analyze flash data with uniform grid
Hi all, Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid? Thanks for your care and consideration. Best wishes, Suoqing
Hi Suoqing, On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update". Thanks, Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Matt, Thanks for your prompt response! I'm not quite sure whether my update is successful or not, but it shows: ---------------------------------------------------------------------------- yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental The current version of the code is: --- 2ace6373d8a3+ (yt) tip --- This installation CAN be automatically updated. Reading configuration from /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc searching for changes no changes found Can't rebuild modules by myself. You will have to do this yourself. Here's a sample commands: $ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg $ hg up $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop Updated successfully. ---------------------------------------------------------------------------- And I've also rebuilt the modules as what the sample tells. ---------------------------------------------------------------------------- (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ hg up 0 files updated, 0 files merged, 0 files removed, 0 files unresolved (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib running develop running build_scripts running egg_info running build_src build_src building py_modules sources building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources building extension "yt.frontends.ramses._ramses_reader" sources building extension "yt.utilities.delaunay._delaunay" sources building extension "yt.utilities.spatial.ckdtree" sources building extension "yt.utilities.spatial._distance_wrap" sources building extension "yt.utilities.lib.CICDeposit" sources building extension "yt.utilities.lib.ContourFinding" sources building extension "yt.utilities.lib.DepthFirstOctree" sources building extension "yt.utilities.lib.fortran_reader" sources building extension "yt.utilities.lib.freetype_writer" sources building extension "yt.utilities.lib.geometry_utils" sources building extension "yt.utilities.lib.Interpolators" sources building extension "yt.utilities.lib.marching_cubes" sources building extension "yt.utilities.lib.misc_utilities" sources building extension "yt.utilities.lib.Octree" sources building extension "yt.utilities.lib.png_writer" sources building extension "yt.utilities.lib.PointsInVolume" sources building extension "yt.utilities.lib.QuadTree" sources building extension "yt.utilities.lib.RayIntegrators" sources building extension "yt.utilities.lib.VolumeIntegrator" sources building extension "yt.utilities.lib.grid_traversal" sources building extension "yt.utilities.data_point_utilities" sources building extension "yt.utilities.hdf5_light_reader" sources building extension "yt.utilities.libconfig_wrapper" sources building extension "yt.visualization._MPL" sources building data_files sources build_src: building npy-pkg config files writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .) yt 2.4dev is already the active version in easy-install.pth Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg Processing dependencies for yt==2.4dev Finished processing dependencies for yt==2.4dev ---------------------------------------------------------------------------- But the file-load error still remains. Best wishes, Suoqing 在 2012-7-28，下午3:35，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update".
Thanks,
Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Suoqing, What is the current output of "yt instinfo"? It should read 2ace6373d8a3 . If it doesn't, you'll need to manually pull again: hg pull https://bitbucket.org/yt_analysis/yt hg up python2.7 setup.py develop -Matt On Sat, Jul 28, 2012 at 3:52 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
Thanks for your prompt response!
I'm not quite sure whether my update is successful or not, but it shows:
---------------------------------------------------------------------------- yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Reading configuration from /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc searching for changes no changes found Can't rebuild modules by myself. You will have to do this yourself. Here's a sample commands:
$ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg $ hg up $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop Updated successfully. ----------------------------------------------------------------------------
And I've also rebuilt the modules as what the sample tells.
---------------------------------------------------------------------------- (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ hg up 0 files updated, 0 files merged, 0 files removed, 0 files unresolved (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib running develop running build_scripts running egg_info running build_src build_src building py_modules sources building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources building extension "yt.frontends.ramses._ramses_reader" sources building extension "yt.utilities.delaunay._delaunay" sources building extension "yt.utilities.spatial.ckdtree" sources building extension "yt.utilities.spatial._distance_wrap" sources building extension "yt.utilities.lib.CICDeposit" sources building extension "yt.utilities.lib.ContourFinding" sources building extension "yt.utilities.lib.DepthFirstOctree" sources building extension "yt.utilities.lib.fortran_reader" sources building extension "yt.utilities.lib.freetype_writer" sources building extension "yt.utilities.lib.geometry_utils" sources building extension "yt.utilities.lib.Interpolators" sources building extension "yt.utilities.lib.marching_cubes" sources building extension "yt.utilities.lib.misc_utilities" sources building extension "yt.utilities.lib.Octree" sources building extension "yt.utilities.lib.png_writer" sources building extension "yt.utilities.lib.PointsInVolume" sources building extension "yt.utilities.lib.QuadTree" sources building extension "yt.utilities.lib.RayIntegrators" sources building extension "yt.utilities.lib.VolumeIntegrator" sources building extension "yt.utilities.lib.grid_traversal" sources building extension "yt.utilities.data_point_utilities" sources building extension "yt.utilities.hdf5_light_reader" sources building extension "yt.utilities.libconfig_wrapper" sources building extension "yt.visualization._MPL" sources building data_files sources build_src: building npy-pkg config files writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .) yt 2.4dev is already the active version in easy-install.pth Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin
Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg Processing dependencies for yt==2.4dev Finished processing dependencies for yt==2.4dev ----------------------------------------------------------------------------
But the file-load error still remains.
