h5repack 1.8.11 with -f destroys comments

Hdf-forum archives
1

'Morning,

I noticed that using the FLET/SHUF/GZIP filters during a whole-file
h5repack operation seems to destroy comments. This feels wrong as a
default behavior and nothing in h5repack -h suggests I can prevent it.

Recreate below using the small attached HDF5 file. The recreate
behaves identically on 1.8.9 and 1.8.11. I didn't see anything in the
1.8.12 and 1.8.13 changelogs that looked like a fix for this, but I
could be wrong.

Known issue? Any workarounds?

- Rhys

$ h5dump --version
h5dump: Version 1.8.11

$ h5dump -H orig.h5
HDF5 "orig.h5" {
GROUP "/" {
   DATASET "chan.visc" {
   COMMENT "Viscous information per documentation of
suzerain_channel_viscous and suzerain_channel_qoi"
      DATATYPE H5T_STD_I32LE
      DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
      ...
   }
}
}

$ h5repack --version
h5repack: Version 1.8.11

$ h5repack -f FLET orig.h5 pack.h5 # or SHUF or GZIP=9

[5023 rhys@setun coleman3k01]$ h5dump -H pack.h5
HDF5 "pack.h5" {
GROUP "/" {
   DATASET "chan.visc" {
      DATATYPE H5T_STD_I32LE
      DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
      ...
   }
}
}

orig.h5 (2.1 KB)

2

Rhys,

Thank you for reporting the issue! You are correct, this is a wrong behavior.

Issue HDFFV-8841 has been created in JIRA and, hopefully, we will be able to address it for the HDF5 1.8.14 release in November.

BTW, only h5dump currently handles object comments. The HDF Group has some work to do :wink: Patches are also welcome!

Elena

···

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Jun 5, 2014, at 8:23 AM, Rhys Ulerich <rhys.ulerich@gmail.com> wrote:

'Morning,

I noticed that using the FLET/SHUF/GZIP filters during a whole-file
h5repack operation seems to destroy comments. This feels wrong as a
default behavior and nothing in h5repack -h suggests I can prevent it.

Recreate below using the small attached HDF5 file. The recreate
behaves identically on 1.8.9 and 1.8.11. I didn't see anything in the
1.8.12 and 1.8.13 changelogs that looked like a fix for this, but I
could be wrong.

Known issue? Any workarounds?

- Rhys

$ h5dump --version
h5dump: Version 1.8.11

$ h5dump -H orig.h5
HDF5 "orig.h5" {
GROUP "/" {
  DATASET "chan.visc" {
  COMMENT "Viscous information per documentation of
suzerain_channel_viscous and suzerain_channel_qoi"
     DATATYPE H5T_STD_I32LE
     DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
     ...
  }
}
}

$ h5repack --version
h5repack: Version 1.8.11

$ h5repack -f FLET orig.h5 pack.h5 # or SHUF or GZIP=9

[5023 rhys@setun coleman3k01]$ h5dump -H pack.h5
HDF5 "pack.h5" {
GROUP "/" {
  DATASET "chan.visc" {
     DATATYPE H5T_STD_I32LE
     DATASPACE SIMPLE { ( 1 ) / ( 1 ) }
     ...
  }
}
}
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