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