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Title: Welcome to “Using Python in an HPC environment” course material — Using Python in an HPC environment 2.0 documentation

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Domain: uppmax.github.io

Links:

Using Python in an HPC environment https://uppmax.github.io/HPC-python/
Pre-requirementshttps://uppmax.github.io/HPC-python/prereqs.html
Prepare the environmenthttps://uppmax.github.io/HPC-python/preparations.html
Schedulehttps://uppmax.github.io/HPC-python/schedule.html
Log in and other preparationshttps://uppmax.github.io/HPC-python/common/login.html
Use the tarball with exerciseshttps://uppmax.github.io/HPC-python/common/use_tarball.html
Use a text editorhttps://uppmax.github.io/HPC-python/common/use_text_editor.html
HPC clustershttps://uppmax.github.io/HPC-python/common/understanding_clusters.html
NAISS projects overviewhttps://uppmax.github.io/HPC-python/common/naiss_projects_overview.html
Link to Day 1 (Intro to Python)https://uppmax.github.io/HPC-python/common/day1.html
Introductionhttps://uppmax.github.io/HPC-python/day2/intro.html
Using packageshttps://uppmax.github.io/HPC-python/day2/use_packages.html
Install packageshttps://uppmax.github.io/HPC-python/day2/install_packages.html
Use isolated environmentshttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html
Basic batch and Slurmhttps://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html
Interactive work on the compute nodeshttps://uppmax.github.io/HPC-python/day2/interactive.html
Desktop On Demandhttps://uppmax.github.io/HPC-python/day2/ondemand-desktop.html
Starting IDEs from command linehttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html
Using IDEshttps://uppmax.github.io/HPC-python/day2/IDEs.html
Summary day 2https://uppmax.github.io/HPC-python/summary2.html
Evaluationhttps://uppmax.github.io/HPC-python/day2/evaluation.html
Python documentations at the different HPC centreshttps://uppmax.github.io/HPC-python/day2/python_at_hpc_centers.html
A Brief Intro to Matplotlibhttps://uppmax.github.io/HPC-python/day3/new-matplotlib-intro.html
Intro to Pandas on HPChttps://uppmax.github.io/HPC-python/day3/pandas.html
A Brief Introduction to the Seaborn Statistical Plotting Libraryhttps://uppmax.github.io/HPC-python/day3/seaborn-new.html
Big data with Pythonhttps://uppmax.github.io/HPC-python/day3/big_data.html
Running Python in batch modehttps://uppmax.github.io/HPC-python/day3/batch-new.html
Summary day 3https://uppmax.github.io/HPC-python/summary3.html
Evaluationhttps://uppmax.github.io/HPC-python/day3/evaluation.html
Parallel computing with Pythonhttps://uppmax.github.io/HPC-python/day4/parallel.html
Using GPUs with Pythonhttps://uppmax.github.io/HPC-python/day4/gpu.html
Machine Learning and Deep Learninghttps://uppmax.github.io/HPC-python/day4/ml.html
Dimensionality Reductionhttps://uppmax.github.io/HPC-python/day4/dim_reduction.html
Evaluationhttps://uppmax.github.io/HPC-python/day4/evaluation.html
Summary day 4https://uppmax.github.io/HPC-python/summary4.html
On Bianca clusterhttps://uppmax.github.io/HPC-python/bianca.html
Other courseshttps://uppmax.github.io/HPC-python/extra/other_courses.html
More about packageshttps://uppmax.github.io/HPC-python/extra/packages_deeper.html
Developing in isolated environmentshttps://uppmax.github.io/HPC-python/extra/isolated_deeper.html
Jupyter at Kebnekaisehttps://uppmax.github.io/HPC-python/extra/jupyterHPC2N.html
On Kebnekaise clusterhttps://uppmax.github.io/HPC-python/kebnekaise.html
