HDF5 TypeError when writing LightRay
Hi all, I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error. TypeError: Object dtype dtype('O') has no native HDF5 equivalent This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation. I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error. AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str) When using python 2.7 the error is the same but with 'unicode' instead of 'str'. Any help would be greatly appreciated. Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
Hi Joseph, I believe you're hitting this issue: https://bitbucket.org/yt_analysis/yt/issues/1330 Which was fixed here: https://bitbucket.org/yt_analysis/yt/pull-requests/2541 We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds: http://yt-project.org/docs/dev/installing.html#nightly-conda-builds If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)? Best, Nathan Goldbaum On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson <jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Nathan, That issue is very likely the problem that I was having with the stable version. I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets. The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant. The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue? Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ 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
You can use the yt curldrop to share the dataset: https://docs.hub.yt/services.html#curldrop But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion. -Nathan On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson <jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ 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
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Nathan, I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error AttributeError: 'str' object has no attribute 'astype' This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716. Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ 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
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Hi Joseph, I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page. -Nathan On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson <jmtomlinson95@gmail.com> wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ 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
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It looks like the failure comes just from doing yt.load with that file. This is, indeed, LightRay related. I can reproduce it here and can look into it. I'm in a place with very unreliable internet, but I'll try to get to this as soon as I can. On Mon, Apr 24, 2017 at 3:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
_______________________________________________ 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
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Nathan, To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/show/7131/. Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Hi all,
I am trying to use the single dataset LightRay module but I am running into an issue. Whenever I use the data_filename parameter, which I believe is necessary for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit lost as to what to do. I am running the latest stable version on anaconda and have tried both h5py 2.7 and 2.6. The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype' from line 326 in _restore_light_ray_solution self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of 'str'.
Any help would be greatly appreciated.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
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Hmm, so this light ray dataset you've shared with me is missing a lot of metadata. Is there any chance you can share the original dataset with me so I can debug the light ray creation process as well? You should be able to use the curldrop to upload the dataset as a tarball. On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson <jmtomlinson95@gmail.com> wrote:
Nathan,
To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/show/7131/.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
Hi Joseph,
I believe you're hitting this issue:
https://bitbucket.org/yt_analysis/yt/issues/1330
Which was fixed here:
https://bitbucket.org/yt_analysis/yt/pull-requests/2541
We haven't had a stable release since that was fixed. If you're running yt from a stable release, can you try installing the development version from source? If you're using conda you can also use the nightly binary builds:
http://yt-project.org/docs/dev/installing.html#nightly-conda-builds
If you are running a recent development version then Britton's fix might need to be eloborated upon. If so, can you create a self-contained, runnable example script that triggers the issue you're seeing (preferably making use of one of the public datasets on yt-project.org/data)?
Best,
Nathan Goldbaum
On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
> Hi all, > > I am trying to use the single dataset LightRay module but I am > running into an issue. > Whenever I use the data_filename parameter, which I believe is > necessary for use with AbsorptionSpectrum, I receive the following error. > > TypeError: Object dtype dtype('O') has no native HDF5 equivalent > > This error does not occur when I run the cookbook example so I am a > bit lost as to what to do. > I am running the latest stable version on anaconda and have tried > both h5py 2.7 and 2.6. > The simulation is a cosmological Enzo simulation. > > I have also tried using the nightly dev build which changes the > error from being on write to being on load with the following error. > > AttributeError: 'str' object has no attribute 'astype' > from line 326 in _restore_light_ray_solution > self.parameters[ksp3] = self.parameters[ksp3].astype(str) > > When using python 2.7 the error is the same but with 'unicode' > instead of 'str'. > > Any help would be greatly appreciated. > > Thanks, > Joe Tomlinson > Senior Undergraduate > Department of Physics, Drexel University > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >
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Hi Joseph, Nathan, The problem seems to be one of two things. First, this is a light ray made by a single dataset, and so an hdf5 attribute that is normally expected to be a list of strings was a single single. Second, this attribute, which records the unique_identifiers for the datasets used to make the light ray is "[None]", so whatever dataset this was is missing a unique_identifier attribute. Fixing the first issue will probably take care of it, but it's probably worth making sure that this dataset type gets unique_attributes made as well. What type of dataset was used to make this light ray? Britton On Mon, Apr 24, 2017 at 4:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hmm, so this light ray dataset you've shared with me is missing a lot of metadata. Is there any chance you can share the original dataset with me so I can debug the light ray creation process as well? You should be able to use the curldrop to upload the dataset as a tarball.
