Trying to install yt on XSEDE Comet
Hi all, I have been having many issues running yt on Comet recently. I initially installed yt using conda, and quickly ran into problems with yt.enable_plugins(). I found that only some of my fields were being added, and I ended up having to manually load in the fields that were not added (although this also proved to be a struggle). I was able to run the same script, using the same plugins file, on a different computer, but with yt version 3.4.0. So today I decided to revert to yt version 3.4.0 and try to run my script. Now, when I "import yt", I get the following error: Traceback (most recent call last): File "trace_halos_full.py", line 3, in <module> import yt File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/__init__.py", line 102, in <module> from yt.visualization.api import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/api.py", line 22, in <module> from .particle_plots import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/particle_plots.py", line 18, in <module> from yt.visualization.fixed_resolution import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", line 23, in <module> from .volume_rendering.api import off_axis_projection File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", line 23, in <module> from .camera import Camera File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", line 21, in <module> from .utils import data_source_or_all File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", line 11, in <module> from yt.utilities.lib import mesh_traversal File "rtcore_scene.pxd", line 61, in init yt.utilities.lib.mesh_traversal ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, try recompiling. Expected 32, got 24 It would be great to hear from other yt users on comet to hear how they installed yt, or if someone can help me out with this error, that would be much appreciated! Please let me know what other info you may need from me. I'll do my best to quickly respond.
Hi Danielle, Oof, that's no fun! It looks to me like there's a strange change in the expected size of the dependency pyembree; perhaps it got installed with a different version that it is now -- I believe they may have rolled a new release. One simple way around this might be to do: "conda uninstall pyembree" and see if that changes the situation. On Fri, Jan 25, 2019 at 10:30 AM Danielle Skinner <drenniks@gatech.edu> wrote:
Hi all,
I have been having many issues running yt on Comet recently. I initially installed yt using conda, and quickly ran into problems with yt.enable_plugins(). I found that only some of my fields were being added, and I ended up having to manually load in the fields that were not added (although this also proved to be a struggle).
I was able to run the same script, using the same plugins file, on a different computer, but with yt version 3.4.0. So today I decided to revert to yt version 3.4.0 and try to run my script. Now, when I "import yt", I get the following error:
Traceback (most recent call last): File "trace_halos_full.py", line 3, in <module> import yt File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/__init__.py", line 102, in <module> from yt.visualization.api import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/api.py", line 22, in <module> from .particle_plots import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/particle_plots.py", line 18, in <module> from yt.visualization.fixed_resolution import \ File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py", line 23, in <module> from .volume_rendering.api import off_axis_projection File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py", line 23, in <module> from .camera import Camera File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/camera.py", line 21, in <module> from .utils import data_source_or_all File "/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py", line 11, in <module> from yt.utilities.lib import mesh_traversal File "rtcore_scene.pxd", line 61, in init yt.utilities.lib.mesh_traversal ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, try recompiling. Expected 32, got 24
It would be great to hear from other yt users on comet to hear how they installed yt, or if someone can help me out with this error, that would be much appreciated! Please let me know what other info you may need from me. I'll do my best to quickly respond. _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
Thanks for the response! Unfortunately, if I want to uninstall pyembree via conda, conda also wants to remove yt....
Oof, that's no fun. I've looked and it seems that in the latest version of yt, we catch ValueError as well, so I'm not sure why it's throwing an error all the way up. Can you check that you're using a recent version of yt from conda-forge? Alternately, you can change /home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py to have this, instead of the current import of mesh_traversal: from yt.utilities.on_demand_imports import NotAModule try: from yt.utilities.lib import mesh_traversal # Catch ValueError in case size of objects in Cython change except (ImportError, ValueError): mesh_traversal = NotAModule("pyembree") On Fri, Jan 25, 2019 at 12:18 PM Danielle Skinner <drenniks@gatech.edu> wrote:
Thanks for the response! Unfortunately, if I want to uninstall pyembree via conda, conda also wants to remove yt.... _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
Also are you installing yt via conda-forge? The anaconda package for yt is out of date and unfortunately we are unable to update it ourselves. On Fri, Jan 25, 2019 at 1:24 PM Matthew Turk <matthewturk@gmail.com> wrote:
Oof, that's no fun.
I've looked and it seems that in the latest version of yt, we catch ValueError as well, so I'm not sure why it's throwing an error all the way up. Can you check that you're using a recent version of yt from conda-forge? Alternately, you can change
/home/drenniks/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/utils.py
to have this, instead of the current import of mesh_traversal:
from yt.utilities.on_demand_imports import NotAModule try: from yt.utilities.lib import mesh_traversal # Catch ValueError in case size of objects in Cython change except (ImportError, ValueError): mesh_traversal = NotAModule("pyembree")
On Fri, Jan 25, 2019 at 12:18 PM Danielle Skinner <drenniks@gatech.edu> wrote:
Thanks for the response! Unfortunately, if I want to uninstall pyembree via conda, conda also wants to remove yt.... _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
I was using the most recent version of yt from conda-forge, but with that version, I was having problems reading in my plugins file. So I decided to revert back to yt version 3.4.0, which I know works for my script on a different computer. So right now, I am on version 3.4.0. But I will try your recommendation about mesh_traversal and report back.
