Andrea Zonca

Mastodon

 

Call for Student Volunteers: Summer 2026 HPC & Data Science Institute

sdsc
hpc
education
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.
Jun 3, 2026
Andrea Zonca

healpy 1.20.0b1 beta — harmonic_ud_grade for artifact-safe map downgrading

python
astrophysics
healpy
healpix
cmb
harmonic_ud_grade changes map NSIDE through spherical-harmonic transforms with pixel-window and beam transfer corrections following Eq. 1 of Planck 2015 X (arXiv:1502.01588).
May 29, 2026
Andrea Zonca

 

SDSC Cyberinfrastructure for AI-Enabled Science: A Beginner’s Guide

hpc
ai
sdsc
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.
May 29, 2026
Andrea Zonca, Mai H. Nguyen

 

PySM 3.4.5: HalfDome TSZ model, scipy pin removed, Python 3.9 dropped

python
astronomy
pysm
PySM 3.4.5 is now available on PyPI and GitHub.
May 28, 2026
Andrea Zonca

 

Synchronizing Google Docs and GitHub with gdrivemd

tools
automation
github
Managing documentation often requires choosing between the collaborative ease of Google Docs and the version-controlled structure of GitHub. The gdrivemd scripts (usable as…
May 24, 2026
Andrea Zonca

healpy harmonic_ud_grade vs skytools change_resolution: A Comparison

python
astrophysics
healpy
healpix
cmb
A comparison of healpy.harmonic_ud_grade and skytools.change_resolution for HEALPix map resolution changes, highlighting API differences, beam/pixel-window support, direct alm input, and agreement levels.
May 20, 2026
Andrea Zonca

 

Do you need JupyterHub for your workshop? JupyterLite runs Python in the browser

jupyter
teaching
python
You’re organizing a Python workshop or teaching a class that uses Jupyter notebooks. The first question that comes up is almost always the same: how do I get everyone…
May 18, 2026
Andrea Zonca

 

up: One command to update all my AI tools

linux
ai
tools
I use a lot of AI coding assistants — Claude Code, Gemini CLI, Codex, Cline, Qwen Code, Crush, and more. Keeping them all updated was a chore: apt upgrade for the system, npm…
May 17, 2026
Andrea Zonca

harmonic_ud_grade vs ud_grade: A Focused Comparison

python
astrophysics
healpy
harmonic_ud_grade vs ud_grade A Focused Comparison.
May 5, 2026
Andrea Zonca

 

SDSC HPC and Data Science Summer Institute 2026

events
HPC
data-science
education
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…
Apr 23, 2026
Andrea Zonca

 

Deploying JupyterHub on OpenStack Magnum with OpenTofu

kubernetes
openstack
jupyterhub
In this tutorial, we will walk through the process of deploying a production-ready JupyterHub on OpenStack Magnum using OpenTofu.
Apr 22, 2026
Andrea Zonca

SPT-3G D1 high-ℓ CMB power spectra vs. Planck 2018

cosmology
python
Load and compare the SPT-3G D1 high-ell TT power spectra with the Planck 2018 CMB power spectrum, illustrating primary vs. secondary CMB anisotropies.
Apr 21, 2026
Andrea Zonca

 

Configure Claude Code with MiniMax on NRP

ai
tools
This guide covers configuring Claude Code to use MiniMax models through the NRP (Nautilus Research Platform) infrastructure, including setting up Brave Search for web queries.
Apr 21, 2026
Andrea Zonca

 

Fixing clipboard issues with Opencode in Byobu/Tmux over SSH on Chromebook

linux
When using a Chromebook (Crostini) and connecting via SSH to a remote server, you might encounter a frustrating clipboard issue. Copy-paste works perfectly when running openc…
Apr 13, 2026
Andrea Zonca

 

Send email using UCSD SMTP with a Gmail-based address

Python
If you have a GMAIL-based UCSD email address and need to send email programmatically or via an email client using SMTP, you can use Google’s SMTP servers.
Apr 13, 2026
Andrea Zonca

Why 3 pixels per beam? The mathematics of HEALPix resolution matching

python
astrophysics
healpy
Exploring why the Planck convention uses FWHM = 3 x pixel size for harmonic-space map downgrading, with equations from the literature and simulated demonstrations.
Apr 6, 2026
Andrea Zonca

 

PySM 3.4.4 released with new SZ models and NumPy 2 support

openscience
pysm
python
PySM 3.4.4 is now available both on PyPI and on conda-forge. This release is mostly about extending the Sunyaev-Zeldovich model suite and making sure PySM works cleanly with…
Apr 2, 2026
Andrea Zonca

 

Deploy a ChatGPT-like LLM on Jetstream with llama.cpp, tested on g3.medium

jetstream
llm
This is a tested follow-up and updated standalone version of Deploy a ChatGPT-like LLM on Jetstream with llama.cpp. I ran the deployment end to end on a fresh Jetstream…
Mar 11, 2026
Andrea Zonca

 

Better way to export a Confluence page to Markdown

documentation
In a previous post, I wrote about Export a Confluence page to Markdown by copying and pasting into Google Docs. I’ve since found a better and much more powerful way using the …
Mar 11, 2026
Andrea Zonca

 

Keep Jupyter notebooks clean in git, but rendered with outputs in Sphinx

python
jupyter
A small Sphinx extension that fetches an executed notebook from a Gist or raw URL, verifies the sources still match, and replaces the local notebook during the docs build.
Mar 10, 2026
Andrea Zonca

 

How to pronounce Andrea in Italian

The Italian pronunciation of Andrea is:
Mar 6, 2026
Andrea Zonca

 

Auto-build JupyterHub images with repo2docker and GitHub Actions

jupyterhub
python
This guide explains how to automatically build a custom, JupyterHub-ready Docker image directly from GitHub using repo2docker, without having to write a complicated…
Mar 4, 2026
Andrea Zonca

 

Deploy nbgrader on Jetstream with a Manila exchange disk (Kubernetes)

kubernetes
jetstream
jupyterhub
nbgrader
This tutorial shows how to deploy nbgrader on Jetstream Kubernetes using a shared Manila disk mounted on all JupyterHub user pods.
Mar 3, 2026
Andrea Zonca

 

Connect Gmail (and more) to Codex CLI and Gemini CLI with Smithery (MCP)

ai
Use Smithery to connect Gmail, Google Sheets, and Calendar to terminal AI assistants via MCP, with OAuth handled in the browser.
Feb 6, 2026
Andrea Zonca

 

Create a Manila share in Exosphere and mount it for all JupyterHub users

kubernetes
jetstream2
jupyterhub
This tutorial shows how to create a Manila share in Exosphere and mount it into all JupyterHub single-user pods on Jetstream 2. This provides a ReadWriteMany (RWX) shared…
Feb 4, 2026
Andrea Zonca

 

Deploy a NFS server to share data between JupyterHub users on Jetstream

kubernetes
jetstream
jupyterhub
linux
This is an updated version of my 2025 tutorial on deploying a NFS server to share data between JupyterHub users on Jetstream.
Feb 4, 2026
Andrea Zonca

 

Deploy nbgrader on Jetstream with ngshare (Kubernetes)

kubernetes
jetstream
jupyterhub
nbgrader
Update (March 3, 2026): See the newer tutorial: Deploy nbgrader on Jetstream with a Manila exchange disk (Kubernetes)
Feb 4, 2026
Andrea Zonca

 

Configure NRP LLM with OpenCode and Crush

ai
The National Research Platform (NRP) provides a free Large Language Model (LLM) service for researchers. This service allows you to access powerful models like GLM 4.7…
Jan 29, 2026
Andrea Zonca

 

Setting up shared NFS home directories & shared data for JupyterHub on Kubernetes

kubernetes
jetstream
jupyterhub
This tutorial provides a walkthrough on how to set up a shared NFS server for JupyterHub users’ home directories and shared data.
Jan 20, 2026
Andrea Zonca

 

Terminal-based AI assistant with GitHub for Education

ai
github
GitHub offers to all academic people a free GitHub Pro account which allows you to use GitHub Copilot Pro, which includes access to the latest and most powerful models from…
Jan 20, 2026
Andrea Zonca

 

Convenience script for system & CLI updates

linux
ai
I use a simple bash alias to keep my environment in sync with one command. It handles standard system updates and refreshes my core AI tools—the Gemini and Codex CLIs.
Jan 10, 2026
Andrea Zonca

 

Voice chatbot with Gemini Live

ai
In this tutorial, we will explore how to create a voice-enabled chatbot using the new “Live” capabilities in Google AI Studio. Our goal is to build an assistant that can…
Jan 4, 2026
Andrea Zonca

 

AI chatbot as a frontend for a Google Form

ai
Using a chatbot as a frontend for a Google Form can significantly improve user engagement and completion rates. Instead of a static form, users interact with a…
Jan 1, 2026
Andrea Zonca

 

Read DICOM (Tomography) files with 3D Slicer

If you receive a USB drive with tomography data (for example from a dentist), the files often come in DICOM format (extension .dcm).
Dec 19, 2025
Andrea Zonca

 

Cosmosage: A specialized AI assistant for cosmology

jetstream
llm
cosmology
Cosmosage is an AI assistant specialized in cosmology. It has been trained on thousands of cosmology papers and textbooks, starting from a large-language model base and…
Dec 17, 2025
Andrea Zonca

 

Cosmosage Unshelver

github
This post describes the Cosmosage Unshelver. You can find the project on GitHub: zonca/openstack_unshelver_webapp. There is an active pull request for further development.…
Dec 16, 2025
Andrea Zonca

 

Copy a single Codex session to another machine

ai
You might want to copy a Codex session to another machine to continue a conversation started on one device, such as moving from a laptop to a desktop or server.
Dec 16, 2025
Andrea Zonca

 