More about MLhttps://uppmax.github.io/HPC-python/day4/ML_deeper.html
On UPPMAX clustershttps://uppmax.github.io/HPC-python/uppmax.html
Using Python in an HPC environmenthttps://uppmax.github.io/HPC-python/
https://uppmax.github.io/HPC-python/
Edit on GitHubhttps://github.com/UPPMAX/HPC-python/blob/main/docs/index.rst
https://uppmax.github.io/HPC-python/#welcome-to-using-python-in-an-hpc-environment-course-material
https://uppmax.github.io/HPC-python/#schedule-autumn-2025
Schedulehttps://uppmax.github.io/HPC-python/schedule.html#schedule
UPPMAXhttps://docs.uppmax.uu.se/software/python/
HPC2Nhttps://docs.hpc2n.umu.se/tutorials/userinstalls/#python__packages
LUNARChttps://lunarc-documentation.readthedocs.io/en/latest/guides/applications/Python/
NSChttps://www.nsc.liu.se/support/
PDChttps://support.pdc.kth.se/doc/applications/python/
C3SEhttps://www.c3se.chalmers.se/documentation/module_system/python/
Code of Conducthttps://github.com/UPPMAX/R-matlab-julia-HPC/blob/main/CODE_OF_CONDUCT.md
https://umeauniversity.sharepoint.com/:w:/s/HPC2N630/IQDToLTHrvKHQ7PSkxBv9v_lAfFXgfgLZVMLRDzQ_jOrfDwhttps://umeauniversity.sharepoint.com/:w:/s/HPC2N630/IQDToLTHrvKHQ7PSkxBv9v_lAfFXgfgLZVMLRDzQ_jOrfDw
Pre-requirementshttps://uppmax.github.io/HPC-python/prereqs.html#prereqs
https://uppmax.github.io/HPC-python/#content-of-the-course
Pre-requirementshttps://uppmax.github.io/HPC-python/prereqs.html
Pre-requirements for Day 1https://uppmax.github.io/HPC-python/prereqs.html#pre-requirements-for-day-1
Pre-requirements for Day 2https://uppmax.github.io/HPC-python/prereqs.html#pre-requirements-for-day-2
Pre-requirements for Day 3https://uppmax.github.io/HPC-python/prereqs.html#pre-requirements-for-day-3
Pre-requirements for Day 4https://uppmax.github.io/HPC-python/prereqs.html#pre-requirements-for-day-4
Prepare the environmenthttps://uppmax.github.io/HPC-python/preparations.html
The steps to makehttps://uppmax.github.io/HPC-python/preparations.html#the-steps-to-make
Schedulehttps://uppmax.github.io/HPC-python/schedule.html
Course dateshttps://uppmax.github.io/HPC-python/schedule.html#course-dates
Day 1: Log in and use basic Python in a cluster environmenthttps://uppmax.github.io/HPC-python/schedule.html#day-1-log-in-and-use-basic-python-in-a-cluster-environment
Day 2: Packages, environments and using compute nodeshttps://uppmax.github.io/HPC-python/schedule.html#day-2-packages-environments-and-using-compute-nodes
Day 3: Basic analysis, Big Data and Batch jobshttps://uppmax.github.io/HPC-python/schedule.html#day-3-basic-analysis-big-data-and-batch-jobs
Day 4: Parallelism, GPUs, and machine learninghttps://uppmax.github.io/HPC-python/schedule.html#day-4-parallelism-gpus-and-machine-learning
Log in and other preparationshttps://uppmax.github.io/HPC-python/common/login.html
Step 1: Log in!https://uppmax.github.io/HPC-python/common/login.html#step-1-log-in
Step 2: Make a work directoryhttps://uppmax.github.io/HPC-python/common/login.html#step-2-make-a-work-directory
Test an editorhttps://uppmax.github.io/HPC-python/common/login.html#test-an-editor
Download and extract the tarball with exerciseshttps://uppmax.github.io/HPC-python/common/login.html#download-and-extract-the-tarball-with-exercises
Use the tarball with exerciseshttps://uppmax.github.io/HPC-python/common/use_tarball.html
Procedurehttps://uppmax.github.io/HPC-python/common/use_tarball.html#procedure
Use a text editorhttps://uppmax.github.io/HPC-python/common/use_text_editor.html
HPC clustershttps://uppmax.github.io/HPC-python/common/understanding_clusters.html
