[yt-users] RadMC3DWriter and Ramses data

Marc Schartmann mschartmann at swin.edu.au
Mon Oct 5 19:01:41 PDT 2015


Thanks again. Now I am getting the following message:


Traceback (most recent call last):
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/runpy.py", line 151, in _run_module_as_main
    mod_name, loader, code, fname = _get_module_details(mod_name)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/runpy.py", line 101, in _get_module_details
    loader = get_loader(mod_name)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 464, in get_loader
    return find_loader(fullname)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 474, in find_loader
    for importer in iter_importers(fullname):
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 430, in iter_importers
    __import__(pkg)
  File "/home/mschartm/python_routines_galnuc/ramses_to_radmc3d.py", line 18, in <module>
    writer = RadMC3DWriter(ds)
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py", line 568, in RadMC3DWriter
    raise YTException(message=message, ds=ds)
yt.utilities.exceptions.YTException: Could not determine output style, Oct-Tree or Layer.


and after choosing the RadMC3DTreeWriter(ds) option "by hand", I get the following:

  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/runpy.py", line 151, in _run_module_as_main
    mod_name, loader, code, fname = _get_module_details(mod_name)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/runpy.py", line 101, in _get_module_details
    loader = get_loader(mod_name)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 464, in get_loader
    return find_loader(fullname)
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 474, in find_loader
    for importer in iter_importers(fullname):
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/pkgutil.py", line 430, in iter_importers
    __import__(pkg)
  File "/home/mschartm/python_routines_galnuc/ramses_to_radmc3d.py", line 18, in <module>
    writer = RadMC3DWriter(ds)
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py", line 565, in RadMC3DWriter
    return RadMC3DTreeWriter(ds)
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py", line 136, in __init__
    self.tree = ds.index.oct_handler.save_octree()
AttributeError: 'RAMSESIndex' object has no attribute 'oct_handler'

Best,

Marc

On 6 Oct 2015, at 12:11 pm, Andrew Myers <atmyers2 at gmail.com<mailto:atmyers2 at gmail.com>> wrote:

I did the merge and updated the pull request so that it has that bugfix. Now the revision hash is 0b2aab9<https://bitbucket.org/atmyers/yt/commits/0b2aab975b9e24b723bebc9df4fc9161b4342da9?at=yt>, but other than that you should be able to update to it using the same process as before.

Best,
Andrew

On Mon, Oct 5, 2015 at 5:31 PM, Nathan Goldbaum <nathan12343 at gmail.com<mailto:nathan12343 at gmail.com>> wrote:
This is an issue that was fixed a while ago, but after Andrew opened his pull request. Since you're updating to the PR head, you're updating to a version before the fix was applied.

You should be able to avoid the error by executing the clean.sh script at the root of the yt repository:

$ bash clean.sh

And then rebuilding yt:

$ python setup.py develop

You could also temporarily merge Andrew's pull request with the latest development version, but you might need to resolve some merge conflicts. Andrew could also do the merge and update his PR.

HTH,

Nathan

On Mon, Oct 5, 2015 at 7:26 PM, Marc Schartmann <mschartmann at swin.edu.au<mailto:mschartmann at swin.edu.au>> wrote:
Thanks!
Unfortunately, it didn’t work out for me.
After merging the PR locally into a new installation of yt (with the standard install script), I get the following
error already after importing yt.



Python 2.7.9 (default, Oct  6 2015, 10:48:03)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import yt
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/__init__.py", line 132, in <module>
    frontends = _frontend_container()
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/api.py", line 48, in __init__
    setattr(self, frontend, importlib.import_module(_mod))
  File "/home/mschartm/data/galnuc_ramses/yt/yt-x86_64/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/artio/api.py", line 17, in <module>
    from .data_structures import \
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/frontends/artio/data_structures.py", line 22, in <module>
    from ._artio_caller import \
  File "yt/geometry/particle_deposit.pxd", line 98, in init yt.frontends.artio._artio_caller (yt/frontends/artio/_artio_caller.c:27347)
ValueError: yt.geometry.particle_deposit.ParticleDepositOperation has the wrong size, try recompiling





On 6 Oct 2015, at 5:42 am, Andrew Myers <atmyers2 at gmail.com<mailto:atmyers2 at gmail.com>> wrote:

Hi Marc,

In that case, you should be able to try out the PR by doing:

1. Make sure yt is activated
2. cd $YT_DEST/src/yt-hg/
3. hg pull -r 7674674 https://bitbucket.org/atmyers/
4. hg update -C 7674674
5. python setup.py develop

The "-C" option to hg update will wipe any uncommited changes in your working copy, so be wary.

-Andrew

On Sun, Oct 4, 2015 at 10:57 PM, Marc Schartmann <mschartmann at swin.edu.au<mailto:mschartmann at swin.edu.au>> wrote:
Thanks a lot.
I installed the Dev branch via the install script.





On 5 Oct 2015, at 2:41 pm, Nathan Goldbaum <nathan12343 at gmail.com<mailto:nathan12343 at gmail.com>> wrote:

There's an open pull request that adds support for actree style outputs to the radmc3d exporter:

https://bitbucket.org/yt_analysis/yt/pull-requests/1688/wip-adding-support-for-octree-style-output

If you merge that pull request in locally you could try it out. If you share how you've set up your yt installation (install script? pip? from a mercurial checkout? anaconda?) one of us could give instructions on how to test out the PR.

On Sun, Oct 4, 2015 at 10:30 PM, Marc Schartmann <mschartmann at swin.edu.au<mailto:mschartmann at swin.edu.au>> wrote:
Dear all,

I am trying to export the density distribution from a RAMSES run to RADMC-3D using RadMC3DWriter.
Whereas the example with the “StarParticle” data set works perfectly, it fails for any RAMSES data
I tried (e.g. the “ramses_mhd_amr” one).

Below is the output, complaining about a missing attribute in the RAMSES frontend.
I am not a yt expert, any help with how to fix this would be appreciated.

Thanks a lot.

Best wishes,

Marc



>>> writer = RadMC3DWriter(ds)
yt : [INFO     ] 2015-10-05 14:20:04,236 Loading field plugins.
yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded angular_momentum (8 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded astro (15 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,237 Loaded cosmology (22 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,238 Loaded fluid (63 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,238 Loaded fluid_vector (95 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded geometric (111 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded local (111 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded magnetic_field (119 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded my_plugins (119 new fields)
yt : [INFO     ] 2015-10-05 14:20:04,239 Loaded species (121 new fields)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/lustre/projects/p054_swin/marc/galnuc_ramses/yt/yt-x86_64/src/yt-hg/yt/analysis_modules/radmc3d_export/RadMC3DInterface.py", line 148, in __init__
    sorted_grids = sorted(ds.index.grids, key=lambda x: x.Level)
AttributeError: 'RAMSESIndex' object has no attribute 'grids'




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