Request access to AWS and Google Cloud resources via CloudBank for scientists

cloudcomputing
openscience
hpc
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…
Dec 15, 2025
Andrea Zonca

Healpy blm_gauss breaking change analysis

python
astrophysics
healpy
Analyzing the breaking change in healpy’s blm_gauss function (1.18.1 to 1.19.0) and its impact on Gaussian beam coefficients.
Dec 11, 2025
Andrea Zonca

 

Release of healpy 1.19.0

healpy
python
I am pleased to announce the release of healpy 1.19.0.
Dec 11, 2025
Andrea Zonca

 

Jupytext for AI agent Jupyter workflows

python
How using Jupytext with AI coding agents can simplify Jupyter Notebook development by avoiding JSON formatting issues.
Dec 11, 2025
Andrea Zonca

 

The Aaron Price Fellows Program: Fostering community leaders

The Aaron Price Fellows Program is an initiative dedicated to preparing highly motivated and diverse public high school students from San Diego to become responsible…
Dec 9, 2025
Andrea Zonca

 

Software Citation Station

software
github
This post introduces the “Software Citation Station” by Tom Wagg, a tool designed to help researchers generate accurate and comprehensive citations for software. It…
Dec 3, 2025
Andrea Zonca

 

How to install codex and gemini cli

ai
This is actually not recommended because it mixes node packages with other packages installed in .local. Recommend instead to use nvm, once configured nvm, then the standard…
Dec 2, 2025
Andrea Zonca

 

Container and product EZID DOIs with Python

python
doi
This post refers to the ezid_api repository.
Dec 2, 2025
Andrea Zonca

 

Take control of your Kaiser Permanente blood test results (no coding knowledge required)

ai
github
Want to make sense of your Kaiser Permanente blood test results without needing to be a coding expert? This guide will walk you through using readily available tools to…
Dec 2, 2025
Andrea Zonca

 

Disable Gemini CLI loading phrases

How to disable the annoying loading phrases in Gemini CLI for a smoother experience.
Dec 2, 2025
Andrea Zonca

 

Auto-build JupyterHub images with GitHub Actions

jupyterhub
python
Overview: https://github.com/zonca/custom-jupyterhub-docker-image is a template that ships a JupyterHub-ready single-user image with common scientific Python tooling and…
Dec 1, 2025
Andrea Zonca

 

Deploy the Dask Operator for JupyterHub on Kubernetes

kubernetes
jetstream2
jupyterhub
python
This post describes how to deploy the Dask Operator for Kubernetes alongside a Helm-based JupyterHub installation. The Operator provides a Kubernetes-native way to create…
Nov 17, 2025
Andrea Zonca

 

Implementing conditional logic in Nextflow workflows

hpc
sdsc
nextflow
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…
Nov 15, 2025
Andrea Zonca

 

Mixing Nextflow executors for hybrid workflows

hpc
sdsc
nextflow
This post demonstrates how to combine different Nextflow executors within a single workflow, a powerful pattern for optimizing resource usage in scientific computing. By…
Nov 15, 2025
Andrea Zonca

 

Hierarchical EZID DOIs with Python

python
doi
This post refers to the ezid_api repository.
Nov 13, 2025
Andrea Zonca

 

Going full agentic for scientific software development

github
ai
python
The landscape of scientific software development is being transformed by AI coding agents. Over the past few weeks, I’ve been exploring GitHub Copilot’s AI coding agent…
Nov 10, 2025
Andrea Zonca

 

Software Citation Station helper script

Proof-of-concept generate_citation.py in the software_citation repo pulls PyPI metadata plus repo CITATION files to produce the Markdown block that Software Citation Station …
Nov 6, 2025
Andrea Zonca

 

Updated tutorial on The Littlest JupyterHub on Jetstream

jupyterhub
jetstream2
I’m excited to share that I’ve contributed an updated tutorial on how to deploy “The Littlest JupyterHub” (TLJH) on a Jetstream instance!
Nov 4, 2025
Andrea Zonca

 

Tampermonkey script for Audible filtering

This Tampermonkey script helps filter Audible search results by hiding items that do not meet certain criteria. Specifically, it hides audiobooks with a rating less than 4.0…
Nov 1, 2025
Zonca

 

Running Nextflow on Expanse with Seqera

hpc
sdsc
nextflow
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…
Oct 27, 2025
Andrea Zonca

 

Auto-merge GitHub pull requests after GitHub Actions pass

github
Pull request auto-merge is a small feature that keeps teams from babysitting green builds. Once every required check is green, GitHub merges the PR for you—no extra clicks…
Oct 20, 2025
Andrea Zonca

 

Manage calendar of a scientific collaboration using Google Groups

openscience
Managing a calendar for a large scientific collaboration can be challenging. Over the years, I have tried different approaches to solve this problem.
Oct 10, 2025
Andrea Zonca

 

Running Nextflow on Expanse

hpc
sdsc
nextflow
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…
Oct 7, 2025
Andrea Zonca

 

Building Singularity containers with Conda environments from requirements.txt

singularity
python
This post introduces a method for building Singularity containers that include a Conda environment based on a requirements.txt file. This approach provides a reproducible…
Oct 7, 2025
Andrea Zonca

EZID DOI management with Python

python
doi
This project offers Python scripts for interacting with the EZID API to create and verify Digital Object Identifiers (DOIs).
Oct 7, 2025
Andrea Zonca

 

PySM 3.4.3 Released

openscience
pysm
python
PySM version 3.4.3 is now live. Install it from PyPI or upgrade existing environments with pip install --upgrade pysm3. Full details are available in the GitHub release notes.
Oct 2, 2025
Andrea Zonca

 

Deploy a ChatGPT-like LLM on Jetstream with llama.cpp

jetstream
llm
Tutorial last updated in December 2025
Sep 30, 2025
Andrea Zonca

PySM methods paper published in ApJ

openscience
pysm
python
The Astrophysical Journal formally published our paper, Full-sky Models of Galactic Microwave Emission and Polarization at Sub-arcminute Scales for the Python Sky Model, on S…
Sep 24, 2025
Andrea Zonca

 

Inspect SMTP sending through UCSD

Python
When configuring email sending through UCSD, it can be surprisingly unclear which SMTP server to use. The official documentation mentions three options: smtp.ucsd.edu, smtp.g…
Sep 23, 2025
Andrea Zonca

OpenStack Unshelver Demo

openstack
jetstream
I recently vibe-coded a lightweight web application, using gpt-5-codex, that revives shelved OpenStack instances on demand. The stack is intentionally minimal: a FastHTML…
Sep 22, 2025
Andrea Zonca

 

Timing the unshelving of a Jetstream 70B LLM instance

jetstream
llm
Following the work documented in Deploy a 70B LLM to Jetstream, the Meta-Llama-3.1-70B-Instruct-GGUF deployment is now running on a g3.xl instance. The goal of this…
Sep 18, 2025
Andrea Zonca

 

Deploy a 70B LLM to Jetstream

jetstream
llm
Deploying large language models on Jetstream is getting easier thanks to the official Jetstream LLM guide. Here I follow that walkthrough but scale the hardware and model so…
Sep 18, 2025
Andrea Zonca

 

Python for HPC

Python
hpc
sdsc
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. This…
Sep 15, 2025
Andrea Zonca

 

Execute Pegasus jobs on Expanse

sdsc
hpc
Pegasus is a workflow management system that helps scientists and engineers execute complex computational workflows. It maps a user’s abstract workflow onto available…
Sep 9, 2025
Andrea Zonca

 

Use VS Code on Expanse

Using VS Code directly on Expanse, or other HPC systems, is generally not recommended due to the high resource usage of the IDE itself. These systems are optimized for…
Aug 8, 2025
Andrea Zonca

 

How to use AI chat assistants while traveling

ai
llm
Traveling often means unreliable or expensive internet access, especially on airplanes or in remote areas. Here are two practical ways to keep using AI chat assistants even…
Jun 17, 2025
Andrea Zonca

 

Voyager enters ACCESS allocations phase

ai
sdsc
As of June 1, 2025, SDSC’s Voyager supercomputer has transitioned from its testbed phase to the ACCESS Allocations Phase. All research use now requires an official ACCESS…
Jun 4, 2025
Andrea Zonca

 

How to use GitHub Copilot for scientific computing

github
ai
python
GitHub Copilot is rapidly transforming the landscape of scientific computing by streamlining code development and accelerating research workflows. This guide outlines how…
May 23, 2025
Andrea Zonca

Python and AI coding summer camp in person in San Diego

python
I’m excited to announce that I’ll be teaching a brand new Python and AI Coding Summer Camp in person in San Diego, hosted at the Italian School of San Diego (Kearny Mesa)!
May 18, 2025
Andrea Zonca

VS Code Copilot agent mode: A productivity showcase

llm
ai
Visual Studio Code, together with GitHub Copilot in agent mode, enables a more focused and efficient development workflow. Below are three practical examples of how this…
May 13, 2025
Andrea Zonca

 

Astrophysics Papers Daily Summaries Notebook with the Jetstream LLM Inference Service

astrophysics
llm
jetstream2
Fetch today’s astro-ph papers from arXiv, summarize abstracts with llm, and output a Markdown summary.
May 8, 2025
Andrea Zonca

 

BK18 added to Panexp model suite and new WebSky radio source models in PySM 3.4.1

pysm
cmb
Following up on my previous post about Panexp model suite simulations, there have been several important updates:
May 1, 2025
Andrea Zonca

 

Deploy a NFS server to share data between JupyterHub users on Jetstream

kubernetes
jetstream
jupyterhub
linux
This is an updated version of my 2023 tutorial on deploying a NFS server to share data between JupyterHub users on Jetstream.
Apr 22, 2025
Andrea Zonca

 

How to request High Performance Computing (HPC) resources

hpc
sdsc
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…
Apr 19, 2025
Andrea Zonca

 

