Hello Erik,

thank you for the information. I will give this a try.

Yours, Roland

Roland

Yes, such a converter exists; it is part of the SimulationIO package < https://github.com/eschnett/SimulationIO%3E, and is called "sio-convert-carpet-output". It should be built by the default makefile target.

You call it as "./sio-convert-carpet-output [--copy|--extlink]? <output file name> {<input file name>}*". There is one output file, and there can be multiple input files (e.g. one for each process). The "copy" option copies datasets, the "extlink" option creates external links to the original HDF5 files. The latter is faster and creates smaller files, but you obviously need to keep the originals around, and need to preserve their path (either their relative or absolute path, depending on what you specified on the command line).

I believe one of these two options is currently broken in the development version, sorry about this. I don't recall which.

-erik

On Fri, Sep 30, 2016 at 5:01 PM, Roland Haas rhaas@illinois.edu wrote:

...

Hello Jonah, Einstein Toolkit users,

I think you were working on a plugin to read S5 files into yt, right? Do you also have a converter tool to convert CarpetIOHDF5 3d output files (vertex centered, mesh refined) to S5 files? If only cell centering is supported this is also fine as or this project a slight inaccuracy does not matter.

I would be working with Nathan Goldbaum locally to read them into yt so once I have them in that format I will hopefully be home free.

Yours, Roland

-- 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.

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Hi Roland,

I think this could be caused by an incompatibility with Llama. Erik can confirm for the development version, but at least for the release version, SimulationIO does not correctly slurp up Llama data. We would like SimulationIO to know the coordinate system, but this hasn't been implemented for arbitrary coordinate maps.

Best,

Jonah

On 16-10-05 06:38 PM, Roland Haas wrote:

Hello Erik, Jonah,

this failed for me when calculating the active regions with:

Calculating active regions... discretization: iteration.0000350208-timelevel.0-map.000-level.00 region: {([0,0,0]:[89,89,50])} terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check: __n (which is 0) >= this->size() (which is 0) Aborted (core dumped)

The code that generated the HDF5 is the 2016_05 CarpetIOHDF5 3d output code for vertex centering and with mesh refinement and Llama.

Is any of those (not master code, Llama?) likely to cause this?

Yours, Roland

...

Roland

Yes, such a converter exists; it is part of the SimulationIO package < https://github.com/eschnett/SimulationIO%3E, and is called "sio-convert-carpet-output". It should be built by the default makefile target.

You call it as "./sio-convert-carpet-output [--copy|--extlink]? <output file name> {<input file name>}*". There is one output file, and there can be multiple input files (e.g. one for each process). The "copy" option copies datasets, the "extlink" option creates external links to the original HDF5 files. The latter is faster and creates smaller files, but you obviously need to keep the originals around, and need to preserve their path (either their relative or absolute path, depending on what you specified on the command line).

I believe one of these two options is currently broken in the development version, sorry about this. I don't recall which.

-erik

On Fri, Sep 30, 2016 at 5:01 PM, Roland Haas rhaas@illinois.edu wrote:

...

Hello Jonah, Einstein Toolkit users,

I think you were working on a plugin to read S5 files into yt, right? Do you also have a converter tool to convert CarpetIOHDF5 3d output files (vertex centered, mesh refined) to S5 files? If only cell centering is supported this is also fine as or this project a slight inaccuracy does not matter.

I would be working with Nathan Goldbaum locally to read them into yt so once I have them in that format I will hopefully be home free.

Yours, Roland

-- 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.

---

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Hi Roland,

Here are build and use instructions for SimulationIO and the SimulationIO converter. You can find much of the same information in the slides for my presentation at the ET workshop:

https://github.com/Yurlungur/simulationio-and-yt

Let me know if you have any trouble.

Best,

Jonah

To build the release version of SimulationIO, use my fork of Erik's repo:

https://github.com/Yurlungur/SimulationIO/tree/release-0.1

And the instructions are here:

https://github.com/Yurlungur/SimulationIO/blob/release-0.1/README.md

This installs the SimulationIO reader and the python API. It also adds the utilities sio-convert-carpet-output and sio-list, which you can use to generate and look at SimulationIO files.

The version of yt with a working SimulationIO frontend is:

https://bitbucket.org/Yurlungur/yt-simulationio

To use it:

hg clone ssh://hg@bitbucket.org/Yurlungur/yt-simulationio

cd yt-simulationio

hg update simulationio

python setup.py install

(add --user or --prefix=path or whatever you prefer)

Then you can load simulationio files by

import yt

ds = yt.load(filename,configuration=configuration)

where configuration is a name for the time level and timestep in the SimulationIO file. You may also need to specify that there are no ghost zones, etc.

On 16-10-05 06:46 PM, Roland Haas wrote:

Hello Erik, Jonah,

yes, Llama seems involved. If I use only the data for the Cartesian grid it aborts with a different error:

opening dataset WEYLSCAL4::Psi4r it=357120 tl=0 m=0 rl=5 c=6... field name: WEYLSCAL4::Psi4r tensor rank: 0 tensor type: Scalar3D tensor indices: [] iteration: 357120 time level: 0 map: 0 refinement level: 5 component: 6 sio-convert-carpet-output: convert-carpet-output.cpp:612: main(int, char**)::<lambda(const H5::Group&, const string&, const H5L_info_t*)>: Assertion `loc == val' failed. Aborted (core dumped)

Yours, Roland

...

Roland

Yes, such a converter exists; it is part of the SimulationIO package < https://github.com/eschnett/SimulationIO%3E, and is called "sio-convert-carpet-output". It should be built by the default makefile target.

You call it as "./sio-convert-carpet-output [--copy|--extlink]? <output file name> {<input file name>}*". There is one output file, and there can be multiple input files (e.g. one for each process). The "copy" option copies datasets, the "extlink" option creates external links to the original HDF5 files. The latter is faster and creates smaller files, but you obviously need to keep the originals around, and need to preserve their path (either their relative or absolute path, depending on what you specified on the command line).

I believe one of these two options is currently broken in the development version, sorry about this. I don't recall which.

-erik

On Fri, Sep 30, 2016 at 5:01 PM, Roland Haas rhaas@illinois.edu wrote:

...

Hello Jonah, Einstein Toolkit users,

I think you were working on a plugin to read S5 files into yt, right? Do you also have a converter tool to convert CarpetIOHDF5 3d output files (vertex centered, mesh refined) to S5 files? If only cell centering is supported this is also fine as or this project a slight inaccuracy does not matter.

I would be working with Nathan Goldbaum locally to read them into yt so once I have them in that format I will hopefully be home free.

Yours, Roland

-- 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

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Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users