Hi Maria,

You can also use kuibit, which knows how to read the various files and combine them.

Assuming `sim` is your SimDir, `sim.gridfunctions.xyz` is a dictionary-like object that contains all the grid functions in those files.

For instance, `sim.gridfunctions.xyz["rho"][0]` is going to be a `HierarchicalGridData` for your 3D rest mass density at iteration 0. This data structure contains all the information for the various refinement levels in the data. You can resample it to `UniformGridData` for visualization purposes.

Processing large 3D data with kuibit can be computationally intensive.

Gabriele

On Wed, Jun 15, 2022, 1:30 PM Roland Haas rhaas@illinois.edu wrote:

Hello all,

Chris' answer is absolutely correct.

The utilities are built by default by Simfactory and by doing `make sim-utils` using a non-simfactory build.

hdf5_merge is the tool to use to combine multiple HDF5 files, eg different variables or multiple segments of the same simulation.

It won't merge output files from multiple processes into a single file (so foo.xyz.file_0.h5 and foo.xyz.file_1.h5 cannot be merged but foo.xyz.file_0.h5 and bar.xyz.file_0.h5 can be merged).

If you need merge files foo.xyz.file_0.h5 and foo.xyz.file_1.h5 into foo.xyz.h5 then you can use the hdf5_slicer utility and its --out3d-cube option (hdf5_slicer --help gives some examples).

Yours, Roland

...

KIa ora Maria,

For me, there are hdf scripts located in Cactus/exe/<Build name>, such as hdf5_merge, which should do what you are after. These potentially may only be there for certain build options but someone more knowledgeable than me can probably expand on that.

Cheers,

Chris

[cid:8795d7d8-3669-4adf-905d-788d81a3ba8c]

[cid:3a28163e-f206-41a5-8619-e8b15edd91b0]

Dr Chris Stevens

Lecturer in Applied Mathematics

Rm 602, Jack Erskine building

School of Mathematics and Statistics

T: +64 3 369 0396 (Internal 90396)

University of Canterbury | Te Whare Wānanga o Waitaha

Private Bag 4800, Christchurch 8140, New Zealand

https://urldefense.com/v3/__http://www.chrisdoesmaths.com__;!!DZ3fjg!7WZG6jd...

...

<

https://urldefense.com/v3/__http://www.chrisdoesmaths.com/__;!!DZ3fjg!7WZG6j...

...

...

Director SCRI Ltd

https://urldefense.com/v3/__http://www.scri.co.nz__;!!DZ3fjg!7WZG6jdWvLk-xY5...

...

<

https://urldefense.com/v3/__http://www.scri.co.nz/__;!!DZ3fjg!7WZG6jdWvLk-xY...

...

...

---

From: users-bounces@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: 16 June 2022 08:02 To: Roland Haas rhaas@illinois.edu Cc: users@einsteintoolkit.org users@einsteintoolkit.org Subject: [Users] Combine multiple h5 files

You don't often get email from babiuc@marshall.edu. Learn why this is important<

https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;...

...

...

Hi,

I have a quick question: my output has a series of ....xyz.file_...h5 and I would like to look at them. Do I have to combine them? If yes, is there a way to combine them in one single file?

Maria

---

Maria C. Babiuc Hamilton, Ph.D. Professor, Department of Physics College of Science, Marshall University, 1 John Marshall Drive, Huntington, WV, 25755 Room S 257, Phone: (304)696-2754

-- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net. _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users