On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Nathan,
To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/show/7131/.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
That issue is very likely the problem that I was having with the stable version.
I tried to recreate the issue I am having with the dev version but the issue does not occur for any of the public enzo datasets.
The error occurs after the ray data has been saved and it reloads it . The saved file is able to be read in h5py and seems correct. A few layers down the error occurs in _parse_parameter_file() and I think this may be the difference between the data I was given and the public sets. I can't really see the difference between the two myself. I've uploaded the file here http://paste.yt-project.org/show/7129/ if it becomes relevant.
The script to generate the error is extremely basic, I didn't upload it because its just two lines, making the LightRay then calling make_light_ray. The error should be reproducible by simply trying to load the resultant hdf5 file, is there somewhere you would prefer me to upload it? It's not too large, less than 1MB. Is there anything else I could provide to help diagnose the issue?
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> Hi Joseph, > > I believe you're hitting this issue: > > https://bitbucket.org/yt_analysis/yt/issues/1330 > > Which was fixed here: > > https://bitbucket.org/yt_analysis/yt/pull-requests/2541 > > We haven't had a stable release since that was fixed. If you're > running yt from a stable release, can you try installing the development > version from source? If you're using conda you can also use the nightly > binary builds: > > http://yt-project.org/docs/dev/installing.html#nightly-conda-builds > > If you are running a recent development version then Britton's fix > might need to be eloborated upon. If so, can you create a self-contained, > runnable example script that triggers the issue you're seeing (preferably > making use of one of the public datasets on yt-project.org/data)? > > Best, > > Nathan Goldbaum > > On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < > jmtomlinson95@gmail.com> wrote: > >> Hi all, >> >> I am trying to use the single dataset LightRay module but I am >> running into an issue. >> Whenever I use the data_filename parameter, which I believe is >> necessary for use with AbsorptionSpectrum, I receive the following error. >> >> TypeError: Object dtype dtype('O') has no native HDF5 equivalent >> >> This error does not occur when I run the cookbook example so I am a >> bit lost as to what to do. >> I am running the latest stable version on anaconda and have tried >> both h5py 2.7 and 2.6. >> The simulation is a cosmological Enzo simulation. >> >> I have also tried using the nightly dev build which changes the >> error from being on write to being on load with the following error. >> >> AttributeError: 'str' object has no attribute 'astype' >> from line 326 in _restore_light_ray_solution >> self.parameters[ksp3] = self.parameters[ksp3].astype(str) >> >> When using python 2.7 the error is the same but with 'unicode' >> instead of 'str'. >> >> Any help would be greatly appreciated. >> >> Thanks, >> Joe Tomlinson >> Senior Undergraduate >> Department of Physics, Drexel University >> >> _______________________________________________ >> 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 > >
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Nathan, Britton The dataset was made using a cosmological enzo simulation. I have uploaded it here use.yt/upload/ad078d12 be aware the tarball is around 5GB. Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University On Mon, Apr 24, 2017 at 5:15 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Joseph, Nathan,
The problem seems to be one of two things. First, this is a light ray made by a single dataset, and so an hdf5 attribute that is normally expected to be a list of strings was a single single. Second, this attribute, which records the unique_identifiers for the datasets used to make the light ray is "[None]", so whatever dataset this was is missing a unique_identifier attribute. Fixing the first issue will probably take care of it, but it's probably worth making sure that this dataset type gets unique_attributes made as well.
What type of dataset was used to make this light ray?
Britton
On Mon, Apr 24, 2017 at 4:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hmm, so this light ray dataset you've shared with me is missing a lot of metadata. Is there any chance you can share the original dataset with me so I can debug the light ray creation process as well? You should be able to use the curldrop to upload the dataset as a tarball.
On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/show/7131/.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
You can use the yt curldrop to share the dataset:
https://docs.hub.yt/services.html#curldrop
But if it's as you said and the issue is fixed already (e.g. you do not have any issues when you build yt from latest version on the "yt" branch in the mercurial repository) then there's no need to go further, since the issue is fixed already. We will hopefully be able to do a yt 3.4 release soon after moving development to github, so that will get this fix out there in a more easily shareable fashion.
