HDF 5 1.8.1 on Ubuntu 8.0.4

Hi list :slight_smile:

I'm trying to use HDF5 1.8.1 on Ubuntu 8.0.4. Unfortunately, I'm experiencing strange problems when writing HDF-files. Although the library does not report any errors, the resulting HDF-files cannot be opened, neither by h5dump or h5ls, nor by hdfview.

I'm writing with the default virtual file driver (sec2) to an ext3-formatted partition. For simplicity reasons, I do not use online compression of data. Indeed, I write 1-dimensional arrays of data to datasets.

Did this issue arise for anyone else?

Best regards,
Thomas

路路路

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A Thursday 30 October 2008, Thomas Vo脽 escrigu茅:

Hi list :slight_smile:

I'm trying to use HDF5 1.8.1 on Ubuntu 8.0.4. Unfortunately, I'm
experiencing strange problems when writing HDF-files. Although the
library does not report any errors, the resulting HDF-files cannot be
opened, neither by h5dump or h5ls, nor by hdfview.

I'm writing with the default virtual file driver (sec2) to an ext3-
formatted partition. For simplicity reasons, I do not use online
compression of data. Indeed, I write 1-dimensional arrays of data to
datasets.

Did this issue arise for anyone else?

I've had reports of people that experienced this, yes. They were
creating HDF5 files with PyTables and h5ls was not able to look into
them. After contacting the THG help desk they confirmed that this was
a know problem and that will be fixed in next HDF5 1.8.2.

How have you created your files? Can you send an example file or a
sample code to generate it?

Cheers,

路路路

--
Francesc Alted

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Hi,

As far as I know (and I run Ubuntu) none of the problems you mention are related to Ubuntu.

To fix some known problems with h5dump and h5ls, I would advice you to download and install the latest snapshot of hdf5-1.8.1

hdfview only supports hdf5-files created with version 1.6.7 or earlier.

Best regards, Richard

Francesc Alted wrote:

路路路

A Thursday 30 October 2008, Thomas Vo锟 escrigu锟:
聽聽

Hi list :slight_smile:

I'm trying to use HDF5 1.8.1 on Ubuntu 8.0.4. Unfortunately, I'm
experiencing strange problems when writing HDF-files. Although the
library does not report any errors, the resulting HDF-files cannot be
opened, neither by h5dump or h5ls, nor by hdfview.

I'm writing with the default virtual file driver (sec2) to an ext3-
formatted partition. For simplicity reasons, I do not use online
compression of data. Indeed, I write 1-dimensional arrays of data to
datasets.

Did this issue arise for anyone else?
聽聽聽聽
I've had reports of people that experienced this, yes. They were creating HDF5 files with PyTables and h5ls was not able to look into them. After contacting the THG help desk they confirmed that this was a know problem and that will be fixed in next HDF5 1.8.2.

How have you created your files? Can you send an example file or a sample code to generate it?

Cheers,

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

Hi,

thanks for the swift responses. I could narrow down the problem to the following line

聽聽error = H5LTset_attribute_string( sensorHandle, f.str().c_str(), "ClassName", sensor->className().c_str() );

the class-name of sensor might be NULL, but the HDF-API does not report any problems. Notice that "f" is an object of type boost::format.

If this line is commented out, everything works fine.

Btw, I'm able to load the result hdf5-1.8.1-files with the hdfview-application.

Best regards,
Thomas

路路路

Am 31.10.2008 um 14:59 schrieb Richard van Hees:

Hi,

As far as I know (and I run Ubuntu) none of the problems you mention are related to Ubuntu.

To fix some known problems with h5dump and h5ls, I would advice you to download and install the latest snapshot of hdf5-1.8.1

hdfview only supports hdf5-files created with version 1.6.7 or earlier.

Best regards, Richard

Francesc Alted wrote:

A Thursday 30 October 2008, Thomas Vo脽 escrigu茅:

Hi list :slight_smile:

I'm trying to use HDF5 1.8.1 on Ubuntu 8.0.4. Unfortunately, I'm
experiencing strange problems when writing HDF-files. Although the
library does not report any errors, the resulting HDF-files cannot be
opened, neither by h5dump or h5ls, nor by hdfview.

I'm writing with the default virtual file driver (sec2) to an ext3-
formatted partition. For simplicity reasons, I do not use online
compression of data. Indeed, I write 1-dimensional arrays of data to
datasets.

Did this issue arise for anyone else?

I've had reports of people that experienced this, yes. They were creating HDF5 files with PyTables and h5ls was not able to look into them. After contacting the THG help desk they confirmed that this was a know problem and that will be fixed in next HDF5 1.8.2.

How have you created your files? Can you send an example file or a sample code to generate it?

Cheers,

----------------------------------------------------------------------
This mailing list is for HDF software users discussion.
To subscribe to this list, send a message to hdf-forum-subscribe@hdfgroup.org.
To unsubscribe, send a message to hdf-forum-unsubscribe@hdfgroup.org.

----------------------------------------------------------------------
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Dear Thomas,

I know that you can load hdf5-files created with hdf5-1.8.1 with
hdfview, but only in special cases. I did not want to go into too many
details (I advice you to take a look at the hdf5-documentation: 鈥淔ormat compatibility issues鈥). In my email I wrote: 鈥hdfview
only supports hdf5-files created with version 1.6.7 or earlier
鈥.

Best regards,

Richard

Thomas Vo脽 wrote:

路路路

Hi,

thanks for the swift responses. I could narrow down the problem to the
following line

error = H5LTset_attribute_string( sensorHandle, f.str().c_str(),

鈥淐lassName鈥, sensor->className().c_str() );

the class-name of sensor might be NULL, but the HDF-API does not report
any problems. Notice that 鈥渇鈥 is an object of type boost::format.

If this line is commented out, everything works fine.

Btw, I鈥檓 able to load the result hdf5-1.8.1-files with the
hdfview-application.

Best regards,

Thomas

Am 31.10.2008 um 14:59 schrieb Richard van Hees:

Hi,

As far as I know (and I run Ubuntu) none of the problems you mention
are related to Ubuntu.

To fix some known problems with h5dump and h5ls, I would advice you to
download and install the latest snapshot of hdf5-1.8.1

hdfview only supports hdf5-files created with version 1.6.7 or earlier.

Best regards, Richard

Francesc Alted wrote:

  A Thursday 30 October 2008, Thomas Vo脽

escrigu茅:

    Hi list :-)

I鈥檓 trying to use HDF5 1.8.1 on Ubuntu 8.0.4. Unfortunately, I鈥檓

experiencing strange problems when writing HDF-files. Although the

library does not report any errors, the resulting HDF-files cannot be

opened, neither by h5dump or h5ls, nor by hdfview.

I鈥檓 writing with the default virtual file driver (sec2) to an ext3-

formatted partition. For simplicity reasons, I do not use online

compression of data. Indeed, I write 1-dimensional arrays of data to

datasets.

Did this issue arise for anyone else?

I鈥檝e had reports of people that experienced this, yes. They were
creating HDF5 files with PyTables and h5ls was not able to look into
them. After contacting the THG help desk they confirmed that this was
a know problem and that will be fixed in next HDF5 1.8.2.

How have you created your files? Can you send an example file or a
sample code to generate it?

Cheers,


This mailing list is for HDF software users discussion.
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