The HPC centers UPPMAX, HPC2N, LUNARC, NSC and Dardelhttps://uppmax.github.io/HPC-python/common/understanding_clusters.html#the-hpc-centers-uppmax-hpc2n-lunarc-nsc-and-dardel
Briefly about the cluster hardware and system at UPPMAX, HPC2N, LUNARC, NSC and PDChttps://uppmax.github.io/HPC-python/common/understanding_clusters.html#briefly-about-the-cluster-hardware-and-system-at-uppmax-hpc2n-lunarc-nsc-and-pdc
NAISS projects overviewhttps://uppmax.github.io/HPC-python/common/naiss_projects_overview.html
Link to Day 1 (Intro to Python)https://uppmax.github.io/HPC-python/common/day1.html
Introductionhttps://uppmax.github.io/HPC-python/day2/intro.html
Why is this course important?https://uppmax.github.io/HPC-python/day2/intro.html#why-is-this-course-important
Exerciseshttps://uppmax.github.io/HPC-python/day2/intro.html#exercises
Using packageshttps://uppmax.github.io/HPC-python/day2/use_packages.html
Why Python packages are importanthttps://uppmax.github.io/HPC-python/day2/use_packages.html#why-python-packages-are-important
Why software modules are importanthttps://uppmax.github.io/HPC-python/day2/use_packages.html#why-software-modules-are-important
How to see which Python packages are installedhttps://uppmax.github.io/HPC-python/day2/use_packages.html#how-to-see-which-python-packages-are-installed
Exerciseshttps://uppmax.github.io/HPC-python/day2/use_packages.html#exercises
Install packageshttps://uppmax.github.io/HPC-python/day2/install_packages.html
Introductionhttps://uppmax.github.io/HPC-python/day2/install_packages.html#introduction
Exercisehttps://uppmax.github.io/HPC-python/day2/install_packages.html#exercise
Use isolated environmentshttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html
Isolated environmentshttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#isolated-environments
Virtual environment - venv & virtualenvhttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#virtual-environment-venv-virtualenv
Condahttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#conda
Install from filehttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#install-from-file
Exerciseshttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#exercises
Summaryhttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#summary
Summaryhttps://uppmax.github.io/HPC-python/day2/use_isolated_environments.html#id10
Basic batch and Slurmhttps://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html
What is a batch job?https://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html#what-is-a-batch-job
What is a cluster?https://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html#what-is-a-cluster
What are some important commands regarding batch jobs?https://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html#what-are-some-important-commands-regarding-batch-jobs
Running your programs and scripts on UPPMAX, HPC2N, LUNARC, NSC, and PDChttps://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html#running-your-programs-and-scripts-on-uppmax-hpc2n-lunarc-nsc-and-pdc
Exerciseshttps://uppmax.github.io/HPC-python/day2/basic_batch_slurm.html#exercises
Interactive work on the compute nodeshttps://uppmax.github.io/HPC-python/day2/interactive.html
Introductionhttps://uppmax.github.io/HPC-python/day2/interactive.html#introduction
The different way HPC2N, UPPMAX, LUNARC, NSC, PDC, and C3SE provide for an interactive sessionhttps://uppmax.github.io/HPC-python/day2/interactive.html#the-different-way-hpc2n-uppmax-lunarc-nsc-pdc-and-c3se-provide-for-an-interactive-session
Start an interactive sessionhttps://uppmax.github.io/HPC-python/day2/interactive.html#start-an-interactive-session