PySM 3.4.1 Released

openscience
pysm
python
PySM version 3.4.1 is now available. It can be downloaded from PyPI. The release notes detail new features and improvements.
Apr 15, 2025
Andrea Zonca

 

healpy 1.18.1 released

healpy
python
Just released healpy 1.18.1, this version includes important bug fixes, please test and open issues at https://github.com/healpy/healpy/issues
Mar 30, 2025
Andrea Zonca

 

New simulations of the Panexp model suite for Planck and WMAP

pysm
cmb
Following up on my recent post about PySM models for Galactic emission, I have recently executed three new simulations of the Panexp model suite:
Mar 30, 2025
Andrea Zonca

 

Gateways 2024 - Tutorial on creating a serverless research data repository based on Globus

data
Following our work published at PEARC 2024 presenting a Data Portal based on a static website built on top of Globus HTTPS services, we presented a tutorial at Gateways 2024.
Mar 26, 2025
Andrea Zonca

 

Jetstream2 Usage Monitoring

jetstream2
Monitoring resource usage on cloud platforms is essential for managing allocations effectively. For users of Jetstream2, the Unidata team has developed a useful script to…
Mar 26, 2025
Andrea Zonca

 

Deployment of BinderHub by Project Pythia on Jetstream 2

kubernetes
jetstream2
Project Pythia has recently published a blog post about their deployment of BinderHub on Jetstream 2. This blog post discusses Project Pythia’s efforts to address “Jupyter…
Mar 26, 2025
Andrea Zonca

 

New paper on arXiv about models of Galactic emission in the microwaves for CMB experiments

openscience
pysm
python
A new paper has been published on Arxiv discussing models of Galactic emission in the microwaves for Cosmic Microwave Background (CMB) experiments:
Mar 3, 2025
Andrea Zonca

Use Jetstream’s DeepSeek R1 as a code assistant on JupyterAI

jetstream
llm
Thanks to Openrouter, there is now a way of using the Jetstream LLM inference system, in particular the powerful Deepseek R1 model, as a code and documentation assistant in…
Feb 4, 2025
Andrea Zonca

Authenticate to GitHub in the browser with the device flow

github
Authenticating to GitHub in the browser using the device flow is essential for applications that cannot directly handle OAuth redirects. This method allows users to…
Jan 29, 2025
Andrea Zonca

 

Save Jupyterlite notebooks to GitHub

github
JupyterLite runs entirely inside the browser, which means it doesn’t have access to the underlying operating system. Its storage is persistent across restarts of the machine…
Jan 29, 2025
Andrea Zonca

 

Using GitHub Releases to keep track of large artifacts

github
GitHub Releases provide a way to attach large artifacts, such as binaries or large autogenerated files, without polluting the repository. A release points to a specific…
Jan 22, 2025
Andrea Zonca

 

Italian and chess classes in San Diego

italian
My wife Maura D’Andrea is Principal and Teacher of Italian school of San Diego.
Jan 1, 2025
Andrea Zonca

 

Deploy Kubernetes and JupyterHub on Jetstream with Magnum and Cluster API

kubernetes
jetstream
jupyterhub
This guide demonstrates how to deploy Kubernetes on Jetstream with Magnum and then install JupyterHub on top using zero-to-jupyterhub. Jetstream recently enabled the Cluster…
Dec 11, 2024
Andrea Zonca

 

Proposal for Simons Observatory data products attribution

data
doi
CC BY 4.0 only requiring attribution and not restricting commercial use or remixes.
Dec 5, 2024
Andrea Zonca

 

Run Windows and WSL on Jetstream

jetstream
Need access to a Windows machine? You can leverage Jetstream 2, spin up a Virtual Machine with Windows Server 2022 and access the Windows graphical desktop through your…
Dec 4, 2024
Andrea Zonca

 

Allow users to self-invite to a Google Calendar event

openscience
Google Calendar is the most popular calendar service, and it is widely used in academia, often Scientific Collaborations maintain one or multiple shared calendars to keep…
Nov 13, 2024
Andrea Zonca

 

Deploy an LLM ChatGPT-like service on Jetstream

jetstream
llm
kubernetes
python
In this tutorial we will deploy a LLM Chat-GPT like service on a GPU node on Jetstream. For experimentation purposes we are using the smaller and cheapest GPU node available…
Oct 31, 2024
Andrea Zonca

Kubernetes monitoring with Prometheus and Grafana

kubernetes
jetstream
jupyterhub
In a production Kubernetes deployment it is necessary to make it easier to monitor the status of the cluster effectively. Kubernetes provides Prometheus to gather data from…
Oct 25, 2024
Andrea Zonca

 

Generate script to mount a Manila share

kubernetes
jetstream2
Jetstream 2 makes creating volumes that are shared across instances as easy as creating standard volumes. This is provided by the Manila service, which creates volumes based…
Oct 9, 2024
Andrea Zonca

 

Configure ssh-agent on Linux

linux
I keep Googling this again and again.
Oct 2, 2024
Andrea Zonca

 

Tutorial on Python for HPC at the SDSC Summer Institute 2024

python
hpc
sdsc
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…
Sep 11, 2024
Andrea Zonca

 

How to use Anki flashcards to help kids learn spelling

documentation
In the Anki Desktop app on your computer, from the main screen, click on the “Create Deck” button to create a new deck, name it “Spelling::Week1” or similar. This is going…
Sep 3, 2024
Andrea Zonca

Generate sample Cosmology data for Cheap and FAIR data portal with PySM

cosmology
healpy
pysm
This notebook generates some figures of Galactic and Extra-Galactic emissions using PySM. Mostly for displaying purposes.
Aug 28, 2024
Andrea Zonca

 

Cosmic Microwave Background data licensing

data
Some thoughts on how to license and attribute data products from the Simons Observatory.
Aug 4, 2024
Andrea Zonca

 

Export a Confluence page to Markdown

documentation
I feel the pain, you have a page trapped in Confluence and you want to set it free. Of course the “Export” features of Confluence are useless.
Aug 4, 2024
Andrea Zonca

 

Ubuntu 22.04 minimal on Jetstream

kubernetes
jetstream2
Update July 2024: Ubuntu 22.04 Minimal image with Generic Kernel
Jul 31, 2024
Andrea Zonca

PEARC24 paper Cheap and FAIR Data Portal

data
In this blog post, we summarize the key points from our recent paper presented at PEARC 2024, titled “Cheap and FAIR: A Serverless Research Data Repository for the Next…
Jul 31, 2024
Andrea Zonca

Generate point source maps with pixell and convert to HEALPix

cosmology
pysm
Testing the pixell sim_objects functionality to create maps of point sources pre-smoothed with a gaussian beam. The purpose is to include this functionality in PySM to be…
Jul 29, 2024
Andrea Zonca

Run (part of) healpy in the browser with pyodide

python
healpy
Thanks to the help of @VeerioSDSC and Rick Wagner, I have been able to run part of healpy in the browser. For now only tested reading FITS maps and plotting with projview.
Jul 17, 2024
Andrea Zonca

 

Conditional authentication on a single endpoint with FastAPI

python
Building on my previous tutorial, I have now implemented a toy FastAPI application which requires authentication based on query parameters.
Jun 27, 2024
Andrea Zonca

 

Deploy a web server with automatic HTTPS for static website and Django app on Jestream 2

jetstream2
python
As part of my work to support the Jetstream 2 Openstack deployment at Indiana University, I have developed a tutorial that explains how to create a Virtual Machine that…
Jun 13, 2024
Andrea Zonca

 

Authenticate FastAPI endpoints with a GitHub organization

python
git
github
FastAPI is a framework that simplifies building APIs in Python. Authentication via Google, Github and many more is provided by FastAPI-SSO.
May 29, 2024
Andrea Zonca

 

AI Code Assistant at NERSC

python
nersc
If you are used to Github Copilot on VS Code or on Google Colaboratory as I am, coding without an AI assistant is so slow!
May 28, 2024
Andrea Zonca

 

Jupyter Notebook frontmatter for Quarto to download source notebook

python
jupyter
Quarto is one of the best platforms to create statically generated blogs with Markdown and Jupyter Notebooks.
May 28, 2024
Andrea Zonca

Interactive 3D plot of a Planck map with Matplotlib

python
astrophysics
This is an update of my older tutorial
May 20, 2024
Andrea Zonca

 

HEALPix in Megapixels

cosmology
healpy
How many megapixels is a HEALPix map?
May 20, 2024
Andrea Zonca

 

Load data from Globus in the browser and plot with pyscript

python
Globus supports a Javascript SDK which allows to authenticate against Globus Auth and then access all the Globus services, for example accessing protected data or setting up…
May 16, 2024
Andrea Zonca

 

Ubuntu 22.04 minimal on Jetstream with GPU support

kubernetes
jetstream2
Just notes on how to create a Ubuntu 22.04 image with GPU support
May 13, 2024
Andrea Zonca

 

News item on SDSC website about Advanced Simons Observatory and PySM

python
pysm
cosmology
In collaboration with the SDSC Communications team I prepared a news item for the SDSC Website announcing my participation in the Advanced Simons Observatory project…
May 12, 2024
Andrea Zonca

 

Italian classes in San Diego

italian
My wife Maura D’Andrea is Principal and Teacher of Italian school of San Diego.
May 11, 2024
Andrea Zonca

Generate point source maps with pixell

cosmology
pysm
Testing the pixell sim_objects functionality to create maps of point sources pre-smoothed with a gaussian beam. The purpose is to include this functionality in PySM to be…
May 2, 2024
Andrea Zonca

 

Setup a conda environment at NERSC

python
nersc
NERSC recommends to use the “Global Common” to store Conda environments, because it is optimized to store lots of small files. Consider that it is mounted read-only on…
May 2, 2024
Andrea Zonca

 

