Tutorials¶

Worked tutorials covering Linux, data transfers, software, and domain science.

• Introduction to Linux - A first tour of the Linux command line for new HPC users.
• Parallel Python with Dask and scikit-learn - Scale scikit-learn workloads across cluster nodes from JupyterHub using Dask.
• MPI parallelization from JupyterHub - Run MPI-parallel Python (mpi4py/ipyparallel) from CARC JupyterHub sessions.
• Parallel R with the future package - Parallelize R code across cores and nodes using the future framework.
• MATLAB deep learning - Train deep learning models in MATLAB using CARC GPU nodes.
• Mathematica on Easley - Derive exact beam-deflection formulas with Mathematica, then run the examples across CPUs, nodes, and a GPU on Easley.
• PyTorch image classifier walkthrough - End-to-end example: train an image classifier with PyTorch on a CARC GPU node.
• Multi-GPU TensorFlow - Distribute TensorFlow training across multiple GPUs on a CARC node.
• Apache Spark - Launch Apache Spark clusters inside Slurm allocations for large-scale data analysis.
• Variant calling with GATK - A genomics variant-calling workflow using GATK best practices on CARC systems.
• Metabarcoding analysis - Process environmental DNA metabarcoding data on CARC clusters.
• RAD-seq analysis with Stacks - Analyze restriction-site associated DNA sequencing (RAD-seq) data with Stacks.
• Genome assembly evaluation with QUAST and BUSCO - Evaluate genome assembly quality and completeness with QUAST and BUSCO.
• Coalescent simulation with msprime - Simulate genealogical histories and genome sequences with msprime.
• Demographic inference with PSMC - Infer population size history from diploid genomes using PSMC.
• Bayesian phylogenetics with BEAST - Run BEAST Bayesian evolutionary analyses on CARC clusters.
• SimCov epidemiological simulation - Run the SimCov agent-based model of SARS-CoV-2 infection dynamics in lung tissue.
• VASP materials simulation - Set up and run VASP density-functional-theory calculations on CARC clusters.
• ORCA quantum chemistry - Run ORCA quantum chemistry calculations in parallel on CARC clusters.
• Parallel CASA for radio astronomy - Run mpiCASA for parallel radio astronomy imaging on CARC clusters.

Data transfer¶

• Data transfer tutorials - Moving data to and from CARC storage.

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