-Nathan
On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
> Nathan, > > That issue is very likely the problem that I was having with the > stable version. > > I tried to recreate the issue I am having with the dev version but > the issue does not occur for any of the public enzo datasets. > > The error occurs after the ray data has been saved and it reloads it > . The saved file is able to be read in h5py and seems correct. > A few layers down the error occurs in _parse_parameter_file() and I > think this may be the difference between the data I was given and the > public sets. > I can't really see the difference between the two myself. I've > uploaded the file here http://paste.yt-project.org/show/7129/ if it > becomes relevant. > > The script to generate the error is extremely basic, I didn't upload > it because its just two lines, making the LightRay then calling > make_light_ray. > The error should be reproducible by simply trying to load the > resultant hdf5 file, is there somewhere you would prefer me to upload it? > It's not too large, less than 1MB. > Is there anything else I could provide to help diagnose the issue? > > Thanks, > Joe Tomlinson > Senior Undergraduate > Department of Physics, Drexel University > > On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> Hi Joseph, >> >> I believe you're hitting this issue: >> >> https://bitbucket.org/yt_analysis/yt/issues/1330 >> >> Which was fixed here: >> >> https://bitbucket.org/yt_analysis/yt/pull-requests/2541 >> >> We haven't had a stable release since that was fixed. If you're >> running yt from a stable release, can you try installing the development >> version from source? If you're using conda you can also use the nightly >> binary builds: >> >> http://yt-project.org/docs/dev/installing.html#nightly-conda-builds >> >> If you are running a recent development version then Britton's fix >> might need to be eloborated upon. If so, can you create a self-contained, >> runnable example script that triggers the issue you're seeing (preferably >> making use of one of the public datasets on yt-project.org/data)? >> >> Best, >> >> Nathan Goldbaum >> >> On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < >> jmtomlinson95@gmail.com> wrote: >> >>> Hi all, >>> >>> I am trying to use the single dataset LightRay module but I am >>> running into an issue. >>> Whenever I use the data_filename parameter, which I believe is >>> necessary for use with AbsorptionSpectrum, I receive the following error. >>> >>> TypeError: Object dtype dtype('O') has no native HDF5 equivalent >>> >>> This error does not occur when I run the cookbook example so I am >>> a bit lost as to what to do. >>> I am running the latest stable version on anaconda and have tried >>> both h5py 2.7 and 2.6. >>> The simulation is a cosmological Enzo simulation. >>> >>> I have also tried using the nightly dev build which changes the >>> error from being on write to being on load with the following error. >>> >>> AttributeError: 'str' object has no attribute 'astype' >>> from line 326 in _restore_light_ray_solution >>> self.parameters[ksp3] = self.parameters[ksp3].astype(str) >>> >>> When using python 2.7 the error is the same but with 'unicode' >>> instead of 'str'. >>> >>> Any help would be greatly appreciated. >>> >>> Thanks, >>> Joe Tomlinson >>> Senior Undergraduate >>> Department of Physics, Drexel University >>> >>> _______________________________________________ >>> 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 > >
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Hi Joseph, Thanks for sharing your dataset, that made it much easier to see what was going wrong. I've issued a pull request here that should fix things: https://bitbucket.org/yt_analysis/yt/pull-requests/2589 The reason we hadn't seen this before is that you are working with a somewhat peculiar Enzo output that doesn't contain any unique identifier metadata. This metadata has been in the Enzo output format for several years now, so I guess this is a somewhat older dataset? In any case it was triggering a bug in yt that was causing ds.unique_identifier to get set to None, which then triggered another bug in the light ray saving machinery when it was passed such a strange unique identifier. I think I've fixed both issues. It would be great if you could give it a test. I'm happy to help out if you have questions about how to do that. -Nathan On Mon, Apr 24, 2017 at 4:20 PM, Joseph Tomlinson <jmtomlinson95@gmail.com> wrote:
Nathan, Britton
The dataset was made using a cosmological enzo simulation. I have uploaded it here use.yt/upload/ad078d12 be aware the tarball is around 5GB.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 5:15 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Joseph, Nathan,
The problem seems to be one of two things. First, this is a light ray made by a single dataset, and so an hdf5 attribute that is normally expected to be a list of strings was a single single. Second, this attribute, which records the unique_identifiers for the datasets used to make the light ray is "[None]", so whatever dataset this was is missing a unique_identifier attribute. Fixing the first issue will probably take care of it, but it's probably worth making sure that this dataset type gets unique_attributes made as well.