Flatcar Container Linux on Jetstream

kubernetes
jetstream2
Virtual Machine images provided by the Jetstream team are fully fledged and therefore quite large.
Apr 30, 2024
Andrea Zonca

 

Automate sending polls via WhatsApp

Polls in WhatsApp are so convenient for the users, but so painful for group admins. Cannot modify them, cannot re-use or replicate them.
Apr 25, 2024
Andrea Zonca

 

2-way synchronization of Overleaf and GitHub via a GitHub Action

git
github
Updated: 2025-02-20
Apr 17, 2024
Andrea Zonca

Generate figures for PySM emissions

cosmology
healpy
pysm
This notebook generates some figures of Galactic and Extra-Galactic emissions using PySM. Mostly for displaying purposes.
Apr 12, 2024
Andrea Zonca

 

Run PyTorch with GPU support on Expanse

hpc
jupyter
python
In this tutorial we will create a Python environment with PyTorch and see how to get Jupyterlab running on a GPU node.
Apr 4, 2024
Andrea Zonca

 

Deploy Kubernetes on Jetstream 2 with GPU support

jetstream2
jupyterhub
kubernetes
This work has been supported by Indiana University and is cross-posted on the Jetstream 2 official documentation website.
Feb 8, 2024
Andrea Zonca

 

Soft scaling Kubernetes on Jetstream

kubernetes
jetstream2
ana-espinoza
Work and post contributed by Ana Espinoza, only tested and benchmarked by Andrea Zonca.
Feb 2, 2024
Andrea Zonca

 

Make a PDF from a series of screenshots

You might need to digitize some web content by taking screenshots and then bundling them up in a PDF.
Jan 12, 2024
Andrea Zonca

 

Received DeSouza award for work on deploying software infrastructure on Jetstream

jupyterhub
jetstream
kubernetes
I am honored to have received the 2023 DeSouza award from Unidata, a NSF-funded center providing data, software and support for the field of Geoscience. The award celebrates…
Nov 2, 2023
Andrea Zonca

 

Buy US Treasury bonds on Fidelity

The Fidelity interface is complicated, here a description of the steps necessary to buy newly issued US Treasury bonds at the next available auction. Currently auctions are…
Oct 27, 2023
Andrea Zonca

 

Gateways 2023 tutorial about Dask and JupyterHub on Kubernetes on Jetstream

jupyterhub
jetstream
kubernetes
python
Video on Youtube
Oct 11, 2023
Andrea Zonca

 

Deploy Dask Gateway with JupyterHub on Kubernetes

kubernetes
jetstream2
jupyterhub
dask
python
In this tutorial we will install Dask Gateway, currently version 2023.9.0, on Kubernetes and configure JupyterHub so Jupyter Notebook users can launch private Dask cluster…
Sep 28, 2023
Andrea Zonca

 

Deploy GitHub Authenticator in JupyterHub

jupyterhub
jetstream
kubernetes
git
github
Updated June 2024: added more options to config file
Sep 27, 2023
Andrea Zonca

 

Setup HTTPS on Kubernetes with cert-manager

kubernetes
jetstream
jupyterhub
Update March 2024: the routing issue that force cert-manager pods to run on the control-plane are back, see this Github issue, so we had to add back the pinning of…
Sep 26, 2023
Andrea Zonca

 

Tutorial on Python for HPC at the SDSC Summer Institute

python
hpc
sdsc
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…
Aug 16, 2023
Andrea Zonca

 

Deploy Kubernetes on Jetstream 2 with Kubespray 2.21.0

kubernetes
jetstream2
Obsolete Tutorial
Jun 19, 2023
Andrea Zonca

 

Hiring a computational scientist at the San Diego Supercomputer Center

hpc
sdsc
Come work in my group of High Performance Computing “consultants” at the San Diego Supercomputer Center, help scientists develop, scale and run Data Intensive computations…
Apr 24, 2023
Andrea Zonca

 

Cosmology webinar Hyper Suprime-Cam

cosmology
Webinar about Cosmology results, in particular tension in \(S_8\) by the Hyper Supreme Cam collaboration:
Apr 23, 2023
Andrea Zonca

 

Get a Letsencrypt certificate for Dreamhost with certbot

Dreamhost has discontinued offering free Letsecrypt certificated in their shared hosting.
Apr 1, 2023
Andrea Zonca

 

Update OpenStack credentials in Kubernetes

kubernetes
jetstream
If you are deploying Kubernetes on top of Openstack, the Openstack External cloud provider stores the ID and Secret necessary to authenticate with the cloud infrastructure…
Mar 23, 2023
Andrea Zonca

Work on a LaTeX document in GitHub Codespaces

git
github
I was exploring using Github Codespaces instead of Overleaf to work on a Latex document.
Mar 16, 2023
Andrea Zonca

 

Gzipping or not gzipping HEALPix maps

healpy
nersc
HEALPix maps are generally stored in FITS format, they can be Gzipped to save disk space. Reading gzipped maps is natively supported in healpy, however, it takes longer…
Mar 6, 2023
Andrea Zonca

 

Share data from NERSC publicly via web

nersc
NERSC allows to make data which is on their Community File System publicly available via a web interface.
Feb 24, 2023
Andrea Zonca

 

Showyourwork! Globus demo

python
Showyourwork! is a great project to make scientific articles reproducible.
Feb 21, 2023
Andrea Zonca

 

Deploy a NFS server to share data between JupyterHub users on Jetstream

kubernetes
jetstream
jupyterhub
linux
Update: See the 2025 updated tutorial for deploying NFS on Jetstream with Kubernetes for the latest instructions.
Feb 6, 2023
Andrea Zonca

 

Work on a LaTeX document with GitHub and Overleaf

git
github
In the past I have written about coordinating a large document using multiple overleaf documents and Github repositories. In this post I will just layout the simpler case…
Feb 2, 2023
Andrea Zonca

 

Deploy Kubernetes on Jetstream 2 with GPU support

jetstream2
jupyterhub
This tutorial is obsolete, see the new version of the tutorial.
Jan 23, 2023
Andrea Zonca

Compare WebSky radio galaxies maps from PySM to Planck

healpy
pysm
I need to check that the amplitude of the maps of Radio Galaxies produced by WebSky are reasonable if compared to experimental results. The main worry is that being point…
Dec 5, 2022
Andrea Zonca

 

Share data between JupyterHub users with Manila shares

jetstream2
kubernetes
This work has been supported by Indiana University and is cross-posted on the Jetstream 2 official documentation website.
Dec 5, 2022
Andrea Zonca

Deploy BinderHub on top of Kubernetes on Jetstream 2

jetstream2
kubernetes
This work has been supported by Indiana University and is cross-posted on the Jetstream 2 official documentation website.
Nov 15, 2022
Andrea Zonca

 

Setup a conda environment at NERSC

python
nersc
Obsolete: see the new version
Nov 8, 2022
Andrea Zonca

 

Build and host Singularity containers on GitHub

singularity
git
github
I present a demo repository configured to build Singularity containers using Github actions and then host them using the Github container registry:
Nov 3, 2022
Andrea Zonca

 

Generate Click command line options dynamically from class arguments

python
In this application I need to use command line options to create class objects. In order not to repeat all class arguments in the Click configuration, I created a simple…
Oct 26, 2022
Andrea Zonca

 

Closures in Numba

python
Closures can be used to dinamically create different versions of a function based on some parameter, a similar functionality can be achieved with functools.partial.
Oct 24, 2022
Andrea Zonca

 

Install the JupyROOT Python kernel in JupyterHub

jupyterhub
kubernetes
After installing ROOT’s conda package, for example with micromamba:
Oct 11, 2022
Andrea Zonca

 

Singularity on Expanse tutorial

singularity
hpc
jetstream2
As one of my last tasks in XSEDE, I updated and improved the tutorial about running Singularity containers in the HPC system Espanse at my institution the San Diego…
Oct 5, 2022
Andrea Zonca

Screenshot of old blog

Migrate from fastpages to quarto preserving git history

Most of my blog posts are in Markdown…however, there are cases where plotting and code are very important, and nothing beats a Jupyter Notebook for that.
Sep 27, 2022
Andrea Zonca

 

Deploy MariaDB on Jetstream 2 on top of Kubernetes

kubernetes
jetstream2
In this tutorial we will install a MariaDB instance backed by a persistent volume on Jetstream 2. It will be in the jhub namespace, so that it can be accessed by the…
Jun 6, 2022
Andrea Zonca

 

Remove unique cell id from Jupyter Notebooks

git
jupyter
I know! Jupyter is littering your git diff with randomly generated cell ids and nbstripout doesn’t remove them, (I’m sure they are useful for some reason).
May 17, 2022
Andrea Zonca

 

Access running GitHub Action with SSH

github
git
Sometimes Github actions are failing and it is difficult to reproduce the error locally, in particular if you have a different OS.
May 2, 2022
Andrea Zonca

 

Monitor Restic backups on Kubernetes

jetstream2
kubernetes
For one of my production JupyterHub deployments on Kubernetes, I have setup an automated system to perform nightly backup of the user data, see the full tutorial on how to…
Apr 27, 2022
Andrea Zonca

 

Jetstream2 SU calculator

jetstream2
Jupyter Notebook to compute daily, monthly, yearly consumption of SU based on the number and type of Virtual Machines:
Apr 15, 2022
Andrea Zonca

 

Custos authentication for JupyterHub

kubernetes
jetstream2
jupyterhub
Custos is a security middleware used to authenticate users to Airavata-based Science Gateways. It is relevant to the Science Gateways community to unify authentication and…
Apr 13, 2022
Andrea Zonca

 

Science Gateway with Dask and Zarr

kubernetes
jetstream2
jupyterhub
dask
python
This material was presented on April 2022 at the MiniGateways 2022 conference organized by the wonderful Science Gateways Community Institute (SGCI).
Apr 5, 2022
Andrea Zonca

 