Best wishes, Suoqing
在 2012-7-28，下午3:35，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update".
Thanks,
Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Matt, It is: yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental The current version of the code is: --- 2ace6373d8a3+ (yt) tip --- This installation CAN be automatically updated. Updated successfully. Best wishes, Suoqing 在 2012-7-28，下午3:54，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
What is the current output of "yt instinfo"? It should read 2ace6373d8a3 . If it doesn't, you'll need to manually pull again:
hg pull https://bitbucket.org/yt_analysis/yt hg up python2.7 setup.py develop
-Matt
On Sat, Jul 28, 2012 at 3:52 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
Thanks for your prompt response!
I'm not quite sure whether my update is successful or not, but it shows:
---------------------------------------------------------------------------- yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Reading configuration from /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc searching for changes no changes found Can't rebuild modules by myself. You will have to do this yourself. Here's a sample commands:
$ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg $ hg up $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop Updated successfully. ----------------------------------------------------------------------------
And I've also rebuilt the modules as what the sample tells.
---------------------------------------------------------------------------- (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ hg up 0 files updated, 0 files merged, 0 files removed, 0 files unresolved (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib running develop running build_scripts running egg_info running build_src build_src building py_modules sources building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources building extension "yt.frontends.ramses._ramses_reader" sources building extension "yt.utilities.delaunay._delaunay" sources building extension "yt.utilities.spatial.ckdtree" sources building extension "yt.utilities.spatial._distance_wrap" sources building extension "yt.utilities.lib.CICDeposit" sources building extension "yt.utilities.lib.ContourFinding" sources building extension "yt.utilities.lib.DepthFirstOctree" sources building extension "yt.utilities.lib.fortran_reader" sources building extension "yt.utilities.lib.freetype_writer" sources building extension "yt.utilities.lib.geometry_utils" sources building extension "yt.utilities.lib.Interpolators" sources building extension "yt.utilities.lib.marching_cubes" sources building extension "yt.utilities.lib.misc_utilities" sources building extension "yt.utilities.lib.Octree" sources building extension "yt.utilities.lib.png_writer" sources building extension "yt.utilities.lib.PointsInVolume" sources building extension "yt.utilities.lib.QuadTree" sources building extension "yt.utilities.lib.RayIntegrators" sources building extension "yt.utilities.lib.VolumeIntegrator" sources building extension "yt.utilities.lib.grid_traversal" sources building extension "yt.utilities.data_point_utilities" sources building extension "yt.utilities.hdf5_light_reader" sources building extension "yt.utilities.libconfig_wrapper" sources building extension "yt.visualization._MPL" sources building data_files sources build_src: building npy-pkg config files writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .) yt 2.4dev is already the active version in easy-install.pth Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin
Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg Processing dependencies for yt==2.4dev Finished processing dependencies for yt==2.4dev ----------------------------------------------------------------------------
But the file-load error still remains.
Best wishes, Suoqing
在 2012-7-28，下午3:35，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
> pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update".
Thanks,
Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Suoqing, The fix I pushed changed line 377 in yt/frontends/flash/data_structures.py from its original value (seen in your traceback) of: self.min_level = self.parameters["lrefine_min"] -1 to: self.min_level = self.parameters.get("lrefine_min", 1) - 1 If your traceback still indicates that the old line is present, something strange is going on. I note that you've modified the source (the "+" at the end of the hash) -- is it possible that the change you've made has somehow interfered? I have checked that my fix should work in the case of the parameter "lrefine_min" not existing. What's the output of: grep lrefine_min /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py thanks, -Matt On Sat, Jul 28, 2012 at 3:57 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
It is:
yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Suoqing
在 2012-7-28，下午3:54，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
What is the current output of "yt instinfo"? It should read 2ace6373d8a3 . If it doesn't, you'll need to manually pull again:
hg pull https://bitbucket.org/yt_analysis/yt hg up python2.7 setup.py develop
-Matt
On Sat, Jul 28, 2012 at 3:52 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
Thanks for your prompt response!
