where's the old wiki?

robl · January 7, 2014, 3:34pm

I came across this URL discussing google protocol buffers and HDF5.
Sounds like just the thing I wanted to send to someone... except it's
not there any longer:

http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

Where does this content live now?

==rob

···

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

Gordon_Smith · January 28, 2014, 2:03pm

This is all I could find:
http://web.archive.org/web/*/http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

···

On Tue, Jan 7, 2014 at 8:34 AM, Rob Latham <robl@mcs.anl.gov> wrote:

I came across this URL discussing google protocol buffers and HDF5.
Sounds like just the thing I wanted to send to someone... except it's
not there any longer:

http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

Where does this content live now?

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org

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

epourmal · February 11, 2014, 9:02pm

Hi Rob,

I came across this URL discussing google protocol buffers and HDF5.
Sounds like just the thing I wanted to send to someone... except it's
not there any longer:

http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

Where does this content live now?

Well… sorry, in some backup file. We are trying to locate it.

Elena

···

On Jan 7, 2014, at 9:34 AM, Rob Latham <robl@mcs.anl.gov> wrote:

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

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

nyama · January 31, 2014, 7:06pm

Hi
I am reading string data from my h5 file sequentially. But some how it fails on the second reading.Error message is:

HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:
#000: ../../src/H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: ../../src/H5Dio.c line 324 in H5D_read(): unable to set up type info
major: Dataset
minor: Unable to initialize object
#002: ../../src/H5Dio.c line 738 in H5D_typeinfo_init(): unable to convert between src and dest datatype
major: Dataset
minor: Feature is unsupported
#003: ../../src/H5T.c line 4449 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object

I can read the string , which failed, individually. But when I try read them sequentially from same object I got the error when I read the second string.
Thank you.

Reader::Reader( std::string lib_name )
{
_hdf5_strtype = H5Tcopy( H5T_C_S1 );

_hdf5_status = H5Tset_size( _hdf5_strtype, 1300 );

_hdf5_file_id = H5Fopen( lib_name.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );

if ( _hdf5_file_id < 0 )
{
cout << "Cannot open template library HDF5 file" << endl;
exit(EXIT_FAILURE);
}
}

int Reader::SetFasta( std::string tpl_name )
{
char dset[1300] = "";

if ( H5Lexists( _hdf5_file_id, tpl_name.c_str(), H5P_DEFAULT ) )
{
_hdf5_group_id = H5Gopen2( _hdf5_file_id, tpl_name.c_str(), H5P_DEFAULT );

_hdf5_dataset_id = H5Dopen2( _hdf5_group_id,"Fasta_seq", H5P_DEFAULT );

_hdf5_status = H5Dread( _hdf5_dataset_id, _hdf5_strtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, dset );

_hdf5_fasta = dset;

return _hdf5_group_id;
}

epourmal · February 17, 2014, 12:10am

All,

Here is a link to the PDF version of the " Google Protocol Buffers and HDF5" document
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/docs/Google-Protocol-Buffers-and-HDF5.pdf

Unfortunately links in the document do not work, but the original Google post can be easily found at

Please let me know if you have any questions.

Have a great week!

Elena

···

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

On Feb 11, 2014, at 3:02 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Hi Rob,

On Jan 7, 2014, at 9:34 AM, Rob Latham <robl@mcs.anl.gov> wrote:

I came across this URL discussing google protocol buffers and HDF5.
Sounds like just the thing I wanted to send to someone... except it's
not there any longer:

http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

Where does this content live now?

Well… sorry, in some backup file. We are trying to locate it.

Elena

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

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

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

j.rowe · February 18, 2014, 4:58am

Interestingly, this document only highlights the differences in the two formats. I have found them quite complimentary for some situations. For example, we use protocol buffers extensively to serialize/deserialize and persist object state or smaller arrays of complex objects (we have found it much faster than xml serialization). These serialized protocol buffer messages can be stored easily enough as byte array attributes inside of an H5 file. The issue of all-or-nothing access is moot since that is how that data is used anyway in the app and I'd much rather work with its flexible xml-style than creating complex hdf5 compound types.

Not sure about other languages, but .NET makes using protocol buffers trivial through the use of attributes (we use "protobuf").

Anyway, just thought I'd pass on how we are successfully using the two together where each has its own strengths.

Warm Regards,
Jim

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Elena Pourmal
Sent: Sunday, February 16, 2014 5:11 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] where's the old wiki?

All,

Here is a link to the PDF version of the " Google Protocol Buffers and HDF5" document
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/docs/Google-Protocol-Buffers-and-HDF5.pdf

Unfortunately links in the document do not work, but the original Google post can be easily found at

Please let me know if you have any questions.

Have a great week!

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

On Feb 11, 2014, at 3:02 PM, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:

Hi Rob,

On Jan 7, 2014, at 9:34 AM, Rob Latham <robl@mcs.anl.gov<mailto:robl@mcs.anl.gov>> wrote:

I came across this URL discussing google protocol buffers and HDF5.
Sounds like just the thing I wanted to send to someone... except it's
not there any longer:

http://wiki.hdfgroup.org/Google+Protocol+Buffers+and+HDF5

Where does this content live now?
Well... sorry, in some backup file. We are trying to locate it.

Elena

==rob

--
Rob Latham
Mathematics and Computer Science Division
Argonne National Lab, IL USA

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