Use the distributed file format Zarr on Jetstream 2 object storage

dask
jetstream2
python
Zarr is a file format designed for cloud computing, see documentation.
Apr 4, 2022
Andrea Zonca

 

Deploy Dask Gateway with JupyterHub on Kubernetes

kubernetes
jetstream2
jupyterhub
dask
python
Tutorial obsolete, see the new version of the tutorial
Apr 4, 2022
Andrea Zonca

 

Deploy JupyterHub on Jetstream 2 on top of Kubernetes

kubernetes
jupyterhub
jetstream2
This tutorial is a followup to: Deploy Kubernetes on Jetstream 2 with Kubespray 2.18.0, so I’ll assume Kubernetes is already deployed with a default storageclass.
Mar 31, 2022
Andrea Zonca

 

Deploy Kubernetes on Jetstream 2 with Kubespray 2.18.0

kubernetes
jetstream2
Obsolete: please use the updated release of this tutorial.
Mar 30, 2022
Andrea Zonca

 

Workflow for Jupyter Notebooks under version control

jupyter
git
I’ll present here my strategy for keeping Jupyter Notebooks under version control.
Mar 22, 2022
Andrea Zonca

 

Deploy Dask Gateway with JupyterHub on Kubernetes

kubernetes
jetstream
jupyterhub
dask
python
Tutorial OBSOLETE Please check the updated version of this tutorial.
Jan 27, 2022
Andrea Zonca

 

Make for repeated commands

linux
I often find myself repeat the same commands in a project, for example in Openstack/Kubernetes, but also when I need to interface with Docker (build/push image).
Jan 7, 2022
Andrea Zonca

 

Fund healpy via GitHub Sponsors

healpy
Github Sponsor page
Nov 8, 2021
Andrea Zonca

 

Kubernetes certifications CKA and CKAD

kubernetes
I recently pursued 2 Kubernetes certifications by Linux Foundation:
Nov 4, 2021
Andrea Zonca

Compare HEALPix and Gauss-Legendre pixelizations for sky emission modelling

healpy
cosmology
pysm
We compare the transform from spherical harmonics space to pixel space and back using HEALPix and Gauss-Legendre pixelization. The context is the evaluation of sky emission…
Nov 2, 2021
Andrea Zonca

 

Deploy Hadoop on Kubernetes on Jetstream

kubernetes
jetstream
We are deploying the good old Hadoop on top of Kubernetes on Jetstream. Don’t ask why.
Oct 12, 2021
Andrea Zonca

Plot HEALPix pixel boundaries

healpy
Some time ago I created a Jupyter Notebook based on plotly to create a 3D visualization of the boundaries of HEALPix pixels on the sphere.
Oct 6, 2021
Andrea Zonca

 

Monitor traffic on Github repositories

github
Github only shows traffic data for the last 2 weeks. Through the API is possible to gather those data every 2 weeks and save them for later collection and reduction.
Oct 1, 2021
Andrea Zonca

 

Manage Globus groups with the Python SDK

python
hpc
Globus is the best tool to transfer quickly Terabytes data between Supercomputers because it automatically parallelizes the transfer to saturate the network (yeah I know I…
Sep 24, 2021
Andrea Zonca

 

New paper about PySM 3

openscience
python
pysm
cosmology
Update November 2021
Aug 4, 2021
Andrea Zonca

 

Upload a JOSS paper to arXiv

github
openscience
If you are in Astrophysics, you probably want to have your JOSS paper published to the Arxiv.
Aug 1, 2021
Andrea Zonca

 

Configure dreamhost email

Configuration to read Dreamhost email from Gmail:
Jun 27, 2021
Andrea Zonca

 

healpy 1.15.0 released

healpy
python
Just released healpy 1.15.0, this is a large release with many important changes, please test and open issues at https://github.com/healpy/healpy/issues
Jun 22, 2021
Andrea Zonca

Investigate rotation of masks in healpy

healpy
cosmology
Investigating a question about healpy on Stackoverflow
Jun 18, 2021
Andrea Zonca

 

Learn Italian in San Diego

italian
My wife Maura D’Andrea recently opened a new Italian language school in San Diego.
Jun 17, 2021
Andrea Zonca

 

Migrate from Google Docs to Overleaf and GitHub

github
Once a document on Google Docs becomes too big and complicated to make sure it is consistent, it is a good idea to migrate it to Latex. In particular we can support both…
May 20, 2021
Andrea Zonca

Correct a power spectrum by the instrument beam with healpy

healpy
cosmology
If you are analyzing a map from an instrument with a specific beam width, you can correct the power spectrum by the smoothing factor caused by that beam and obtain a better…
Apr 27, 2021
Andrea Zonca

 

Backup Kubernetes volumes to OpenStorageNetwork object store

jetstream
kubernetes
In my specific scenario, I have users running JupyterHub on top of Kubernetes on the Jetstream XSEDE Cloud resouce. Each user has a persistent volume as their home folder of…
Apr 19, 2021
Andrea Zonca

Science Gateways Tech blog - Kubernetes and JupyterHub on Jetstream

kubernetes
jetstream
This is cross-posted from the Science Gateways Community institute tech blog, thanks to Marlon Pierce and Katherine Lawrence for their feeback.
Mar 28, 2021
Andrea Zonca

 

Stream video from object store on Jetstream

jetstream
In this tutorial we will serve video stored in Jetstream’s object store (like Amazon S3) as HTTP live streaming to a user’ browser. This makes it difficult for the user to…
Mar 25, 2021
Andrea Zonca

Tutorial on how to rotate maps in healpy

In this notebook we will explore different ways of rotating maps in healpy.
Mar 11, 2021
Andrea Zonca

Compute the Planck CMB temperature power spectrum with healpy anafast

healpy
cosmology
In this notebook we will load the Planck CMB-only temperature map and try to reproduce the Planck CMB power spectrum in temperature just using healpy.
Feb 28, 2021
Andrea Zonca

 

Coordinate a large Latex document with multiple Overleaf projects and Github

git
github
In case we need to build a large document (~hundreds of pages) and we have a large number of collaborators (more than 50), it is convenient to have each section of the…
Jan 28, 2021
Andrea Zonca

 

Deploy Kubernetes on Jetstream with Kubespray 2.15.0

kubernetes
jetstream
Note: Jetstream 1 has been retired. For current Kubernetes deployments, see Jetstream 2 documentation.
Jan 20, 2021
Andrea Zonca

 

Autoscaling script for JupyterHub on top of Kubespray

kubernetes
jetstream
I think the most reliable way of deploying Kubernetes on Openstack is Kubespray, see my latest tutorial about it focused on Jetstream.
Jan 20, 2021
Andrea Zonca

 

CFITSIO file writing with checkpointing

astrophysics
I wrote a prototype implementation of writing FITS files in C checkpointing using the FITS flush function so that if the code segfaults, the file is not corrupted, see:
Nov 30, 2020
Andrea Zonca

 

Paper review workflow with Overleaf, git and Google Docs

openscience
git
In this blog post I propose a workflow to use the collaborative features of Google Docs to review a paper being written in Overleaf (unless you have Overleaf Pro which has…
Nov 18, 2020
Andrea Zonca

 

Install HEALPix and PolSpice in a conda environment

healpy
hpc
nersc
Some notes on how to install HEALPix and PolSpice inside a conda environment, with some details about doing it at NERSC, but most of the tutorial is independent of that.
Oct 14, 2020
Andrea Zonca

Example of the healpy query disc function

python
healpy
cosmology
lonlat=True switches ang2vec from requiring colatitude \(\theta\) and longitude \(\phi\) in radians to longitude and latitude in degrees (notice that also the order changes)
Oct 2, 2020
Andrea Zonca

 

Read and process Planck CMB power spectra with healpy

healpy
cosmology
In this tutorial we will load CMB power spectra generated by the cosmological parameters measured by Planck, we will create a realization of the Spherical Harmonics…
Sep 30, 2020
Andrea Zonca

 

Edit video recordings with ffmpeg

A few scripts to speedup, concatenate and possibly other operations using ffmpeg on linux (also works on Chromebooks) from the command line:
Sep 25, 2020
Andrea Zonca

 

How to share Jupyter Notebooks

jupyter
github
I tend to preserve and post online all the work I do for later reference and sharing. Jupyter Notebooks are a bit more complex than standard source code because they are…
Sep 15, 2020
Andrea Zonca

 

Simple WCS with astropy modeling and gwcs

astrophysics
Some notes on how to convert a FITS WCS to a WCS from gwcs (Generalized WCS) to be used within the JWST pipeline
Sep 10, 2020
Andrea Zonca

 

Gateways 2020 paper about Kubernetes and JupyterHub on Jetstream

jupyterhub
jetstream
kubernetes
My paper in collaboration with Richard Signell (USGS), Julien Chastang (UCAR), John Michael Lowe (IU/Jetstream), Jeremy Fischer (IU/Jetstream) and Robert Sinkovits (SDSC)…
Sep 4, 2020
Andrea Zonca

Unit conversion with broadband detectors looking at the CMB

healpy
cosmology
We measure the sky with out broadband instrument, we assume we only measure the CMB solar dipole, initially the units are arbitrary, for example Volts of our instrument.
Sep 4, 2020
Andrea Zonca

Unit conversion with broadband detectors looking at foregrounds

cosmology
We measure the sky with out broadband instrument, we assume we only measure the CMB solar dipole, initially the units are arbitrary, for example Volts of our instrument.
Sep 4, 2020
Andrea Zonca

 

Redirect readthedocs documentation to another website

python
This is useful if you switch to hosting your own documentation, for example using Sphinx Multiversion on Github pages, tutorial coming soon.
Sep 1, 2020
Andrea Zonca

 

Migrate from Travis-CI and ReadTheDocs to GitHub Actions

python
github
For a number of years I have been concerned about the duplication of work having to maintain continuous integration environments both on Travis-CI to run the unit tests and…
Sep 1, 2020
Andrea Zonca

