It is surprising to see how many such frameworks are available. I'd suggest that we create a wiki page that briefly describes them, and points to instructions for downloading and examples.
Incidentally, we are also developing such a framework here at Perimeter. The basic idea is to have a generic way of describing the data in a simulation, introducing concepts such as discretizations of a manifold, bases for the tangent space, tensor types, fields, etc. < https://github.com/eschnett/SimulationIO%3E. We (i.e. Jonah Miller) are now testing and benchmarking it against real-world data, developing a yt < http://yt-project.org%3E reader in the process.
The SimulationIO library is supposed to be used directly for writing and reading data from Cactus. Currently, that hasn't been implemented yet, and so there is a converter from Carpet output that either collects all the metadata (with external links to the original datasets) or creates a single output file. Obviously the file format is still based on HDF5 -- the main advantage is that the metadata are much easier to access and interpret than having to loop over the components and parsing their names.
I assume Jonah will describe this at the Einstein Toolkit.
-erik
On Tue, May 17, 2016 at 2:17 PM, Federico Guercilena < guercilena@th.physik.uni-frankfurt.de> wrote:
Hello,
I'd like to point out also my python library/script called "rugutils". This one started off inspired by David's scidata (and pygraph), but has developed into a set of tools to look in a quick and hassle-free way at Carpet data. It's written in python 3.5
https://bitbucket.org/fguercilena/rugutils https://docs.einsteintoolkit.org/et-docs/Analysis_and_post-processing
Federico
2016-05-17 19:44 GMT+02:00 Roland Haas rhaas@aei.mpg.de:
Hello Frank, Michael,
@Michael: both of what Frank or David describe should work. If you know how to compile the VisIt reader yourselv, you can also try the copy of CarpetHDF5 at https://bitbucket.org/rhaas80/carpethdf5 either the "multifile" branch (which is the default one that has all features) or the "for_VisIt" branch which has fewer features and is what I wanted at one point propose for inclusion in VisIt. Both will let you create .visit files listing your hdf5 files and VisIt will treat them a a single database. You will have to create .visit files that look like this:
!NBLOCKS 3 output-0000/rho.file_0.h5 output-0000/rho.file_1.h5 output-0000/rho.file_2.h5 output-0001/rho.file_0.h5 output-0001/rho.file_1.h5 output-0001/rho.file_2.h5
for a 3 process run and similar for runs with more processes. You can probably (I have not tested this) also list both rho and eps:
!NBLOCKS 3 output-0000/rho.file_0.h5 output-0000/rho.file_1.h5 output-0000/rho.file_2.h5 output-0000/eps.file_0.h5 output-0000/eps.file_1.h5 output-0000/eps.file_2.h5 output-0001/rho.file_0.h5 output-0001/rho.file_1.h5 output-0001/rho.file_2.h5 output-0001/eps.file_0.h5 output-0001/eps.file_1.h5 output-0001/eps.file_2.h5
possibly you have to set NBLOCKS to 6 (2*3) for this, though I have not tested this either.
@Frank:
Also, in case you have an old version of VisIt, you might need to enable the use of soft links in the VisIt Carpet reader. I am currently not sure if that change made it back upstream yet. The corresponding patch is:
Index: avtCarpetHDF5FileFormat.C
--- avtCarpetHDF5FileFormat.C (revision 57) +++ avtCarpetHDF5FileFormat.C (working copy) @@ -1044,7 +1044,7 @@ sprintf(fullname, "%s%s%s", rootname,
rootname[strlen(rootname)-1]=='/' ? "" : "/",member_name);
// we are interested in datasets only - skip anything else
- H5Gget_objinfo (group_id, member_name, 0, &object_info);
- H5Gget_objinfo (group_id, member_name, 1, &object_info); if (object_info.type != H5G_DATASET) { if (object_info.type == H5G_GROUP)
As far as I can tell this code change has not even made it into the ET maintained copy of the reader: https://svn.cactuscode.org/VizTools/CarpetHDF5/
where if this does not cause any other problems I think it would be welcome as well.
Yours, Roland
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