I'm not quite sure whether my update is successful or not, but it shows:
---------------------------------------------------------------------------- yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Reading configuration from /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc searching for changes no changes found Can't rebuild modules by myself. You will have to do this yourself. Here's a sample commands:
$ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg $ hg up $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop Updated successfully. ----------------------------------------------------------------------------
And I've also rebuilt the modules as what the sample tells.
---------------------------------------------------------------------------- (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ hg up 0 files updated, 0 files merged, 0 files removed, 0 files unresolved (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib running develop running build_scripts running egg_info running build_src build_src building py_modules sources building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources building extension "yt.frontends.ramses._ramses_reader" sources building extension "yt.utilities.delaunay._delaunay" sources building extension "yt.utilities.spatial.ckdtree" sources building extension "yt.utilities.spatial._distance_wrap" sources building extension "yt.utilities.lib.CICDeposit" sources building extension "yt.utilities.lib.ContourFinding" sources building extension "yt.utilities.lib.DepthFirstOctree" sources building extension "yt.utilities.lib.fortran_reader" sources building extension "yt.utilities.lib.freetype_writer" sources building extension "yt.utilities.lib.geometry_utils" sources building extension "yt.utilities.lib.Interpolators" sources building extension "yt.utilities.lib.marching_cubes" sources building extension "yt.utilities.lib.misc_utilities" sources building extension "yt.utilities.lib.Octree" sources building extension "yt.utilities.lib.png_writer" sources building extension "yt.utilities.lib.PointsInVolume" sources building extension "yt.utilities.lib.QuadTree" sources building extension "yt.utilities.lib.RayIntegrators" sources building extension "yt.utilities.lib.VolumeIntegrator" sources building extension "yt.utilities.lib.grid_traversal" sources building extension "yt.utilities.data_point_utilities" sources building extension "yt.utilities.hdf5_light_reader" sources building extension "yt.utilities.libconfig_wrapper" sources building extension "yt.visualization._MPL" sources building data_files sources build_src: building npy-pkg config files writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .) yt 2.4dev is already the active version in easy-install.pth Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin
Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg Processing dependencies for yt==2.4dev Finished processing dependencies for yt==2.4dev ----------------------------------------------------------------------------
But the file-load error still remains.
Best wishes, Suoqing
在 2012-7-28，下午3:35，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
>> pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update".
Thanks,
Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi Matt, I'm grateful for your help.
The fix I pushed changed line 377 in
Yes, after I modified this by hand, it works well. Thanks!
I note that you've modified the source (the "+" at the end of the hash) -- is it possible that the change you've made has somehow interfered?
I recall that before I've applied a patch provided by Nathan on the same file, which might lead to this strange things. Thanks again! Best wishes, Suoqing 在 2012-7-28，下午4:01，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
The fix I pushed changed line 377 in yt/frontends/flash/data_structures.py from its original value (seen in your traceback) of:
self.min_level = self.parameters["lrefine_min"] -1
to:
self.min_level = self.parameters.get("lrefine_min", 1) - 1
If your traceback still indicates that the old line is present, something strange is going on. I note that you've modified the source (the "+" at the end of the hash) -- is it possible that the change you've made has somehow interfered?
I have checked that my fix should work in the case of the parameter "lrefine_min" not existing. What's the output of:
grep lrefine_min /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py
thanks,
-Matt
On Sat, Jul 28, 2012 at 3:57 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
It is:
yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Updated successfully.
Best wishes, Suoqing
在 2012-7-28，下午3:54，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
What is the current output of "yt instinfo"? It should read 2ace6373d8a3 . If it doesn't, you'll need to manually pull again:
hg pull https://bitbucket.org/yt_analysis/yt hg up python2.7 setup.py develop
-Matt
On Sat, Jul 28, 2012 at 3:52 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi Matt,
Thanks for your prompt response!
I'm not quite sure whether my update is successful or not, but it shows:
---------------------------------------------------------------------------- yt module located at: /aphelion/jisuoqing/yt-x86_64/src/yt-hg The supplemental repositories are located at: /aphelion/jisuoqing/yt-x86_64/src/yt-supplemental
The current version of the code is:
--- 2ace6373d8a3+ (yt) tip ---
This installation CAN be automatically updated. Reading configuration from /aphelion/jisuoqing/yt-x86_64/src/yt-hg/.hg/hgrc searching for changes no changes found Can't rebuild modules by myself. You will have to do this yourself. Here's a sample commands:
$ cd /aphelion/jisuoqing/yt-x86_64/src/yt-hg $ hg up $ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop Updated successfully. ----------------------------------------------------------------------------
And I've also rebuilt the modules as what the sample tells.
