hpc
44 posts
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Python for HPC at SDSC Summer Institute 2026
I updated the Python for HPC session I taught at the SDSC Summer Institute 2026 (August 7, 2026). The material was heavily rewritten for this year - a substantial rework, not a refresh of the 2025 version.
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Request an HPC@UC allocation on Expanse at SDSC
How UC researchers can request a 500K core-hour allocation on SDSC's Expanse supercomputer through the HPC@UC program, including eligibility, the application process, and trial accounts.
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Running AlphaFold3 and OpenFold3 protein-ligand structure prediction on SDSC Expanse
I built two self-contained, reproducible projects that run realistic (non-toy) protein structure prediction on a single SDSC Expanse GPU node: one with DeepMind AlphaFold3 (via nf-core/proteinfold) and one with the fully open OpenFold3 (MCL1 protein-ligand ensemble).
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Call for Student Volunteers: Summer 2026 HPC & Data Science Institute
We are looking for UC San Diego undergraduates to volunteer as student helpers for the SDSC Summer Institute 2026 — gain hands-on experience in high-performance computing and earn official CCR credit on your transcript.
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SDSC Cyberinfrastructure for AI-Enabled Science: A Beginner's Guide
A beginner-friendly overview of SDSC's computing platforms for AI research — Expanse, Voyager, Cosmos, NRP, and the National Data Platform — with step-by-step access instructions and links to get started.
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SDSC HPC and Data Science Summer Institute 2026
The SDSC HPC and Data Science Summer Institute 2026 is a week-long, in-person training event focused on introductory-to-intermediate topics in High Performance Computing (HPC), Data Science, and Artificial Intelligence (AI).
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Request access to AWS and Google Cloud resources via CloudBank for scientists
CloudBank provides a simplified way for scientists and educators to access commercial cloud resources, including Amazon Web Services (AWS) and Google Cloud. Access is free, but requires writing a proposal to justify the requested resources.
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Implementing conditional logic in Nextflow workflows
This post serves as a follow-up to my previous tutorial, "Running Nextflow on Expanse", where I covered the foundational aspects of deploying Nextflow workflows on an HPC environment.
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Mixing Nextflow executors for hybrid workflows
This post demonstrates how to combine different Nextflow executors within a single workflow, a powerful pattern for optimizing resource usage in scientific computing.
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Running Nextflow on Expanse with Seqera
This tutorial will guide you through setting up Nextflow on Expanse using the Seqera platform. Nextflow is a powerful and flexible workflow management system that enables scalable and reproducible scientific workflows.
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Running Nextflow on Expanse
This tutorial will guide you through setting up Nextflow on Expanse. Nextflow is a powerful and flexible workflow management system that enables scalable and reproducible scientific workflows.
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Python for HPC
Python is often the first choice for prototyping research ideas, but scaling that prototype to thousands of cores and multi‑node workflows needs a different toolkit.
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Execute Pegasus jobs on Expanse
Pegasus is a workflow management system that helps scientists and engineers execute complex computational workflows. Pegasus supports different data staging mechanisms, primarily sharedfs and condorio. The sharedfs mode is used when the head node and all worker nodes share a common file system, allowing jobs to directly access data. However, there is currently a bug that prevents sharedfs from working as expected. In contrast, the condorio mode is designed for environments where worker nodes do not share a file system, relying on HTCondor's built-in file transfer capabilities for all data I/O. Since Pegasus 5.0, condorio is the default. Our current setup on Expanse, utilizing HTCondor Annex, operates in condorio mode, leveraging Condor's efficient data transfer for distributed execution.
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How to request High Performance Computing (HPC) resources
I am often asked how a scientist located in the US can access supercomputing resources. I decided to write a blog post with an overview of the options, consider that I'm writing this in April 2025, so please cross-check on the official websites.
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Tutorial on Python for HPC at the SDSC Summer Institute 2024
Each August the San Diego Supercomputer Center organizes a week-long summer school that teaches a large number of topics related to Supercomputing and AI to early career scientists.