What type of dataset was used to make this light ray?
Britton
On Mon, Apr 24, 2017 at 4:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hmm, so this light ray dataset you've shared with me is missing a lot of metadata. Is there any chance you can share the original dataset with me so I can debug the light ray creation process as well? You should be able to use the curldrop to upload the dataset as a tarball.
On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/show/7131/.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum <nathan12343@gmail.com
wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
I apologize if I was unclear. I am still having an issue even on the latest dev version. I was having a separate issue on the stable branch that I believe was the issue you linked me previously. The issue I am currently having is that whenever yt tries to load a LightRay from my dataset it throws the error
AttributeError: 'str' object has no attribute 'astype'
This occurs from simply loading the hdf5 file generated from a call to make_light_ray. It should be easily reproducible by attempting to load the file I uploaded at use.yt/upload/9fe32716.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
> You can use the yt curldrop to share the dataset: > > https://docs.hub.yt/services.html#curldrop > > But if it's as you said and the issue is fixed already (e.g. you do > not have any issues when you build yt from latest version on the "yt" > branch in the mercurial repository) then there's no need to go further, > since the issue is fixed already. We will hopefully be able to do a yt 3.4 > release soon after moving development to github, so that will get this fix > out there in a more easily shareable fashion. > > -Nathan > > On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < > jmtomlinson95@gmail.com> wrote: > >> Nathan, >> >> That issue is very likely the problem that I was having with the >> stable version. >> >> I tried to recreate the issue I am having with the dev version but >> the issue does not occur for any of the public enzo datasets. >> >> The error occurs after the ray data has been saved and it reloads >> it . The saved file is able to be read in h5py and seems correct. >> A few layers down the error occurs in _parse_parameter_file() and I >> think this may be the difference between the data I was given and the >> public sets. >> I can't really see the difference between the two myself. I've >> uploaded the file here http://paste.yt-project.org/show/7129/ if >> it becomes relevant. >> >> The script to generate the error is extremely basic, I didn't >> upload it because its just two lines, making the LightRay then calling >> make_light_ray. >> The error should be reproducible by simply trying to load the >> resultant hdf5 file, is there somewhere you would prefer me to upload it? >> It's not too large, less than 1MB. >> Is there anything else I could provide to help diagnose the issue? >> >> Thanks, >> Joe Tomlinson >> Senior Undergraduate >> Department of Physics, Drexel University >> >> On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum < >> nathan12343@gmail.com> wrote: >> >>> Hi Joseph, >>> >>> I believe you're hitting this issue: >>> >>> https://bitbucket.org/yt_analysis/yt/issues/1330 >>> >>> Which was fixed here: >>> >>> https://bitbucket.org/yt_analysis/yt/pull-requests/2541 >>> >>> We haven't had a stable release since that was fixed. If you're >>> running yt from a stable release, can you try installing the development >>> version from source? If you're using conda you can also use the nightly >>> binary builds: >>> >>> http://yt-project.org/docs/dev/installing.html#nightly-conda >>> -builds >>> >>> If you are running a recent development version then Britton's fix >>> might need to be eloborated upon. If so, can you create a self-contained, >>> runnable example script that triggers the issue you're seeing (preferably >>> making use of one of the public datasets on yt-project.org/data)? >>> >>> Best, >>> >>> Nathan Goldbaum >>> >>> On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < >>> jmtomlinson95@gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I am trying to use the single dataset LightRay module but I am >>>> running into an issue. >>>> Whenever I use the data_filename