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Merge pull request #18220 from anuprulez/patch-5
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Update GPU JupyterLab tool
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martenson authored Jun 11, 2024
2 parents 5b4268c + a55a569 commit ed117ef
Showing 1 changed file with 24 additions and 3 deletions.
27 changes: 24 additions & 3 deletions tools/interactive/interactivetool_ml_jupyter_notebook.xml
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="interactive_tool_ml_jupyter_notebook" tool_type="interactive" name="GPU enabled Interactive Jupyter Notebook for Machine Learning" version="@VERSION@" profile="22.01">
<tool id="interactive_tool_ml_jupyter_notebook" tool_type="interactive" name="GPU-enabled Interactive Jupyter Notebook for Machine Learning" version="@VERSION@" profile="22.01">
<macros>
<token name="@VERSION@">0.2</token>
<token name="@VERSION@">0.4</token>
</macros>
<requirements>
<container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration-@VERSION@</container>
<container type="docker">quay.io/galaxy/docker-ml-jupyterlab:galaxy-integration-@VERSION@</container>
</requirements>
<entry_points>
<entry_point name="GPU enabled Interactive Jupyter Notebook for Machine Learning" requires_domain="True">
Expand Down Expand Up @@ -80,6 +80,15 @@ except FileNotFoundError:
</configfiles>

<command><![CDATA[
## Check if the node has GPU. Activate CPU or GPU version of tensorflow
if nvidia-smi 2> /dev/null; then
echo An NVDIA GPU was detected. ;
ln -s \$PYTHON_LIB_PATH/tensorflow-GPU-cached \$PYTHON_LIB_PATH/tensorflow ;
else
echo No compatible GPU present. ;
ln -s \$PYTHON_LIB_PATH/tensorflow-CPU-cached \$PYTHON_LIB_PATH/tensorflow ;
fi &&
python staging_script.py &&
export GALAXY_WORKING_DIR=`pwd` &&
mkdir -p ./jupyter/outputs &&
Expand All @@ -88,6 +97,10 @@ except FileNotFoundError:
export HOME=/home/\$NB_USER/ &&
export PATH=/home/\$NB_USER/.local/bin:\$PATH &&
cp '${galaxy_input_startup_script}' /home/\$NB_USER/.ipython/profile_default/startup/02-load.py &&
## Disable popups informing that "a new release is available"
jupyter labextension disable "@jupyterlab/apputils-extension:announcements" &&
#set $output_notebook_name = 'jupyterlab_notebook.ipynb'
#if $mode.mode_select == 'scratch':
cp -r /home/\$NB_USER/data ./ &&
Expand All @@ -96,6 +109,10 @@ except FileNotFoundError:
cp -r /home/\$NB_USER/usecases ./ &&
cp -r /home/\$NB_USER/home_page.ipynb ./ &&
jupyter lab --no-browser --NotebookApp.shutdown_button=True
#elif $mode.mode_select == 'github':
cp /home/\$NB_USER/home_page.ipynb ./ &&
git clone $mode.repo_url &&
jupyter lab --no-browser --NotebookApp.shutdown_button=True
#else:
#import re
#set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))
Expand All @@ -119,9 +136,13 @@ except FileNotFoundError:
<conditional name="mode">
<param name="mode_select" type="select" label="Do you already have a notebook?" help="Select a set of default notebooks or load an existing one.">
<option value="scratch">Start with default notebooks</option>
<option value="pull_repo">Start with a code repository</option>
<option value="previous">Load an existing notebook</option>
</param>
<when value="scratch"/>
<when value="pull_repo">
<param name="repo_url" type="text" value="" label="Online code repository (Git-based) URL" optional="False" help="Provide URL of Git-based code repository (for example: GitHub repository URL such as https://github.com/anuprulez/gpu_jupyterlab_ct_image_segmentation)"/>
</when>
<when value="previous">
<param name="ipynb" type="data" format="ipynb" label="IPython Notebook" required="true"/>
<param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one." help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
Expand Down

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