 

Renew letsencrypt certificate with NGINX

linux
If you have a default domain already configured with NGINX, the easiest way to renew manually a domain is to temporarily disable your custom domain and then use certbot-auto …
Aug 24, 2020
Andrea Zonca

 

Investigate broken implementation of bandpass unit conversion in PySM 3

cosmology
pysm
Investigation of the broken implementation of the bandpass unit conversion function in PySM 3 and check of its impact on existing Simons Observatory and CMB-S4 simulated…
Aug 24, 2020
Andrea Zonca

 

Deploy Dask Gateway with JupyterHub on Kubernetes

kubernetes
cloudcomputing
jetstream
jupyterhub
dask
This tutorial is obsolete, please follow https://zonca.dev/2022/01/dask-gateway-jupyterhub.html
Aug 11, 2020
Andrea Zonca

 

Dask array rounding

python
dask
Dask array rounding float32
Aug 4, 2020
Andrea Zonca

 

Deploy a NFS server to share data between JupyterHub users on Jetstream

kubernetes
jetstream
jupyterhub
linux
Important: This tutorial is obsolete, please refer to the new version from February 2023
Jul 10, 2020
Andrea Zonca

Handle white noise with healpy 3 not-uniform and partial sky coverage

cosmology
python
healpy
Simulate white noise maps and use hitmaps
Jun 21, 2020
Andrea Zonca

Handle white noise with healpy 2 partial sky coverage

cosmology
python
healpy
Simulate white noise maps and use hitmaps
Jun 20, 2020
Andrea Zonca

Handle white noise with healpy 1 Full sky coverage

cosmology
python
healpy
Simulate white noise maps and use hitmaps
Jun 19, 2020
Andrea Zonca

 

Deploy Kubernetes on Jetstream with Kubespray

kubernetes
jetstream
Note: Jetstream 1 has been retired. For current Kubernetes deployments, see Jetstream 2 documentation.
Jun 15, 2020
Andrea Zonca

 

My own git cheatsheet

git
I noticed I always google the same procedures…
Jun 1, 2020
Andrea Zonca

 

Import and export list of blocked users on Twitter

python
Back in 2015, Twitter provided the feature to export and import lists of blocked users, unfortunately they discontinued this service.
Jun 1, 2020
Andrea Zonca

 

Minimal example of readthedocs configuration for conda

python
Prompted by the announced better support of conda in readthedocs, more memory! I setup a Python package with conda to automatically build the documentation on readthedocs.
May 27, 2020
Andrea Zonca

 

Deploy Kubernetes and JupyterHub on Jetstream with Magnum

kubernetes
jetstream
jupyterhub
This tutorial deploys Kubernetes on Jetstream with Magnum and then JupyterHub on top of that using zero-to-jupyterhub.
May 21, 2020
Andrea Zonca

White noise NET in radio-astronomy and cosmology

cosmology
python
healpy
Create a white noise map and compare with power spectrum expected from the NET
Apr 24, 2020
Andrea Zonca

 

ECSS Symposium introduction to cloud computing with Jetstream and deployment of Kubernetes

jupyterhub
jetstream
kubernetes
Note: XSEDE has been replaced by ACCESS.
Apr 20, 2020
Andrea Zonca

 

Use the Jetstream object store

jetstream
I plan to collect here notes about using the Openstack object store on Jetstream.
Apr 1, 2020
Andrea Zonca

 

Raise and check a flag array with numpy

python
Handle flag array bits with numpy bitwise operations
Mar 16, 2020
Andrea Zonca

 

Setup HTTPS on Kubernetes with Let’s Encrypt

kubernetes
jetstream
jupyterhub
This tutorial is obsolete since September 2023, see the updated tutorial.
Mar 13, 2020
Andrea Zonca

 

Kill Jupyter Notebook servers

python
jupyter
Just today I learned how to properly stop previously running Jupyter Notebook servers, here for future reference:
Mar 12, 2020
Andrea Zonca

Migrate from Pelican to Fastpages

python
I have been using the Pelican static website generator for a few years, hosting the content on Github, automatically build on push via Travis-CI and deploy on Github pages to …
Mar 9, 2020
Andrea Zonca

 

Deploy CVMFS on Kubernetes

kubernetes
jetstream
jupyterhub
CVMFS is a software distribution service, it is used by High Energy Physics experiments at CERN to synchronize software environments across the whole collaborations.
Feb 26, 2020
Andrea Zonca

screenshot of add to Google Calendar

Organize calendars for a large scientific collaboration

openscience
Many scientific collaborations have a central calendar, often hosted on Google Calendar, to coordinate Teleconferences, meetings and events across timezones.
Dec 2, 2019
Andrea Zonca

 

Simulate users on JupyterHub

kubernetes
jetstream
jupyterhub
Updated January 2021
Oct 30, 2019
Andrea Zonca

 

Execute Jupyter Notebooks not interactively

jupyter
Over the years, I have explored how to scale up easily computation through Jupyter Notebooks by executing them not-interactively, possibily parametrized and remotely. This…
Sep 23, 2019
Andrea Zonca

 

Deploy Cluster Autoscaler for Kubernetes on Jetstream

kubernetes
jetstream
jupyterhub
The Kubernetes Cluster Autoscaler is a service that runs within a Kubernetes cluster and when there are not enough resources to accomodate the pods that are queued to run…
Sep 12, 2019
Andrea Zonca

 

Create a Github account for your research group with free private repositories

github
git
openscience
Github allows a research group to create their own webpage where they can host, share and develop their software using the git version control system and the powerful Github…
Aug 24, 2019
Andrea Zonca

 

Ship large files with Python packages

python
It is often useful to ship large data files together with a Python package, a couple of scenarios are:
Aug 21, 2019
Andrea Zonca

 

Deploy Kubernetes and JupyterHub on Jetstream with Magnum

kubernetes
jetstream
jupyterhub
Note: Jetstream 1 has been retired. See Jetstream 2 documentation for current tutorials.
Jun 14, 2019
Andrea Zonca

 

Webinar about distributed computing with Python

python
hpc
Recording available of the webinar I gave about “Distributed computing with Python”:
May 30, 2019
Andrea Zonca

Kubernetes monitoring with Prometheus and Grafana

kubernetes
jetstream
jupyterhub
See the updated version of this tutorial
Apr 20, 2019
Andrea Zonca

 

Inherit group permission in folder

hpc
linux
I have googled this so many times…
Mar 24, 2019
Andrea Zonca

 

Scale Kubernetes manually on Jetstream

kubernetes
jetstream
jupyterhub
We would like to modify the number of Openstack virtual machines available to Kubernetes. Ideally we would like to do this automatically based on the load on JupyterHub…
Feb 22, 2019
Andrea Zonca

 

Kubernetes monitoring with Dashboard, Prometheus, and Grafana

kubernetes
jetstream
jupyterhub
Install with helm:
Feb 22, 2019
Andrea Zonca

 

Deploy Kubernetes with Kubespray 2.8.2 and JupyterHub with helm recipe 0.8 on Jetstream

kubernetes
jetstream
Note: Jetstream 1 has been retired. See Jetstream 2 documentation for current tutorials.
Feb 22, 2019
Andrea Zonca

 

Use the distributed file format Zarr on Jetstream Swift object storage, 2019

jupyterhub
jetstream
dask
This is an updated version of the 2018 edition
Jan 24, 2019
Andrea Zonca

Deploy Pangeo on Kubernetes deployment on Jetstream created with Kubespray

kubernetes
jetstream
jupyterhub
The Pangeo collaboration for Big Data Geoscience maintains a helm chart with a prefigured JupyterHub deployment on Kubernetes which also supports launching private dask…
Dec 20, 2018
Andrea Zonca

 

Setup two factor authentication for UCSD, and Lastpass

Starting at the end of January 2019 UCSD requires every employee to have activated two factor authentication.
Dec 12, 2018
Andrea Zonca

 

Deploy JupyterHub on a Supercomputer for a workshop or tutorial 2018 edition

jupyterhub
hpc
I described how to deploy JupyterHub with each user session running on a different node of a Supercomputer in my paper for PEARC18, however things are moving fast in the…
Nov 7, 2018
Andrea Zonca

 

Deploy JupyterHub on a Supercomputer for a workshop or tutorial 2018 edition

jupyterhub
hpc
I described how to deploy JupyterHub with each user session running on a different node of a Supercomputer in my paper for PEARC18, however things are moving fast in the…
Nov 7, 2018
Andrea Zonca

 

Advanced pandas with astrophysics example notebook

jupyter
astrophysics
Taught a lesson today on advanced python and pandas based on an example application in Astrophysics with simulations of data from the Planck Satellite, features also a…
Oct 26, 2018
Andrea Zonca

 

Bring your computing to the San Diego Supercomputer Center

hpc
Note (2024 update): This post was written in 2018. Comet has been retired and XSEDE has been replaced by ACCESS. SDSC’s current flagship system is Expanse. Please visit the S…
Oct 24, 2018
Andrea Zonca

 

Deploy JupyterHub on Kubernetes deployment on Jetstream created with Kubespray 3/3

kubernetes
jetstream
jupyterhub
All of the following assumes you are logged in to the master node of the Kubernetes cluster deployed with kubespray and checked out the repository:
Sep 24, 2018
Andrea Zonca

 

Explore a Kubernetes deployment on Jetstream with Kubespray 2/3

kubernetes
jetstream
This is the second part of the tutorial on deploying Kubernetes with kubespray and JupyterHub on Jetstream.
Sep 23, 2018
Andrea Zonca

 

Deploy Kubernetes on Jetstream with Kubespray 1/3

kubernetes
jetstream
Note: Jetstream 1 has been retired. For current Kubernetes deployments, see Jetstream 2 documentation.
Sep 23, 2018
Andrea Zonca

