE_LAYOUT {

      CHUNKED ( 1, 1, 1786 )

      SIZE 219264490 (1.699:1 COMPRESSION)

   }

   FILTERS {

      COMPRESSION DEFLATE { LEVEL 6 }

   }

   FILLVALUE {

      FILL_TIME H5D_FILL_TIME_IFSET

      VALUE 0

   }

   ALLOCATION_TIME {

H5D_ALLOC_TIME_INCR

   }

   SUBSET {

      START ( 174, 0, 0 );

      STRIDE ( 1, 1, 1 );

      COUNT ( 2, 5, 5 );

      BLOCK ( 1, 1, 1 );

      DATA {

      (174,0,0): 5596.14, 5155, 7550.53, 8183.16, 6550.84,

      (174,1,0): 4673.81, 6764.91, 2571.05, 424.237, 3440.45,

      (174,2,0): 1976.77, 2333.76, 5337.73, 5999.94, 3304.85,

      (174,3,0): 1500.24, 2544.14, 5753.82, 5693.52, 3100.93,

      (174,4,0): 2546.38, 2239.06, 5786.03, 2432.32, 447.349

      (175,0,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

      (175,1,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

      (175,2,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

      (175,3,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

      (175,4,0): 2560, 2239.06, 5786.03, 2432.32, 447.349

      }

   }

}

}

Any idea on when I'm doing wrong or how to get the proper data?

Thanks,

  Peter Steinberg

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

3

Do you have an FTP site I can use?

The files range from 200 MB to over 1 GB.

Peter

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Peter Cao
Sent: Tuesday, June 11, 2013 9:04 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Issues reading an HDF5 file

Hi Peter,

Thank you for reporting the problem.

Could you send "bad.h5" to our help desk (help@hdfgroup.org<mailto:help@hdfgroup.org>) so that
we can debug it?

Thanks
--pc
On 6/10/2013 3:01 PM, Steinberg, Peter wrote:
I'm trying to read some small slabs from a database and am getting invalid data returned.
Opening the dataset in HDFView also shows incorrect values.

Trying it via the utilities, this command shows a similar failure:
h5dump -p -d "/Regions/Region1/Dataset" -s "175,0,0" -c "1,5,5" bad.h5
Output:
                HDF5 "bad.h5" {
                DATASET "/Regions/Region1/Dataset" {
                   DATATYPE H5T_IEEE_F32LE
                   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }
   STORAGE_LAYOUT {
      CHUNKED ( 1, 1, 1786 )
      SIZE 219264490 (1.699:1 COMPRESSION)
   }
   FILTERS {
      COMPRESSION DEFLATE { LEVEL 6 }
   }
   FILLVALUE {
      FILL_TIME H5D_FILL_TIME_IFSET
      VALUE 0
   }
   ALLOCATION_TIME {
      H5D_ALLOC_TIME_INCR
   }
                   SUBSET {
                      START ( 175, 0, 0 );
                      STRIDE ( 1, 1, 1 );
                      COUNT ( 1, 5, 5 );
                      BLOCK ( 1, 1, 1 );
                      DATA {
                      (175,0,0): 5.00226e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,1,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,2,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,3,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022,
                      (175,4,0): 5.02496e-011, 4.82024e+030, 7.46402e-007, 1.81771e+031, 6.82915e+022
                      }
                   }
                }
                }

Expanding the selection slight gives the correct data:
h5dump -p -d "/Regions/Region1/Dataset" -s "174,0,0" -c "2,5,5" bad.h5
Output:
HDF5 "bad.h5" {
DATASET "/Regions/Region1/Dataset" {
   DATATYPE H5T_IEEE_F32LE
   DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }
   STORAGE_LAYOUT {
      CHUNKED ( 1, 1, 1786 )
      SIZE 219264490 (1.699:1 COMPRESSION)
   }
   FILTERS {
      COMPRESSION DEFLATE { LEVEL 6 }
   }
   FILLVALUE {
      FILL_TIME H5D_FILL_TIME_IFSET
      VALUE 0
   }
   ALLOCATION_TIME {
      H5D_ALLOC_TIME_INCR
   }
   SUBSET {
      START ( 174, 0, 0 );
      STRIDE ( 1, 1, 1 );
      COUNT ( 2, 5, 5 );
      BLOCK ( 1, 1, 1 );
      DATA {
      (174,0,0): 5596.14, 5155, 7550.53, 8183.16, 6550.84,
      (174,1,0): 4673.81, 6764.91, 2571.05, 424.237, 3440.45,
      (174,2,0): 1976.77, 2333.76, 5337.73, 5999.94, 3304.85,
      (174,3,0): 1500.24, 2544.14, 5753.82, 5693.52, 3100.93,
      (174,4,0): 2546.38, 2239.06, 5786.03, 2432.32, 447.349
      (175,0,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,1,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,2,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,3,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,
      (175,4,0): 2560, 2239.06, 5786.03, 2432.32, 447.349
      }
   }
}
}

Any idea on when I'm doing wrong or how to get the proper data?

Thanks,
  Peter Steinberg

_______________________________________________

Hdf-forum is for HDF software users discussion.

Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>

http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

4

Yes, we have ftp site. Our help desk will be able to help you on this.

Thanks
--pc

···

On 6/11/2013 9:08 AM, Steinberg, Peter wrote:

Do you have an FTP site I can use?

The files range from 200 MB to over 1 GB.

Peter

*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] *On Behalf Of *Peter Cao
*Sent:* Tuesday, June 11, 2013 9:04 AM
*To:* hdf-forum@lists.hdfgroup.org
*Subject:* Re: [Hdf-forum] Issues reading an HDF5 file

Hi Peter,

Thank you for reporting the problem.

Could you send "bad.h5" to our help desk (help@hdfgroup.org <mailto:help@hdfgroup.org>) so that
we can debug it?

Thanks
--pc

On 6/10/2013 3:01 PM, Steinberg, Peter wrote:

    I'm trying to read some small slabs from a database and am getting
    invalid data returned.

    Opening the dataset in HDFView also shows incorrect values.

    Trying it via the utilities, this command shows a similar failure:

    h5dump -p -d "/Regions/Region1/Dataset" -s "175,0,0" -c "1,5,5"
    bad.h5

    Output:

                    HDF5 "bad.h5" {

                    DATASET "/Regions/Region1/Dataset" {

                       DATATYPE H5T_IEEE_F32LE

                       DATASPACE SIMPLE { ( 266, 196, 1786 ) / (
    H5S_UNLIMITED, H5S_UNLIMITED, H5S_UNLIMITED ) }

    STORAGE_LAYOUT {

          CHUNKED ( 1, 1, 1786 )

          SIZE 219264490 (1.699:1 COMPRESSION)

       }

       FILTERS {

    COMPRESSION DEFLATE { LEVEL 6 }

       }

       FILLVALUE {

          FILL_TIME H5D_FILL_TIME_IFSET

          VALUE 0

       }

    ALLOCATION_TIME {

    H5D_ALLOC_TIME_INCR

       }

                       SUBSET {

                          START ( 175, 0, 0 );

                          STRIDE ( 1, 1, 1 );

                          COUNT ( 1, 5, 5 );

                          BLOCK ( 1, 1, 1 );

                          DATA {

                          (175,0,0): 5.00226e-011, 4.82024e+030,
    7.46402e-007, 1.81771e+031, 6.82915e+022,

                          (175,1,0): 5.02496e-011, 4.82024e+030,
    7.46402e-007, 1.81771e+031, 6.82915e+022,

                          (175,2,0): 5.02496e-011, 4.82024e+030,
    7.46402e-007, 1.81771e+031, 6.82915e+022,

                          (175,3,0): 5.02496e-011, 4.82024e+030,
    7.46402e-007, 1.81771e+031, 6.82915e+022,

                          (175,4,0): 5.02496e-011, 4.82024e+030,
    7.46402e-007, 1.81771e+031, 6.82915e+022

                          }

                       }

                    }

                    }

    Expanding the selection slight gives the correct data:

    h5dump -p -d "/Regions/Region1/Dataset" -s "174,0,0" -c "2,5,5" bad.h5

    Output:

    HDF5 "bad.h5" {

    DATASET "/Regions/Region1/Dataset" {

       DATATYPE H5T_IEEE_F32LE

       DATASPACE SIMPLE { ( 266, 196, 1786 ) / ( H5S_UNLIMITED,
    H5S_UNLIMITED, H5S_UNLIMITED ) }

    STORAGE_LAYOUT {

          CHUNKED ( 1, 1, 1786 )

          SIZE 219264490 (1.699:1 COMPRESSION)

       }

       FILTERS {

    COMPRESSION DEFLATE { LEVEL 6 }

       }

       FILLVALUE {

          FILL_TIME H5D_FILL_TIME_IFSET

          VALUE 0

       }

    ALLOCATION_TIME {

    H5D_ALLOC_TIME_INCR

       }

       SUBSET {

          START ( 174, 0, 0 );

          STRIDE ( 1, 1, 1 );

          COUNT ( 2, 5, 5 );

          BLOCK ( 1, 1, 1 );

          DATA {

          (174,0,0): 5596.14, 5155, 7550.53, 8183.16, 6550.84,

          (174,1,0): 4673.81, 6764.91, 2571.05, 424.237, 3440.45,

          (174,2,0): 1976.77, 2333.76, 5337.73, 5999.94, 3304.85,

          (174,3,0): 1500.24, 2544.14, 5753.82, 5693.52, 3100.93,

          (174,4,0): 2546.38, 2239.06, 5786.03, 2432.32, 447.349

          (175,0,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

          (175,1,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

          (175,2,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

          (175,3,0): 2560, 2239.06, 5786.03, 2432.32, 447.349,

          (175,4,0): 2560, 2239.06, 5786.03, 2432.32, 447.349

          }

       }

    }

    }

    Any idea on when I'm doing wrong or how to get the proper data?

    Thanks,

      Peter Steinberg

    _______________________________________________

    Hdf-forum is for HDF software users discussion.

    Hdf-forum@lists.hdfgroup.org <mailto:Hdf-forum@lists.hdfgroup.org>

    http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org