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<p>I'm getting started on that :-)</p>
<p>Roland.<br>
</p>
<div class="moz-cite-prefix">Le 21/11/2024 à 16:22, FARHI Emmanuel a
écrit :<br>
</div>
<blockquote type="cite"
cite="mid:596858572.537493.1732202568096.JavaMail.zimbra@synchrotron-soleil.fr">
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<div>Ouch !<br>
</div>
<div><br data-mce-bogus="1">
</div>
<div>We do have pyvkfft and pycuda, but it seems we have missed
the scikit-cuda dependency for Nabu, which is indicated as
optional in:</div>
<ul>
<li><a
href="https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/pyproject.toml?ref_type=heads"
moz-do-not-send="true" class="moz-txt-link-freetext">https://gitlab.esrf.fr/tomotools/nabu/-/blob/master/pyproject.toml?ref_type=heads</a><br
data-mce-bogus="1">
</li>
<li><a
href="https://tomotools.gitlab-pages.esrf.fr/nabu/install.html"
moz-do-not-send="true" class="moz-txt-link-freetext">https://tomotools.gitlab-pages.esrf.fr/nabu/install.html</a><br
data-mce-bogus="1">
</li>
</ul>
<div>Not so optional in fact...<br data-mce-bogus="1">
</div>
<div>It may be the same story with the missing <code
class="docutils literal notranslate"><span class="pre">pycudwt</span></code>
for wavelets<br data-mce-bogus="1">
</div>
<div><br data-mce-bogus="1">
</div>
<div>The good news is that the scikit-cuda source does not seem
to require too many hidden dependencies, see:</div>
<ul>
<li><a href="https://github.com/lebedov/scikit-cuda"
moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/lebedov/scikit-cuda</a><br
data-mce-bogus="1">
</li>
</ul>
<div>Regarding the pycudwt, the pypi and source code are a: </div>
<ul>
<li><a href="https://pypi.org/project/pycudwt/"
moz-do-not-send="true" class="moz-txt-link-freetext">https://pypi.org/project/pycudwt/</a>
<br data-mce-bogus="1">
</li>
<li><a href="https://github.com/pierrepaleo/pypwt"
moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/pierrepaleo/pypwt</a><br
data-mce-bogus="1">
</li>
</ul>
<div>Roland, do you think you can push sk-cuda and <code
class="docutils literal notranslate"><span class="pre">pycudwt</span></code>
into NEW ?<br data-mce-bogus="1">
</div>
<div><br data-mce-bogus="1">
</div>
<div>I hope there are no other hidden dependencies.<br
data-mce-bogus="1">
</div>
<div><br data-mce-bogus="1">
</div>
<div>Emmanuel.<br data-mce-bogus="1">
</div>
<div><br data-mce-bogus="1">
</div>
<hr id="zwchr" data-marker="__DIVIDER__">
<div data-marker="__HEADERS__"><b>De: </b>"Andrew KING"
<a class="moz-txt-link-rfc2396E" href="mailto:andrew.king@synchrotron-soleil.fr"><andrew.king@synchrotron-soleil.fr></a><br>
<b>À: </b>"FARHI Emmanuel"
<a class="moz-txt-link-rfc2396E" href="mailto:emmanuel.farhi@synchrotron-soleil.fr"><emmanuel.farhi@synchrotron-soleil.fr></a><br>
<b>Cc: </b>"PIAULT Pierre"
<a class="moz-txt-link-rfc2396E" href="mailto:pierre.piault@synchrotron-soleil.fr"><pierre.piault@synchrotron-soleil.fr></a>, "PICCA
Frederic-Emmanuel"
<a class="moz-txt-link-rfc2396E" href="mailto:frederic-emmanuel.picca@synchrotron-soleil.fr"><frederic-emmanuel.picca@synchrotron-soleil.fr></a><br>
<b>Envoyé: </b>Jeudi 21 Novembre 2024 15:19:19<br>
<b>Objet: </b>Re: nabu on grades<br>
</div>
<div><br>
</div>
<div data-marker="__QUOTED_TEXT__">
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style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"
class="1">
<div>Hi Emmanuel,<br>
</div>
<br>
<div> I have just tried Nabu again - I get another error
relating to cuda - see messages copied below...<br>
</div>
<br>
<div>Can you have a look?<br>
</div>
<div>Thanks, Andy<br>
</div>
<div><br>
king@grades-vm:~/persistent_area/benchmark$ nabu
0231_WF6_UJcani_LHS_T1_7p2_top_30k_400ms3600pr_tomo_BINNING/nabu.conf
<br>
Browsing dataset<br>
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<br>
Updating dataset information with user configuration<br>
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<br>
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<br>
Overwriting pixel_size = 1.3e-06<br>
Doing dataset estimations<br>
Doing coupled validation<br>
Going to reconstruct slices (0, 1023)<br>
Unsharp mask margin: 21 pixels<br>
Estimated margin: 21 pixels<br>
Processing sub-volume ((0, 3600), (0, 1024), (0, 1024))<br>
Creating a new pipeline object<br>
Set sub-region to ((0, 3600), (0, 1024), (0, 1024))<br>
Traceback (most recent call last):<br>
File "/usr/bin/nabu", line 8, in <module><br>
sys.exit(main())<br>
^^^^^^<br>
File
"/usr/lib/python3/dist-packages/nabu/app/reconstruct.py",
line 114, in main<br>
R.reconstruct()<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py",
line 621, in reconstruct<br>
self._reconstruct_chunked()<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py",
line 573, in _reconstruct_chunked<br>
self._instantiate_pipeline_if_necessary(task,
prev_task)<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py",
line 551, in _instantiate_pipeline_if_necessary<br>
self._instantiate_pipeline(current_task)<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/reconstruction.py",
line 543, in _instantiate_pipeline<br>
pipeline = self._pipeline_cls(*args,
logger=self.logger, margin=task["margin"], **kwargs)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked_cuda.py",
line 61, in __init__<br>
super().__init__(<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py",
line 106, in __init__<br>
self._init_pipeline()<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py",
line 276, in _init_pipeline<br>
self._init_phase()<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/utils.py",
line 20, in wrapper<br>
return func(*args, **kwargs)<br>
^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/nabu/pipeline/fullfield/chunked.py",
line 481, in _init_phase<br>
self.phase_retrieval =
self.PaganinPhaseRetrievalClass(<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/nabu/preproc/phase_cuda.py",
line 45, in __init__<br>
self._init_fft(fft_backend)<br>
File
"/usr/lib/python3/dist-packages/nabu/preproc/phase_cuda.py",
line 66, in _init_fft<br>
self.cufft = fft_cls(shape=self.data_padded.shape,
dtype=np.float32, r2c=True)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/nabu/processing/fft_base.py",
line 46, in __init__<br>
self._configure_batched_transform()<br>
File
"/usr/lib/python3/dist-packages/nabu/processing/fft_cuda.py",
line 48, in _configure_batched_transform<br>
raise ImportError("Please install pycuda and
scikit-cuda to use the CUDA back-end")<br>
ImportError: Please install pycuda and scikit-cuda to use
the CUDA back-end<br>
<br>
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