End an interactive sessionhttps://uppmax.github.io/HPC-python/day2/interactive.html#end-an-interactive-session
Check to be in an interactive sessionhttps://uppmax.github.io/HPC-python/day2/interactive.html#check-to-be-in-an-interactive-session
Check that the number of cores booked is correcthttps://uppmax.github.io/HPC-python/day2/interactive.html#check-that-the-number-of-cores-booked-is-correct
Running a Python script in an interactive sessionhttps://uppmax.github.io/HPC-python/day2/interactive.html#running-a-python-script-in-an-interactive-session
Conclusionhttps://uppmax.github.io/HPC-python/day2/interactive.html#conclusion
Desktop On Demandhttps://uppmax.github.io/HPC-python/day2/ondemand-desktop.html
What is Desktop On Demand? Is it right for my job?https://uppmax.github.io/HPC-python/day2/ondemand-desktop.html#what-is-desktop-on-demand-is-it-right-for-my-job
Starting the On-Demand Interfacehttps://uppmax.github.io/HPC-python/day2/ondemand-desktop.html#starting-the-on-demand-interface
Setting Job Parametershttps://uppmax.github.io/HPC-python/day2/ondemand-desktop.html#setting-job-parameters
Job Parameters - GPUshttps://uppmax.github.io/HPC-python/day2/ondemand-desktop.html#job-parameters-gpus
Starting IDEs from command linehttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html
Introductionhttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#introduction
Prepare environment!https://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#prepare-environment
Jupyterhttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#jupyter
Spyderhttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#spyder
VS Codehttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#vs-code
Exercises with step-by-step instructionshttps://uppmax.github.io/HPC-python/day2/IDEs_cmd.html#exercises-with-step-by-step-instructions
Using IDEshttps://uppmax.github.io/HPC-python/day2/IDEs.html
Jupyterhttps://uppmax.github.io/HPC-python/day2/IDEs.html#jupyter
Spyderhttps://uppmax.github.io/HPC-python/day2/IDEs.html#spyder
VS Codehttps://uppmax.github.io/HPC-python/day2/IDEs.html#vs-code
Exerciseshttps://uppmax.github.io/HPC-python/day2/IDEs.html#exercises
Summary day 2https://uppmax.github.io/HPC-python/summary2.html
Evaluationhttps://uppmax.github.io/HPC-python/day2/evaluation.html
Python documentations at the different HPC centreshttps://uppmax.github.io/HPC-python/day2/python_at_hpc_centers.html
A Brief Intro to Matplotlibhttps://uppmax.github.io/HPC-python/day3/new-matplotlib-intro.html
Load and Runhttps://uppmax.github.io/HPC-python/day3/new-matplotlib-intro.html#load-and-run
Basic Terms and Application Programming Interface (API)https://uppmax.github.io/HPC-python/day3/new-matplotlib-intro.html#basic-terms-and-application-programming-interface-api
Standard Available Plot Typeshttps://uppmax.github.io/HPC-python/day3/new-matplotlib-intro.html#standard-available-plot-types
Intro to Pandas on HPChttps://uppmax.github.io/HPC-python/day3/pandas.html
Load and Runhttps://uppmax.github.io/HPC-python/day3/pandas.html#load-and-run
Introductory Topics (Review)https://uppmax.github.io/HPC-python/day3/pandas.html#introductory-topics-review
HPC-Specific Topicshttps://uppmax.github.io/HPC-python/day3/pandas.html#hpc-specific-topics
A Brief Introduction to the Seaborn Statistical Plotting Libraryhttps://uppmax.github.io/HPC-python/day3/seaborn-new.html
Load and Run Seabornhttps://uppmax.github.io/HPC-python/day3/seaborn-new.html#load-and-run-seaborn