 

PEARC18 paper on deploying Jupyterhub at scale on XSEDE

singularity
jetstream
jupyterhub
kubernetes
Bob Sinkovits and I are presenting a paper at PEARC18 about:
Jul 23, 2018
Andrea Zonca

 

Updated Singularity images for Comet

singularity
hpc
Back in January 2017 I wrote a blog post about running Singularity on Comet.
Jul 22, 2018
Andrea Zonca

 

Create DockerHub auto build

github
It is very convenient to create Autobuild repositories on DockerHub linked to a Github repository with a Dockerfile. Then every time you commit to Github, Dockerhub is going…
Jul 19, 2018
Andrea Zonca

 

How to organize code and data for simulations at NERSC

hpc
python
nersc
I recently improved my strategy for organizing code and data for simulations run at NERSC, I’ll write it here for reference.
Jun 20, 2018
Andrea Zonca

 

Setup private dask clusters in Kubernetes alongside JupyterHub on Jetstream

jupyterhub
kubernetes
jetstream
dask
In this post we will leverage software made available by the Pangeo community to allow each user of a Jupyterhub instance deployed on Jetstream on top of Kubernetes to…
Jun 7, 2018
Andrea Zonca

 

How to post a PEARC18 paper pre-print to Arxiv

openscience
Follows the step-by-step version:
May 12, 2018
Andrea Zonca

 

Launch a shared dask cluster in Kubernetes alongside JupyterHub on Jetstream

jupyterhub
jetstream
dask
Let’s assume we have already a Kubernetes deployment and have installed JupyterHub, see for example my previous tutorial on Jetstream. Now that users can login and access a…
May 4, 2018
Andrea Zonca

 

Install a BOINC server on Jetstream

jetstream
cloudcomputing
BOINC is the leading platform for volunteer computing.
Mar 29, 2018
Andrea Zonca

 

Use the distributed file format Zarr on Jetstream Swift object storage

jupyter
jetstream
cloudcomputing
Updated again in January 2019
Mar 3, 2018
Andrea Zonca

 

Use the distributed file format Zarr on Jetstream Swift object storage

jupyter
jetstream
Zarr is a pretty new file format designed for cloud computing, see documentation and a webinar for more details.
Mar 3, 2018
Andrea Zonca

 

Install custom Python environment on Jupyter Notebooks at NERSC

jupyterhub
python
hpc
nersc
NERSC has provided a JupyterHub instance for quite some time to all NERSC users. It is currently running on a dedicated large-memory node on Cori, so now it can access also…
Dec 21, 2017
Andrea Zonca

 

ECSS Symposium about Jupyterhub deployments on XSEDE

jupyterhub
jetstream
cloudcomputing
Note: XSEDE has been replaced by ACCESS.
Dec 15, 2017
Andrea Zonca

 

Deploy scalable Jupyterhub with Kubernetes on Jetstream

jupyterhub
jetstream
cloudcomputing
The best infrastructure available to deploy Jupyterhub at scale is Kubernetes. Kubernetes provides a fault-tolerant system to deploy, manage and scale containers. The…
Dec 5, 2017
Andrea Zonca

 

Store a conda environment inside a Notebook

jupyter
python
Last August, during the Container Analysis Environments Workshop held at Urbana-Champaign, we had discussion about reproducibility in the Jupyter Notebooks. There came out…
Dec 4, 2017
Andrea Zonca

 

How to modify Singularity images on a Supercomputer

singularity
hpc
Singularity allows to run your own OS within most Supercomputers, see my previous post about Running Ubuntu on Comet via Singularity
Nov 6, 2017
Andrea Zonca

 

Deploy scalable Jupyterhub on Docker Swarm mode

jupyterhub
jetstream
cloudcomputing
Jupyterhub genrally requires roughly 500MB per user for light data processing and many GB for heavy data processing, therefore it is often necessary to deploy it across…
Oct 26, 2017
Andrea Zonca

 

Setup automated testing on a Github repository with Travis-ci

github
git
Start from the CUDA 8 image from NVIDIA:
Oct 25, 2017
Andrea Zonca

 

Setup automated testing on a Github repository with Travis-ci

github
git
It is good practice in software development to implement extensive testing of the codebase in order to catch quickly any bug introduced into the code when implementing new…
Sep 6, 2017
Andrea Zonca

 

Deployment of Jupyterhub with Globus Auth to spawn notebook on Comet in Singularity containers

jupyterhub
singularity
hpc
Follow the instructions at https://github.com/zonca/singularity-comet to build images from the ubuntu_anaconda_jupyterhub.def and centos_anaconda_jupyterhub.def definition…
Aug 11, 2017
Andrea Zonca

 

How to create pull requests on Github

git
github
cloudcomputing
Pull Requests are the web-based version of sending software patches via email to code maintainers. They allow athat has no access to a code repository to submit a code…
Jun 30, 2017
Andrea Zonca

 

How to create pull requests on Github

git
github
Pull Requests are the web-based version of sending software patches via email to code maintainers. They allow a person that has no access to a code repository to submit a…
Jun 30, 2017
Andrea Zonca

 

Deploy Jupyterhub on a supercomputer with SSH authentication

python
jupyterhub
hpc
The best way to deploy Jupyterhub with an interface to a Supercomputer is through the use of batchspawner. I have a sample deployment explained in an older blog post: https:…
May 16, 2017
Andrea Zonca

 

Configure Globus on your local machine for GridFTP with XSEDE authentication

linux
All the commands are executed on your local machine, the purpose of this tutorial is to be able to use globus-url-copy to copy efficiently data back and forth between your…
Apr 19, 2017
Andrea Zonca

 

Sample deployment of Jupyterhub in HPC on SDSC Comet

python
jupyterhub
hpc
I have deployed an experimental Jupyterhub service (ask me privately if you would like access) installed on a SDSC Cloud virtual machine that spawns single user Jupyter…
Feb 26, 2017
Andrea Zonca

 

Customize your Python environment in Jupyterhub

python
jupyterhub
Usecase: You have access to a Jupyterhub server and you would like to install some packages but cannot use pip install and modify the systemwide Python installation.
Feb 24, 2017
Andrea Zonca

 

Automated deployment of Jupyterhub with Ansible

jupyterhub
cloudcomputing
Last year I wrote some tutorials on simple deployments of Jupyterhub on Ubuntu 16.04 on the OpenStack deployment SDSC Cloud, even if most of the steps would also be suitable…
Feb 3, 2017
Andrea Zonca

 

How to publish your research software to Github

git
github
openscience
Nowadays many journals require that the software used to produce results described in a scientific paper be made available publicly for other peers to be able to reproduce…
Feb 1, 2017
Andrea Zonca

 

Run Ubuntu in HPC with Singularity

singularity
hpc
If your answer to any of those question is yes, read on! Otherwise, well, still read on, it’s awesome!
Jan 13, 2017
Andrea Zonca

 

Jupyterhub Docker Spawner with GPU support

python
jupyterhub
Docker Spawner allows users of Jupyterhub to run Jupyter Notebook inside isolated Docker Containers. Access to the host NVIDIA GPU was not allowed until NVIDIA release the NV…
Oct 12, 2016
Andrea Zonca

 

Jupyterhub deployment on multiple nodes with Docker Swarm

jupyterhub
cloudcomputing
This post is part of a series on deploying Jupyterhub on OpenStack tailored at workshops, in the previous posts I showed:
May 24, 2016
Andrea Zonca

 

Quick Jupyterhub deployment for workshops with pre-built image

python
jupyterhub
This tutorial explains how to use a OpenStack image I already built to quickly deploy a Jupyterhub Virtual Machine that can provide a good initial setup for a workshop…
Apr 28, 2016
Andrea Zonca

 

Deploy Jupyterhub on a virtual machine for a workshop

python
jupyterhub
This tutorial describes the steps to install a Jupyterhub instance on a single machine suitable for hosting a workshop, suitable for having people login with training…
Apr 16, 2016
Andrea Zonca

 

Use your own Python installation (kernel) in Jupyterhub

python
jupyterhub
Updated February 2017
Oct 5, 2015
Andrea Zonca

IPython/Jupyter notebook setup on NERSC Edison

jupyter
python
hpc
nersc
This tutorial explains the setup to run an IPython Notebook on a computing node on the supercomputer Edison at NERSC and forward its port encrypted with SSH to the browser…
Sep 24, 2015
Andrea Zonca

 

IPython/Jupyter notebook setup on SDSC Comet

python
hpc
jupyter
This tutorial explains the setup to run an IPython Notebook on a computing node on the supercomputer Comet at the San Diego Supercomputer Center and forward the port…
Sep 17, 2015
Andrea Zonca

Run Jupyterhub on a supercomputer

python
jupyterhub
hpc
Summary: I developed a plugin for Jupyterhub: RemoteSpawner, it has a proof-of-concept interface with the Supercomputer Gordon at UC San Diego to spawn IPython Notebook…
Apr 2, 2015
Andrea Zonca

 

Accelerate groupby operation on pixels with Numba

python
astrophysics
Download the original IPython notebook
Mar 24, 2015
Andrea Zonca

Screenshot Chromebook click for full resolution

Software Carpentry setup for Chromebook

linux
python
In this post I’ll provide instructions on how to install the main requirements of a Software Carpentry workshop on a Chromebook. Bash, git, IPython notebook and R.
Feb 10, 2015
Andrea Zonca

 

Zero based indexing

python
For Europeans zero based indexing feels reasonable if we think of floors in a house, the lowest floor is ground floor, then 1st floor and so on.
Oct 22, 2014
Andrea Zonca

 

Write unit tests as cells of IPython notebooks

python
jupyter
Plugin for py.test to write unit tests as cells in IPython notebooks:
Sep 30, 2014
Andrea Zonca

 