parameter, which I believe is >>>> necessary for use with AbsorptionSpectrum, I receive the following error. >>>> >>>> TypeError: Object dtype dtype('O') has no native HDF5 equivalent >>>> >>>> This error does not occur when I run the cookbook example so I am >>>> a bit lost as to what to do. >>>> I am running the latest stable version on anaconda and have tried >>>> both h5py 2.7 and 2.6. >>>> The simulation is a cosmological Enzo simulation. >>>> >>>> I have also tried using the nightly dev build which changes the >>>> error from being on write to being on load with the following error. >>>> >>>> AttributeError: 'str' object has no attribute 'astype' >>>> from line 326 in _restore_light_ray_solution >>>> self.parameters[ksp3] = self.parameters[ksp3].astype(str) >>>> >>>> When using python 2.7 the error is the same but with 'unicode' >>>> instead of 'str'. >>>> >>>> Any help would be greatly appreciated. >>>> >>>> Thanks, >>>> Joe Tomlinson >>>> Senior Undergraduate >>>> Department of Physics, Drexel University >>>> >>>> _______________________________________________ >>>> 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 > >
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Nathan, You are correct, the enzo simulation is from before 2012 PR2589 does indeed fix the issue I was having. Thank you for your assistance. Joe Tomlinson On Mon, Apr 24, 2017 at 6:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hi Joseph,
Thanks for sharing your dataset, that made it much easier to see what was going wrong. I've issued a pull request here that should fix things:
https://bitbucket.org/yt_analysis/yt/pull-requests/2589
The reason we hadn't seen this before is that you are working with a somewhat peculiar Enzo output that doesn't contain any unique identifier metadata. This metadata has been in the Enzo output format for several years now, so I guess this is a somewhat older dataset? In any case it was triggering a bug in yt that was causing ds.unique_identifier to get set to None, which then triggered another bug in the light ray saving machinery when it was passed such a strange unique identifier.
I think I've fixed both issues. It would be great if you could give it a test. I'm happy to help out if you have questions about how to do that.
-Nathan
On Mon, Apr 24, 2017 at 4:20 PM, Joseph Tomlinson <jmtomlinson95@gmail.com
wrote:
Nathan, Britton
The dataset was made using a cosmological enzo simulation. I have uploaded it here use.yt/upload/ad078d12 be aware the tarball is around 5GB.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 5:15 PM, Britton Smith <brittonsmith@gmail.com> wrote:
Hi Joseph, Nathan,
The problem seems to be one of two things. First, this is a light ray made by a single dataset, and so an hdf5 attribute that is normally expected to be a list of strings was a single single. Second, this attribute, which records the unique_identifiers for the datasets used to make the light ray is "[None]", so whatever dataset this was is missing a unique_identifier attribute. Fixing the first issue will probably take care of it, but it's probably worth making sure that this dataset type gets unique_attributes made as well.
What type of dataset was used to make this light ray?
Britton
On Mon, Apr 24, 2017 at 4:02 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
Hmm, so this light ray dataset you've shared with me is missing a lot of metadata. Is there any chance you can share the original dataset with me so I can debug the light ray creation process as well? You should be able to use the curldrop to upload the dataset as a tarball.
On Mon, Apr 24, 2017 at 3:59 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
Nathan,
To just generate the error run http://paste.yt-project.org/show/7130/ after downloading the hdf5 file I uploaded. The generation of the hdf5 file requires the actual dataset I'm working with, but it is generated with http://paste.yt-project.org/sh ow/7131/.
Thanks, Joe Tomlinson Senior Undergraduate Department of Physics, Drexel University
On Mon, Apr 24, 2017 at 4:51 PM, Nathan Goldbaum < nathan12343@gmail.com> wrote:
Hi Joseph,
I'm unfamiliar with the LightRay interface - can you make a short sample script that triggers the issue you're seeing? I want to make sure we're on the same page.
