[Debian-pan-maintainers] nabu on grades

[FARHI Emmanuel]

Ouch ! 

We do have pyvkfft and pycuda, but it seems we have missed the scikit-cuda dependency for Nabu, which is indicated as optional in: 


    * [ https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/pyproject.toml?ref_type=heads | https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/pyproject.toml?ref_type=heads ] 
    * [ https://tomotools.gitlab-pages.esrf.fr/nabu/install.html | https://tomotools.gitlab-pages.esrf.fr/nabu/install.html ] 

Not so optional in fact... 
It may be the same story with the missing pycudwt for wavelets 

The good news is that the scikit-cuda source does not seem to require too many hidden dependencies, see: 


    * [ https://github.com/lebedov/scikit-cuda | https://github.com/lebedov/scikit-cuda ] 

Regarding the pycudwt, the pypi and source code are a: 


    * [ https://pypi.org/project/pycudwt/ | https://pypi.org/project/pycudwt/ ] 
    * [ https://github.com/pierrepaleo/pypwt | https://github.com/pierrepaleo/pypwt ] 

Roland, do you think you can push sk-cuda and pycudwt into NEW ? 

I hope there are no other hidden dependencies. 

Emmanuel. 


De: "Andrew KING" <andrew.king at synchrotron-soleil.fr> 
À: "FARHI Emmanuel" <emmanuel.farhi at synchrotron-soleil.fr> 
Cc: "PIAULT Pierre" <pierre.piault at synchrotron-soleil.fr>, "PICCA Frederic-Emmanuel" <frederic-emmanuel.picca at synchrotron-soleil.fr> 
Envoyé: Jeudi 21 Novembre 2024 15:19:19 
Objet: Re: nabu on grades 

Hi Emmanuel, 

I have just tried Nabu again - I get another error relating to cuda - see messages copied below... 

Can you have a look? 
Thanks, Andy 

king at grades-vm:~/persistent_area/benchmark$ nabu 0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/nabu.conf 
Browsing dataset 
dataset /tmp/sshfs-persistent_area/benchmark/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING1.nx has broken virtual-dataset at /flyscan/instrument/detector/data. ('/tmp/sshfs-persistent_area/benchmark/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/tmp/sshfs-persistent_area/benchmark/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING.nxs',) missing 
Updating dataset information with user configuration 
Loaded darks from /tmp/sshfs-persistent_area/benchmark/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING1_darks.hdf5 
Loaded flats from /tmp/sshfs-persistent_area/benchmark/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING1_flats.hdf5 
Overwriting pixel_size = 1.3e-06 
Doing dataset estimations 
Doing coupled validation 
Going to reconstruct slices (0, 1023) 
Unsharp mask margin: 21 pixels 
Estimated margin: 21 pixels 
Processing sub-volume ((0, 3600), (0, 1024), (0, 1024)) 
Creating a new pipeline object 
Set sub-region to ((0, 3600), (0, 1024), (0, 1024)) 
Traceback (most recent call last): 
File "/usr/bin/nabu", line 8, in <module> 
sys.exit(main()) 
^^^^^^ 
File "/usr/lib/python3/dist-packages/nabu/app/reconstruct.py", line 114, in main 
R.reconstruct() 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py", line 621, in reconstruct 
self._reconstruct_chunked() 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py", line 573, in _reconstruct_chunked 
self._instantiate_pipeline_if_necessary(task, prev_task) 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py", line 551, in _instantiate_pipeline_if_necessary 
self._instantiate_pipeline(current_task) 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py", line 543, in _instantiate_pipeline 
pipeline = self._pipeline_cls(*args, logger=self.logger, margin=task["margin"], **kwargs) 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked_cuda.py", line 61, in __init__ 
super().__init__( 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py", line 106, in __init__ 
self._init_pipeline() 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py", line 276, in _init_pipeline 
self._init_phase() 
File "/usr/lib/python3/dist-packages/nabu/pipeline/utils.py", line 20, in wrapper 
return func(*args, **kwargs) 
^^^^^^^^^^^^^^^^^^^^^ 
File "/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py", line 481, in _init_phase 
self.phase_retrieval = self.PaganinPhaseRetrievalClass( 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/usr/lib/python3/dist-packages/nabu/preproc/phase_cuda.py", line 45, in __init__ 
self._init_fft(fft_backend) 
File "/usr/lib/python3/dist-packages/nabu/preproc/phase_cuda.py", line 66, in _init_fft 
self.cufft = fft_cls(shape=self.data_padded.shape, dtype=np.float32, r2c=True) 
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 
File "/usr/lib/python3/dist-packages/nabu/processing/fft_base.py", line 46, in __init__ 
self._configure_batched_transform() 
File "/usr/lib/python3/dist-packages/nabu/processing/fft_cuda.py", line 48, in _configure_batched_transform 
raise ImportError("Please install pycuda and scikit-cuda to use the CUDA back-end") 
ImportError: Please install pycuda and scikit-cuda to use the CUDA back-end 



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