---------------------------------------------------------------------------- (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ hg up 0 files updated, 0 files merged, 0 files removed, 0 files unresolved (yt-x86_64)[jisuoqing@hpcmanage yt-hg]$ /aphelion/jisuoqing/yt-x86_64/bin/python2.7 setup.py develop PNG_LOCATION: png.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib FTYPE_LOCATION: freetype.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib HDF5_LOCATION: hdf5.cfg: /aphelion/jisuoqing/yt-x86_64/include, /aphelion/jisuoqing/yt-x86_64/lib running develop running build_scripts running egg_info running build_src build_src building py_modules sources building extension "yt.analysis_modules.halo_finding.fof.EnzoFOF" sources building extension "yt.analysis_modules.halo_finding.hop.EnzoHop" sources building extension "yt.frontends.ramses._ramses_reader" sources building extension "yt.utilities.delaunay._delaunay" sources building extension "yt.utilities.spatial.ckdtree" sources building extension "yt.utilities.spatial._distance_wrap" sources building extension "yt.utilities.lib.CICDeposit" sources building extension "yt.utilities.lib.ContourFinding" sources building extension "yt.utilities.lib.DepthFirstOctree" sources building extension "yt.utilities.lib.fortran_reader" sources building extension "yt.utilities.lib.freetype_writer" sources building extension "yt.utilities.lib.geometry_utils" sources building extension "yt.utilities.lib.Interpolators" sources building extension "yt.utilities.lib.marching_cubes" sources building extension "yt.utilities.lib.misc_utilities" sources building extension "yt.utilities.lib.Octree" sources building extension "yt.utilities.lib.png_writer" sources building extension "yt.utilities.lib.PointsInVolume" sources building extension "yt.utilities.lib.QuadTree" sources building extension "yt.utilities.lib.RayIntegrators" sources building extension "yt.utilities.lib.VolumeIntegrator" sources building extension "yt.utilities.lib.grid_traversal" sources building extension "yt.utilities.data_point_utilities" sources building extension "yt.utilities.hdf5_light_reader" sources building extension "yt.utilities.libconfig_wrapper" sources building extension "yt.visualization._MPL" sources building data_files sources build_src: building npy-pkg config files writing yt.egg-info/PKG-INFO writing top-level names to yt.egg-info/top_level.txt writing dependency_links to yt.egg-info/dependency_links.txt writing entry points to yt.egg-info/entry_points.txt reading manifest file 'yt.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'yt.egg-info/SOURCES.txt' running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext customize UnixCCompiler customize UnixCCompiler using build_ext running scons Creating /aphelion/jisuoqing/yt-x86_64/lib/python2.7/site-packages/yt.egg-link (link to .) yt 2.4dev is already the active version in easy-install.pth Installing yt script to /aphelion/jisuoqing/yt-x86_64/bin Installing pyro_queue.py script to /aphelion/jisuoqing/yt-x86_64/bin Installing iyt script to /aphelion/jisuoqing/yt-x86_64/bin Installing yt_lodgeit.py script to /aphelion/jisuoqing/yt-x86_64/bin
Installed /aphelion/jisuoqing/yt-x86_64/src/yt-hg Processing dependencies for yt==2.4dev Finished processing dependencies for yt==2.4dev ----------------------------------------------------------------------------
But the file-load error still remains.
Best wishes, Suoqing
在 2012-7-28，下午3:35，Matthew Turk <matthewturk@gmail.com> 写道：
Hi Suoqing,
On Sat, Jul 28, 2012 at 3:26 PM, Ji Suoqing <jisuoqing@gmail.com> wrote:
Hi all,
Currently I'm trying to analyze Flash4-beta data with YT, and for the data file uniform grid rather than AMR is used. I always get such error when I load the file:
>>> pf=load('relax_hdf5_chk_0000') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/convenience.py", line 71, in load return output_type_registry[candidates[0]](*args, **kwargs) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 214, in __init__ StaticOutput.__init__(self, filename, data_style) File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/data_objects/static_output.py", line 92, in __init__ self._parse_parameter_file() File "/aphelion/jisuoqing/yt-x86_64/src/yt-hg/yt/frontends/flash/data_structures.py", line 377, in _parse_parameter_file self.min_level = self.parameters["lrefine_min"] -1 KeyError: 'lrefine_min'
So, does YT provides a way to deal with the uniform grid?
If FLASH4 either doesn't set that parameter anymore or had conditional parameter setting, that will need to be taken into account in the future. I've checked and it looks like this parameter is optional (it will default to L0) and so I've added a check for it. If it's not present, it sets it to be the most lenient. This was done in the current development branch, in changeset 2ace6373d8a3, so you will need to update with "yt update".
Thanks,
Matt
Thanks for your care and consideration.
Best wishes, Suoqing _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
participants (2)
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Ji Suoqing -
Matthew Turk