-Nathan
On Mon, Apr 24, 2017 at 3:49 PM, Joseph Tomlinson < jmtomlinson95@gmail.com> wrote:
> Nathan, > > I apologize if I was unclear. I am still having an issue even on the > latest dev version. I was having a separate issue on the stable branch that > I believe was the issue you linked me previously. > The issue I am currently having is that whenever yt tries to load a > LightRay from my dataset it throws the error > > AttributeError: 'str' object has no attribute 'astype' > > This occurs from simply loading the hdf5 file generated from a call > to make_light_ray. It should be easily reproducible by attempting to load > the file I uploaded at use.yt/upload/9fe32716. > > Thanks, > Joe Tomlinson > Senior Undergraduate > Department of Physics, Drexel University > > > On Mon, Apr 24, 2017 at 4:40 PM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> You can use the yt curldrop to share the dataset: >> >> https://docs.hub.yt/services.html#curldrop >> >> But if it's as you said and the issue is fixed already (e.g. you do >> not have any issues when you build yt from latest version on the "yt" >> branch in the mercurial repository) then there's no need to go further, >> since the issue is fixed already. We will hopefully be able to do a yt 3.4 >> release soon after moving development to github, so that will get this fix >> out there in a more easily shareable fashion. >> >> -Nathan >> >> On Mon, Apr 24, 2017 at 3:34 PM, Joseph Tomlinson < >> jmtomlinson95@gmail.com> wrote: >> >>> Nathan, >>> >>> That issue is very likely the problem that I was having with the >>> stable version. >>> >>> I tried to recreate the issue I am having with the dev version but >>> the issue does not occur for any of the public enzo datasets. >>> >>> The error occurs after the ray data has been saved and it reloads >>> it . The saved file is able to be read in h5py and seems correct. >>> A few layers down the error occurs in _parse_parameter_file() and >>> I think this may be the difference between the data I was given and the >>> public sets. >>> I can't really see the difference between the two myself. I've >>> uploaded the file here http://paste.yt-project.org/show/7129/ if >>> it becomes relevant. >>> >>> The script to generate the error is extremely basic, I didn't >>> upload it because its just two lines, making the LightRay then calling >>> make_light_ray. >>> The error should be reproducible by simply trying to load the >>> resultant hdf5 file, is there somewhere you would prefer me to upload it? >>> It's not too large, less than 1MB. >>> Is there anything else I could provide to help diagnose the issue? >>> >>> Thanks, >>> Joe Tomlinson >>> Senior Undergraduate >>> Department of Physics, Drexel University >>> >>> On Mon, Apr 24, 2017 at 2:09 PM, Nathan Goldbaum < >>> nathan12343@gmail.com> wrote: >>> >>>> Hi Joseph, >>>> >>>> I believe you're hitting this issue: >>>> >>>> https://bitbucket.org/yt_analysis/yt/issues/1330 >>>> >>>> Which was fixed here: >>>> >>>> https://bitbucket.org/yt_analysis/yt/pull-requests/2541 >>>> >>>> We haven't had a stable release since that was fixed. If you're >>>> running yt from a stable release, can you try installing the development >>>> version from source? If you're using conda you can also use the nightly >>>> binary builds: >>>> >>>> http://yt-project.org/docs/dev/installing.html#nightly-conda >>>> -builds >>>> >>>> If you are running a recent development version then Britton's >>>> fix might need to be eloborated upon. If so, can you create a >>>> self-contained, runnable example script that triggers the issue you're >>>> seeing (preferably making use of one of the public datasets on >>>> yt-project.org/data)? >>>> >>>> Best, >>>> >>>> Nathan Goldbaum >>>> >>>> On Mon, Apr 24, 2017 at 1:04 PM, Joseph Tomlinson < >>>> jmtomlinson95@gmail.com> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I am trying to use the single dataset LightRay module but I am >>>>> running into an issue. >>>>> Whenever I use the data_filename parameter, which I believe is >>>>> necessary for use with AbsorptionSpectrum, I receive the following error. >>>>> >>>>> TypeError: Object dtype dtype('O') has no native HDF5 equivalent >>>>> >>>>> This error does not occur when I run the cookbook example so I >>>>> am a bit lost as to what to do. >>>>> I am running the latest stable version on anaconda and have >>>>> tried both h5py 2.7 and 2.6. >>>>> The simulation is a cosmological Enzo simulation. >>>>> >>>>> I have also tried using the nightly dev build which changes the >>>>> error from being on write to being on load with the following error. >>>>> >>>>> AttributeError: 'str' object has no attribute 'astype' >>>>> from line 326 in _restore_light_ray_solution >>>>> self.parameters[ksp3] = self.parameters[ksp3].astype(str) >>>>> >>>>> When using python 2.7 the error is the same but with 'unicode' >>>>> instead of 'str'. >>>>> >>>>> Any help would be greatly appreciated. >>>>> >>>>> Thanks, >>>>> Joe Tomlinson >>>>> Senior Undergraduate >>>>> Department of Physics, Drexel University >>>>> >>>>> _______________________________________________ >>>>> 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 > >
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participants (3)
-
Britton Smith -
Joseph Tomlinson -
Nathan Goldbaum