Common Featureshttps://uppmax.github.io/HPC-python/day3/seaborn-new.html#common-features
Plotting with Seabornhttps://uppmax.github.io/HPC-python/day3/seaborn-new.html#plotting-with-seaborn
Big data with Pythonhttps://uppmax.github.io/HPC-python/day3/big_data.html
High-Performance Data Analytics (HPDA)https://uppmax.github.io/HPC-python/day3/big_data.html#high-performance-data-analytics-hpda
Why we need to take special actionshttps://uppmax.github.io/HPC-python/day3/big_data.html#why-we-need-to-take-special-actions
What the constraints arehttps://uppmax.github.io/HPC-python/day3/big_data.html#what-the-constraints-are
Solutions and toolshttps://uppmax.github.io/HPC-python/day3/big_data.html#solutions-and-tools
Allocating RAMhttps://uppmax.github.io/HPC-python/day3/big_data.html#allocating-ram
Exercise: Memory allocation (10 min)https://uppmax.github.io/HPC-python/day3/big_data.html#exercise-memory-allocation-10-min
File formatshttps://uppmax.github.io/HPC-python/day3/big_data.html#file-formats
Exercise file formats (10 minutes)https://uppmax.github.io/HPC-python/day3/big_data.html#exercise-file-formats-10-minutes
Computing efficiency with Pythonhttps://uppmax.github.io/HPC-python/day3/big_data.html#computing-efficiency-with-python
Exercises: Packageshttps://uppmax.github.io/HPC-python/day3/big_data.html#exercises-packages
Summaryhttps://uppmax.github.io/HPC-python/day3/big_data.html#summary
Running Python in batch modehttps://uppmax.github.io/HPC-python/day3/batch-new.html
Running your programs and scripts on UPPMAX, HPC2N, LUNARC, C3SE, NSC, and PDChttps://uppmax.github.io/HPC-python/day3/batch-new.html#running-your-programs-and-scripts-on-uppmax-hpc2n-lunarc-c3se-nsc-and-pdc
Example Python batch scriptshttps://uppmax.github.io/HPC-python/day3/batch-new.html#example-python-batch-scripts
Summary day 3https://uppmax.github.io/HPC-python/summary3.html
Evaluationhttps://uppmax.github.io/HPC-python/day3/evaluation.html
Parallel computing with Pythonhttps://uppmax.github.io/HPC-python/day4/parallel.html
What is parallel programming?https://uppmax.github.io/HPC-python/day4/parallel.html#what-is-parallel-programming
Why is parallel programming needed?https://uppmax.github.io/HPC-python/day4/parallel.html#why-is-parallel-programming-needed
Parallelizing code in Pythonhttps://uppmax.github.io/HPC-python/day4/parallel.html#parallelizing-code-in-python
2D integrationhttps://uppmax.github.io/HPC-python/day4/parallel.html#d-integration
Serial optimizationshttps://uppmax.github.io/HPC-python/day4/parallel.html#serial-optimizations
Shared Memoryhttps://uppmax.github.io/HPC-python/day4/parallel.html#shared-memory
Distributed Memoryhttps://uppmax.github.io/HPC-python/day4/parallel.html#distributed-memory
Monitoring resources’ usagehttps://uppmax.github.io/HPC-python/day4/parallel.html#monitoring-resources-usage
Exerciseshttps://uppmax.github.io/HPC-python/day4/parallel.html#exercises
Using GPUs with Pythonhttps://uppmax.github.io/HPC-python/day4/gpu.html
Introductionhttps://uppmax.github.io/HPC-python/day4/gpu.html#introduction
GPUs on UPPMAX, HPC2N, LUNARC, NSC, PDC, and C3SE systemshttps://uppmax.github.io/HPC-python/day4/gpu.html#gpus-on-uppmax-hpc2n-lunarc-nsc-pdc-and-c3se-systems
Numba examplehttps://uppmax.github.io/HPC-python/day4/gpu.html#numba-example
Exerciseshttps://uppmax.github.io/HPC-python/day4/gpu.html#exercises
Additional informationhttps://uppmax.github.io/HPC-python/day4/gpu.html#additional-information
Machine Learning and Deep Learninghttps://uppmax.github.io/HPC-python/day4/ml.html
Introductionhttps://uppmax.github.io/HPC-python/day4/ml.html#introduction
