<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Sep 2, 2014 at 3:09 AM, Åsmund Ervik <span dir="ltr"><<a href="mailto:asmund.ervik@ntnu.no" target="_blank">asmund.ervik@ntnu.no</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
<br>
On 01. sep. 2014 16:15, Matthew Knepley wrote:<br>
> On Mon, Sep 1, 2014 at 9:02 AM, Åsmund Ervik <<a href="mailto:asmund.ervik@ntnu.no">asmund.ervik@ntnu.no</a>> wrote:<br>
><br>
>> On 01. sep. 2014 14:02, Matthew Knepley wrote:<br>
>>> On Mon, Sep 1, 2014 at 6:57 AM, Åsmund Ervik <<a href="mailto:asmund.ervik@ntnu.no">asmund.ervik@ntnu.no</a>><br>
>> wrote:<br>
>>><br>
>>>><br>
>>>> No, I am not able to, that is why I switched to "--with-hdf5-dir=". Like<br>
>>>> I said in the first email, the version of HDF5 (1.8.10) that ships with<br>
>>>> PETSc 3.5.1 does not compile on my machine. This is apparently a known<br>
>>>> bug that was fixed upstream, cf.<br>
>>>><br>
>>>> <a href="https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777" target="_blank">https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=711777</a><br>
>>>><br>
>>>> This is the reason why I asked whether I can somehow tell<br>
>>>> "--download-hdf5" to download a more recent version. 1.8.11 should do<br>
>> it.<br>
>>><br>
>>><br>
>>> People who leave commented out code in there should be tarred, feathered,<br>
>>> and run out of town on a rail. You can just go in and delete that line,<br>
>> and<br>
>>> then<br>
>>> reconfigure. It will use the source that is already downloaded.<br>
>><br>
>> Okay, I also had to do the same for two lines in<br>
>> h5dump/h5dump_ddl.c:1344 and then I was able to configure with<br>
>> "--download-hdf5". I am now able to run vec/ex10.c using HDF5 with success!<br>
>><br>
>> Thanks a lot :) (and double on the tar and feathers for people who use<br>
>> C++ comments in C code).<br>
>><br>
>> After some tinkering I am now able to produce 3D plots of scalar fields<br>
>> from my code, and this looks good in Visit and in Tec360 Ex. However, it<br>
>> only works for scalars where only a single DOF is associated to a DMDA.<br>
>> Vector valued fields don't work either. But I am able to save two<br>
>> separate scalar fields to the same HDF5 file, as long as both are the<br>
>> single DOF associated to a DMDA.<br>
>><br>
><br>
> It seems like these programs expect a different organization than we use for<br>
> multiple DOF. Do you know what they want?<br>
<br>
The Tec360 Manual says the following:<br>
"The HDF5 loader add-on allows you to import general HDF5 files into<br>
Tecplot 360. The loader provides a mechanism for importing generic data<br>
from multiple HDF5 datasets or groups. The HDF5 loader will load<br>
datasets within user selected groups, load one or more user selected<br>
datasets to one zone, load multiple user selected datasets to multiple<br>
zones, execute macros after data has been loaded, create implicit X, Y,<br>
and Z grid vectors as needed, sub-sample loaded data, and reference user<br>
selected vectors for X, Y, and Z grids. Datasets must be ordered data.<br>
The HDF5 library used is version 1.8.5."<br>
<br>
This did not leave me any wiser, but perhaps it means something to you.<br>
FYI, the error I get when trying to import vectors or multiple scalars<br>
is "rank N data not supported" where N >= 4.<br></blockquote><div><br></div><div>We add the DOF as another dimension, but clearly in 3D this means a 4D</div><div>structure, which Tec360 does not support, so they are looking for exactly</div>
<div>what you did with VecStrideScatter. That sounds like bad design on their</div><div>part to me.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
><br>
><br>
>> Also, if I call PetscViewerHDF5IncrementTimestep() the resulting HDF5<br>
>> files can no longer be visualized even for the scalars, both Tec360 and<br>
>> Visit give error messages.<br>
>><br>
><br>
> HDF5 is a generic format, and programs like Visit and Tec360 assume some<br>
> organization inside. For time we just add an array dimension, but they<br>
> might do<br>
> something else. I recommend looking at bin/pythonscripts/petsc_ge_xdmf.py,<br>
> which creates .xdmf to describe our HDF5 organization.<br>
<br>
Xdmf seems handy, and I would like to use this feature, but I'm not<br>
really sure how to. I tried running "petsc_ge_xdmf.py Myfile.h5" but I<br>
get the error below. Am I using the script wrong? Or perhaps it is<br>
assuming that the data is from a DMplex? I'm using DMDA.<br>
<br>
Traceback (most recent call last):<br>
File "./petsc_gen_xdmf.py", line 220, in <module><br>
generateXdmf(sys.argv[1])<br>
File "./petsc_gen_xdmf.py", line 194, in generateXdmf<br>
geom = h5['geometry']<br>
File "/usr/lib/python2.7/site-packages/h5py/_hl/group.py", line 153,<br>
in __getitem__<br>
oid = h5o.open(<a href="http://self.id" target="_blank">self.id</a>, self._e(name), lapl=self._lapl)<br>
File "h5o.pyx", line 183, in h5py.h5o.open (h5py/h5o.c:3844)<br>
KeyError: "Unable to open object (Object 'geometry' doesn't exist)"</blockquote><div><br></div><div>Yes, this is designed for unstructured grids. I just meant you could look at it</div><div>and modify. It pretty short.</div>
<div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
Åsmund<br>
<br>
</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener
</div></div>