Ah I see. Can we get a separate bug report on github about the plugins file issue? Also there were several bugfix releases after 3.4.0, you probably want to update to the latest of those. On Fri, Jan 25, 2019 at 1:59 PM Danielle Skinner <drenniks@gatech.edu> wrote:
I was using the most recent version of yt from conda-forge, but with that version, I was having problems reading in my plugins file. So I decided to revert back to yt version 3.4.0, which I know works for my script on a different computer. So right now, I am on version 3.4.0.
But I will try your recommendation about mesh_traversal and report back. _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
I will create a bug report once I switch back to version 3.5.0. I will do that soon. I only switched back to 3.4.0 because I knew this version worked previously. Is there another way you would suggest installing yt on Comet other than conda?
Assuming you have a python environment with yt’s hard dependencies installed (numpy, sympy, matplotlib), “pip install —user” should work to install yt from inside a checkout of the yt git repository. I would be surprised if 3.4.0 worked but one of the subsequent bugfix releases in the 3.4.x series did not work. On Fri, Jan 25, 2019 at 2:16 PM Danielle Skinner <drenniks@gatech.edu> wrote:
I will create a bug report once I switch back to version 3.5.0. I will do that soon. I only switched back to 3.4.0 because I knew this version worked previously.
Is there another way you would suggest installing yt on Comet other than conda? _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
sorry, “pip install . —user” On Fri, Jan 25, 2019 at 2:29 PM Nathan Goldbaum <nathan12343@gmail.com> wrote:
Assuming you have a python environment with yt’s hard dependencies installed (numpy, sympy, matplotlib), “pip install —user” should work to install yt from inside a checkout of the yt git repository.
I would be surprised if 3.4.0 worked but one of the subsequent bugfix releases in the 3.4.x series did not work.
On Fri, Jan 25, 2019 at 2:16 PM Danielle Skinner <drenniks@gatech.edu> wrote:
I will create a bug report once I switch back to version 3.5.0. I will do that soon. I only switched back to 3.4.0 because I knew this version worked previously.
Is there another way you would suggest installing yt on Comet other than conda? _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org
Okay I have made that change in utils.py but now get this error when I import yt (and I am using version 3.4.0) ValueError Traceback (most recent call last) <ipython-input-1-2d2292a375dc> in <module> ----> 1 import yt ~/software/anaconda3/lib/python3.6/site-packages/yt/__init__.py in <module> 100 101 # Now individual component imports from the visualization API --> 102 from yt.visualization.api import \ 103 FixedResolutionBuffer, ObliqueFixedResolutionBuffer, \ 104 write_bitmap, write_image, \ ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/api.py in <module> 20 make_colormap 21 ---> 22 from .particle_plots import \ 23 ParticleProjectionPlot, \ 24 ParticlePhasePlot, \ ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/particle_plots.py in <module> 16 import numpy as np 17 ---> 18 from yt.visualization.fixed_resolution import \ 19 ParticleImageBuffer 20 from yt.funcs import \ ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/fixed_resolution.py in <module> 21 ensure_list, \ 22 deprecate ---> 23 from .volume_rendering.api import off_axis_projection 24 from .fixed_resolution_filters import apply_filter, filter_registry 25 from yt.data_objects.image_array import ImageArray ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/api.py in <module> 23 from .camera import Camera 24 from .transfer_function_helper import TransferFunctionHelper ---> 25 from .volume_rendering import volume_render, create_scene 26 from .off_axis_projection import off_axis_projection 27 from .scene import Scene ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/volume_rendering.py in <module> 13 14 ---> 15 from .scene import Scene 16 from .render_source import VolumeSource, \ 17 MeshSource ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/scene.py in <module> 28 YTArray 29 from .camera import Camera ---> 30 from .render_source import \ 31 OpaqueSource, \ 32 BoxSource, \ ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/render_source.py in <module> 40 ytcfg["yt", "ray_tracing_engine"] = "yt" 41 try: ---> 42 from yt.utilities.lib import mesh_construction 43 except ImportError: 44 mesh_construction = NotAModule("pyembree") rtcore_scene.pxd in init yt.utilities.lib.mesh_construction() ValueError: pyembree.rtcore_scene.EmbreeScene has the wrong size, try recompiling. Expected 32, got 24 I suppose I could make a similar change as what you suggested to ~/software/anaconda3/lib/python3.6/site-packages/yt/visualization/volume_rendering/render_source.py
participants (3)
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Danielle Skinner -
Matthew Turk -
Nathan Goldbaum