Comparison of ML/DL Librarieshttps://uppmax.github.io/HPC-python/day4/ml.html#comparison-of-ml-dl-libraries
Scikit-Learnhttps://uppmax.github.io/HPC-python/day4/ml.html#scikit-learn
PyTorch and TensorFlowhttps://uppmax.github.io/HPC-python/day4/ml.html#pytorch-and-tensorflow
Tips and Tricks (Lessons Learned):https://uppmax.github.io/HPC-python/day4/ml.html#tips-and-tricks-lessons-learned
Miscellaneous exampleshttps://uppmax.github.io/HPC-python/day4/ml.html#miscellaneous-examples
Exerciseshttps://uppmax.github.io/HPC-python/day4/ml.html#exercises
Dimensionality Reductionhttps://uppmax.github.io/HPC-python/day4/dim_reduction.html
visualisation <–> Sciencehttps://uppmax.github.io/HPC-python/day4/dim_reduction.html#visualisation-science
What is a typical machine learning task?https://uppmax.github.io/HPC-python/day4/dim_reduction.html#what-is-a-typical-machine-learning-task
Some Dimensionality Reduction Techniques:https://uppmax.github.io/HPC-python/day4/dim_reduction.html#some-dimensionality-reduction-techniques
Face Recognition (FR) Use casehttps://uppmax.github.io/HPC-python/day4/dim_reduction.html#face-recognition-fr-use-case
Exercisehttps://uppmax.github.io/HPC-python/day4/dim_reduction.html#exercise
Evaluationhttps://uppmax.github.io/HPC-python/day4/evaluation.html
Summary day 4https://uppmax.github.io/HPC-python/summary4.html
On Bianca clusterhttps://uppmax.github.io/HPC-python/bianca.html
Other courseshttps://uppmax.github.io/HPC-python/extra/other_courses.html
Material for improving your Python skillshttps://uppmax.github.io/HPC-python/extra/other_courses.html#material-for-improving-your-python-skills
Material for improving your general programming skillshttps://uppmax.github.io/HPC-python/extra/other_courses.html#material-for-improving-your-general-programming-skills
More about packageshttps://uppmax.github.io/HPC-python/extra/packages_deeper.html
Using setup.pyhttps://uppmax.github.io/HPC-python/extra/packages_deeper.html#using-setup-py
Developing in isolated environmentshttps://uppmax.github.io/HPC-python/extra/isolated_deeper.html
Creator/developerhttps://uppmax.github.io/HPC-python/extra/isolated_deeper.html#creator-developer
Userhttps://uppmax.github.io/HPC-python/extra/isolated_deeper.html#user
Jupyter at Kebnekaisehttps://uppmax.github.io/HPC-python/extra/jupyterHPC2N.html
Running JupyterLab at HPC2N - extra Python packagehttps://uppmax.github.io/HPC-python/extra/jupyterHPC2N.html#running-jupyterlab-at-hpc2n-extra-python-package
Linkshttps://uppmax.github.io/HPC-python/extra/jupyterHPC2N.html#links
On Kebnekaise clusterhttps://uppmax.github.io/HPC-python/kebnekaise.html
Accessing Kebnekaisehttps://uppmax.github.io/HPC-python/kebnekaise.html#accessing-kebnekaise
Loading Pythonhttps://uppmax.github.io/HPC-python/kebnekaise.html#loading-python
Starting Python and running Python scriptshttps://uppmax.github.io/HPC-python/kebnekaise.html#starting-python-and-running-python-scripts
More about MLhttps://uppmax.github.io/HPC-python/day4/ML_deeper.html
Horovodhttps://uppmax.github.io/HPC-python/day4/ML_deeper.html#horovod
On UPPMAX clustershttps://uppmax.github.io/HPC-python/uppmax.html
UPPMAX clustershttps://uppmax.github.io/HPC-python/uppmax.html#uppmax-clusters
UPPMAX packageshttps://uppmax.github.io/HPC-python/uppmax.html#uppmax-packages
Next https://uppmax.github.io/HPC-python/prereqs.html
Sphinxhttps://www.sphinx-doc.org/
themehttps://github.com/readthedocs/sphinx_rtd_theme
Read the Docshttps://readthedocs.org

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