[MOAB-dev] h5m: class attribute in tags
Grindeanu, Iulian R.
iulian at mcs.anl.gov
Thu Nov 12 10:23:16 CST 2015
Hi Nico,
moab stores dense tags in a hdf5 dataspace of dimension 1, not 2
I do not understand in your code where you create the dataspace for tag A. I did not dig too much, and I still did not install it.
So, dimension size should be the number of nodes (for dense node tags)
data type, instead of being a 64-bit floating point, should be an array of 64-bit floating-point (3), for your example
Coordinates, on the other hand, are stored in a 2 dimensional dataspace, and also connectivities
________________________________
From: Nico Schlömer [nico.schloemer at gmail.com]
Sent: Thursday, November 12, 2015 4:10 AM
To: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] h5m: class attribute in tags
> How do you install h5py? serial or parallel? I was trying to play with your meshio, but I need more stuff installed
The `requirements.txt` should list ist all;
```
pip install -r requirements.txt
```
might also help. h5py is needed in serial.
Thanks for the explanation about the tags. I'm now at another error message, namely
```
[0]MOAB ERROR: Incorrect DataSpace for DataSet.!
[0]MOAB ERROR: is_error() line 105 in ReadHDF5.hpp
```
No idea what that wants to say. I'm getting it for the data at [1]. Any idea what might be going wrong?
The respective code is at [2] btw.
Cheers,
Nico
[1] http://chunk.io/f/2f94e4ab6bbe458fbdc1d3a3f7edb624
[2] https://github.com/nschloe/meshio/blob/master/meshio/writer.py#L106
On Wed, Nov 11, 2015 at 10:25 PM Grindeanu, Iulian R. <iulian at mcs.anl.gov<mailto:iulian at mcs.anl.gov>> wrote:
How do you install h5py? serial or parallel? I was trying to play with your meshio, but I need more stuff installed
I was wrong before,
class attribute is an integer attribute, with a value corresponding to the storage type
/** \brief Was dense tag data in mesh database */
#define mhdf_DENSE_TYPE 2
/** \brief Was sparse tag data in mesh database */
#define mhdf_SPARSE_TYPE 1
/** \brief Was bit-field tag data in mesh database */
#define mhdf_BIT_TYPE 0
/** \brief Unused */
#define mhdf_MESH_TYPE 3
the storage type is set here:
./src/io/mhdf/src/tags.c
hid_t create_tag_common( mhdf_FileHandle file_handle,
const char* tag_name,
enum mhdf_TagDataType tag_type,
int size,
int storage,
const void* default_value,
int default_value_size_in,
const void* global_value,
int global_value_size_in,
hid_t hdf_type,
hid_t hdf_base_type,
mhdf_Status* status )
about line 340:
rval = mhdf_create_scalar_attrib( tag_id,
TAG_TYPE_ATTRIB, // this is "class"
H5T_NATIVE_INT,
&storage,
status );
tag_id is the group id associated with the tag
the storage type is retrieved in the hdf5 writer with a code like this
// Get tag properties
rval = iFace->tag_get_type(tag_data.tag_id, mb_storage);CHK_MB_ERR_0(rval);
switch (mb_storage) {
case MB_TAG_DENSE:
storage = mhdf_DENSE_TYPE;
break;
case MB_TAG_SPARSE:
storage = mhdf_SPARSE_TYPE;
break;
case MB_TAG_BIT:
storage = mhdf_BIT_TYPE;
break;
case MB_TAG_MESH:
storage = mhdf_MESH_TYPE;
break;
default:
return error(MB_FAILURE);
}
________________________________
From: Nico Schlömer [nico.schloemer at gmail.com<mailto:nico.schloemer at gmail.com>]
Sent: Wednesday, November 11, 2015 1:01 PM
To: Grindeanu, Iulian R.; moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>
Subject: Re: [MOAB-dev] h5m: class attribute in tags
> Or do you try to understand how are the data / tags stored?
Indeed. I've converted a bunch of files to h5m using MeshIO [1], but found that they couldn't be read into MOAB because of a missing class attribute.
> class would correspond to the type of the tag (integer, double, opaque, etc)
Could you give more detail here?
Cheers,
Nico
[1] https://pypi.python.org/pypi/meshio
On Wed, Nov 11, 2015 at 7:55 PM Grindeanu, Iulian R. <iulian at mcs.anl.gov<mailto:iulian at mcs.anl.gov>> wrote:
Hi Nico,
Not sure what are you trying to do here.
Do you need to improve the h5m reader writer? Or do you try to understand how are the data / tags stored?
Do you have a specific problem/bug ?
Suggestions for improvement?
All these attributes are part of specific moab conventions and hdf5 format. Not much documentation, except what you already found.
class would correspond to the type of the tag (integer, double, opaque, etc)
default would be the default value
global is used if the tag is "global", in the sense it refers to the whole mesh instance
"The tag sub-group may have any or all of the following four attributes: default, global, is_handle, and variable_length. The default attribute, if present, must contain a single tag value that is to be considered the 'default' value of the tag. The global attribute, if present, must contain a single tag value that is the value of the tag as set on the mesh instance (MOAB terminology) or root set (ITAPS terminology.) The presence of the is_handle attribute (the value, if any, is meaningless) indicates that the tag values are to be considered entity IDs."
________________________________
From: moab-dev-bounces at mcs.anl.gov<mailto:moab-dev-bounces at mcs.anl.gov> [moab-dev-bounces at mcs.anl.gov<mailto:moab-dev-bounces at mcs.anl.gov>] on behalf of Nico Schlömer [nico.schloemer at gmail.com<mailto:nico.schloemer at gmail.com>]
Sent: Wednesday, November 11, 2015 3:43 AM
To: moab-dev at mcs.anl.gov<mailto:moab-dev at mcs.anl.gov>
Subject: [MOAB-dev] h5m: class attribute in tags
Hi everyone,
In h5m files [1], I see that tstt->tags typically have three attributes:
* class
* default
* global
Where can I find documentation on these attributes?
Cheers,
Nico
[1] https://trac.mcs.anl.gov/projects/ITAPS/wiki/MOAB/h5m
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