MLWorkflow

Machine Learning Workflow Automation

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Summary

• Preprocess list of geotiff files for machine learning algorithms
• support state-of-art machine learning algorithms including XGBoost, Random Forest, and SVR.
• perform feature ranking
• perform hyper-parameter tuning with algorithms including Bayesian Search
• create model analysis and visualizations

Setting up on NCI:

ssh <USERNAME>@gadi.nci.org.au

# working dir
export MLHOME=/g/data/ge3
cd $MLHOME

# load req packages
module purge
module load pbs
module load python3-as-python
module load gdal/3.0.2

# get updated code 
mkdir -p $MLHOME/github
cd $MLHOME/github
rm -rf MLWorkflow
git clone git@github.com:GeoscienceAustralia/MLWorkflow.git

# create python environment
rm -rf $MLHOME/venvs/MLWorkflow
python3 -m venv $MLHOME/venvs/MLWorkflow
source $MLHOME/venvs/MLWorkflow/bin/activate
pip install --upgrade pip setuptools wheel
pip install -r $MLHOME/github/MLWorkflow/requirements.txt
chmod 0700 $MLHOME    

# make scripts excuatable 
cd $MLHOME/github/MLWorkflow
sed -i -e 's/\r$//' run*
chmod +x run*

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How to Install the Software at NCI GADI

ssh abc123@gadi.nci.org.au

module purge
module load pbs
module load python3-as-python
module load gdal/3.0.2

export MLHOME=/g/data/ge3/$USER   # this can be pointed any dir with enough storage space. 
# user-specific work space in which github code, virtual environment is located 

mkdir -p $MLHOME/github
cd $MLHOME/github
rm -rf MLWorkflow
git clone git@github.com:GeoscienceAustralia/MLWorkflow.git
# to test bleeding edge features checkout develop branch 
# git clone -b develop --single-branch git@github.com:GeoscienceAustralia/MLWorkflow.git

cd MLWorkflow
rm -rf $MLHOME/venvs/MLWorkflow
python3 -m venv $MLHOME/venvs/MLWorkflow
source $MLHOME/venvs/MLWorkflow/bin/activate
pip install --upgrade pip setuptools wheel
pip install -r $MLHOME/github/MLWorkflow/requirements.txt
pip install -e .
chmod 0700 $MLHOME    
sed -i -e 's/\r$//' run*
chmod +x run*

cd /g/data/ge3/$USER/github/MLWorkflow

# Change the output folder in the configration file, so that a writable dir can be used
## outputfolder =  /g/data/ge3/sg4953/results/debugging
## outputfolder =  /g/data/ge3/fxz547/results/debugging

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How to Run Jupyter Notebook at NCI GADI

qsub run_jupyter.sh
less 5_connection_strings.txt
# copy string in local terminal 
# navigate to http://localhost:8385 in browser 
# choose the notebook you want to run

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Running Software on NCI

qsub -v inputConfigFile="$MLHOME//github/MLWorkflow/configurations_examples/default_configuration.ini" run_small_workflow.sh
qsub -v inputConfigFile="/g/data/ge3/sg4953/github/MLWorkflow/configurations_examples/reference_configuration_6.ini" run_large_workflow.sh
less 1_connection_strings.txt

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Running Software on Local Linux Machine

# input datasets
# refer to bin/download_datasets.sh to download sample input dataset 

# download software 
mkdir -p $MLHOME/projects
cd $MLHOME/projects
rm -rf MLWorkflow
git clone git@github.com:GeoscienceAustralia/MLWorkflow.git -b develop

git clone git@github.com:GeoscienceAustralia/MLWorkflow.git -b sheece-tests

# setup python environment 
cd $MLHOME
rm -rf $MLHOME/venvs/MLWorkflow
python3 -m venv $MLHOME/venvs/MLWorkflow
source $MLHOME/venv/MLWorkflow/bin/activate
rm -rf ~/.cache/pip
pip install -r $MLHOME/MLWorkflow/requirements.txt

cd $MLHOME/projects/MLWorkflow
source $MLHOME/venvs/MLWorkflow/bin/activate

ray start --head

python -m mlwkf -c experements/small_test.ini 

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Remove Temporary Files after running the pipeline

rm *setupRayWorkerNode.sh -f
rm *connection_strings* -f
rm mlflowpbs* -f
rm core.ray:* -f
rm core.raylet* -f

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Compile

find . -name '*.py'
python3 -m compileall .
find . -name '*.pyc' -delete
find . -name '*.py' -delete
find . -name '__pycache__' -delete

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Testing

pytest -rx -s tests