How to perform code review for scientific software

github
git
openscience
Code review is the formal process where a programmer inspects in detail a piece of software developed by somebody else in order to improve code quality by catching bugs…
Aug 28, 2014
Andrea Zonca

 

Create a Github account for your research group with free private repositories

github
git
openscience
See the updated version at https://zonca.github.io/2019/08/github-for-research-groups.html
Aug 19, 2014
Andrea Zonca

 

Thoughts on a career as a computational scientist

hpc
Recently I’ve been asked what are the prospects of a wannabe computational scientist, both in terms of training and in terms of job opportunities.
Jun 5, 2014
Andrea Zonca

 

Machine learning at scale with Python

python
hpc
My talk for the San Diego Data Science meetup: http://www.meetup.com/San-Diego-Data-Science-R-Users-Group/events/170967362/
Mar 20, 2014
Andrea Zonca

 

Python on Gordon

hpc
python
Gordon has already a python environment setup which can be activated by loading the python module:
Mar 20, 2014
Andrea Zonca

 

Build Software Carpentry lessons with Pelican

python
openscience
Software Carpentry offers bootcamps for scientist to teach basic programming skills. All the material, mainly about bash, git, Python and R is available on Github under…
Feb 26, 2014
Andrea Zonca

 

openproceedings - Github/FigShare based publishing platform for conference proceedings

python
openscience
Github provides a great interface for gathering, peer reviewing and accepting papers for conference proceedings, the second step is to publish them on a website either in…
Feb 13, 2014
Andrea Zonca

 

wget file from google drive

linux
Sometimes it is useful, even more if you have a chromebook, to upload a file to Google Drive and then use wget to retrieve it from a server remotely.
Jan 31, 2014
Andrea Zonca

IPython notebook on Gordon

Run IPython Notebook on a HPC cluster via PBS

python
hpc
The IPython notebook is a great tool for data exploration and visualization. It is suitable in particular for analyzing a large amount of data remotely on a computing node…
Dec 18, 2013
Andrea Zonca

 

Joining San Diego Supercomputer Center

TL;DR Left UCSB after 4 years, got staff position at San Diego Supercomputer Center within UCSD, will be helping research groups analyze their data on Gordon and more. Still…
Dec 10, 2013
Andrea Zonca

 

Published paper on destriping Cosmic Microwave Background polarimeter data

python
cosmology
TL;DR version:
Nov 20, 2013
Andrea Zonca

Jiffylab Login page

Jiffylab multiuser IPython notebooks

python
jiffylab is a very interesting project by Preston Holmes to provide sandboxed IPython notebooks instances on a server using docker. There are several user cases, for example:
Oct 14, 2013
Andrea Zonca

 

How to log exceptions in Python

python
Sometimes it is useful to just catch any exception, write details to a log file and continue execution.
Oct 1, 2013
Andrea Zonca

 

Google Plus comments plugin for Pelican

python
github
There has been recently several discussions about whether comments are any useful on blogs I think it is important to find better ways to connect blogs to social networks.…
Sep 27, 2013
Andrea Zonca

 

How to automatically build your Pelican blog and publish it to Github Pages

python
git
Something I like a lot about Jekyll, the Github static blog generator, is that you just push commits to your repository and Github takes care of re-building and publishing…
Sep 26, 2013
Andrea Zonca

 

clviewer, interactive plot of CMB spectra

python
astrophysics
Today it was HackDay at .Astronomy, so I felt compelled to hack something around myself, creating something I have been thinking for a while after my previous work on Interac…
Sep 17, 2013
Andrea Zonca

Planck CMB map at high resolution

python
astrophysics
healpy
Prompted by a colleague, I created a high-resolution version of the Cosmic Microwave Background map in MollWeide projection released by the Planck collaboration, available…
Sep 10, 2013
Andrea Zonca

Run Hadoop Python jobs on Amazon with mrjob

git
python
MrJob makes the implementation of the reducer particularly simple. Using hadoop-streaming directly, we needed also to first parse back the output of the mapper into python…
Sep 2, 2013
Andrea Zonca

 

Interactive figures in the browser - CMB power spectra

astrophysics
healpy
For a long time I’ve been curious about trying out d3.js , the javascript plotting library which is becoming the standard for interactive plotting in the browser.
Aug 30, 2013
Andrea Zonca

 

Planck CTP angular power spectrum ell binning

healpy
Planck released a binning of the angular power spectrum in the Explanatory supplement,
unfortunately the file is in PDF format, non easily machine-readable:

http://www.s…
Aug 20, 2013
Andrea Zonca

HEALPix map of the Earth using healpy

healpy
HEALPix maps can also be used to create equal-area pixelized maps of the Earth, RGB colors are not supported in healpy, so we need to convert the image to colorscale.
The…
Aug 8, 2013
Andrea Zonca

 

Export google analytics data via API with Python

python
Fun weekend hacking project: export google analytics data using the google APIs.

Clone the latest version of the API client from:

https://code.google.com/p/google-api-p…
Aug 4, 2013
Andrea Zonca

Processing sources in Planck maps with Hadoop and Python

hpc
python
The purpose of this post is to investigate how to process in parallel sources extracted from full sky maps, in this case the maps release by Planck, using Hadoop instead of…
Jul 15, 2013
Andrea Zonca

 

How to use the IPython notebook on a small computing cluster

hpc
python
The IPython notebook is a powerful and easy to use interface for using Python and particularly useful when running remotely, because it allows the interface to run locally…
Jun 22, 2013
Andrea Zonca

 

IPython parallell setup on Carver at NERSC

hpc
python
IPython parallel is one of the easiest ways to spawn several Python sessions on a Supercomputing cluster and process jobs in parallel.

On Carver, the basic setup is…
Apr 11, 2013
Andrea Zonca

 

Simple Mixin usage in python

python
One situation where Mixins are useful in Python is when you need to modify  a method of similar classes that you are importing from a package.
Apr 8, 2013
Andrea Zonca

 

Noise in spectra and map domain

healpy
astrophysics
\(C_\ell\) of the variance map is just the variance map multiplied by the pixel area divided by the integration time.

\[C_\ell = \Omega_{\rm pix} \langle…
Apr 8, 2013
Andrea Zonca

 

Basic fork/pull git workflow

git
Typical simple workflow for a (github) repository with few users.
Apr 6, 2013
Andrea Zonca

Interactive 3D plot of a sky map

python
astrophysics
update May 2024: See the new version of this tutorial
Mar 12, 2013
Andrea Zonca

 

How to cite HDF5 in bibtex

here the bibtex entry:


reference:
https://www.hdfgroup.org/solutions/hdf5/
Feb 27, 2013
Andrea Zonca

 

Compile healpix C++ to javascript

linux
Compile C++ -> LLVM with clang

Convert LLVM -> Javascript:
https://github.com/kripken/emscripten/wiki/Tutorial
Jan 28, 2013
Andrea Zonca

 

Elliptic beams, FWHM and ellipticity

astrophysics
The relationship between the Full Width Half Max, FWHM (min, max, and average) and the
ellipticity is:

FWHM = sqrt(FWHM_min * FWHM_max)
e = FWHM_max/FWHM_min

Jan 18, 2013
Andrea Zonca

 

Ubuntu PPA for HEALPix and healpy

healpy
linux

Dec 17, 2012
Andrea Zonca

 

Butterworth filter with Python

python
Using IPython notebook of course:

http://nbviewer.ipython.org/3843014/
Oct 6, 2012
Andrea Zonca

 

IPython.parallel for Planck data analysis at NERSC

python
Planck is a Space mission for high precision measurements of the Cosmic Microwave Background (CMB), data are received as timestreams of output voltages from the 2…
Sep 27, 2012
Andrea Zonca

 

homepage on about.me

moved my homepage to about.me:

http://about.me/andreazonca

it is quite nice, and essential, as most of it is just links to other websites, i.e. arXiv for…
Sep 26, 2012
Andrea Zonca

 

doctests and unittests happiness 2

python
Download sourceContribute
Aug 16, 2012
Andrea Zonca

 

compile python module with mpi support

CC=mpicc LDSHARED=“mpicc -shared” python setup.py build_ext -i
Jul 6, 2012
Andrea Zonca

 

some python resources

python
python tutorial:
https://docs.python.org/3/tutorial/
numpy tutorial [arrays]:
https://numpy.org/doc/stable/user/quickstart.html
plotting tutorial:
https://matplotl…
Nov 1, 2011
Andrea Zonca

 

cfitsio wrapper in python

python
After several issues with pyfits, and tired of it being so overengineered, I’ve wrote my own fits I/O package in python, wrapping the C library cfitsio with ctypes.

Pretty…
Jun 21, 2011
Andrea Zonca

 

unit testing happiness

python
Download sourceContribute
Jun 21, 2011
Andrea Zonca

Pink noise (1/f noise) simulations in numpy

python
https://gist.github.com/979729

May 18, 2011
Andrea Zonca

 

Vim regular expressions

linux
very good reference of the usage of regular expressions in VIM:

http://www.softpanorama.org/Editors/Vimorama/vim_regular_expressions.shtml
Apr 29, 2011
Andrea Zonca

 

set python logging level

python
often using logging.basicConfig is useless because if the logging module is already configured upfront by one of the imported libraries this is ignored.

The solution is…
Apr 13, 2011
Andrea Zonca

 

pyfits memory leak in new_table

python
astrophysics
I found a memory leakage issue in pyfits.new_table, data were NOT deleted when the table was deleted, I prepared a test on github, using objgraph , which shows that data…
Mar 28, 2011
Andrea Zonca

 

ipython and PyTrilinos

python
Download sourceContribute
Feb 16, 2011
Andrea Zonca

 

git make local branch tracking origin

git
git branch –set-upstream master origin/master

you obtain the same result as initial cloning
Feb 2, 2011
Andrea Zonca

 

memory map npy files

python
Mem-map the stored array, and then access the second row directly from disk:

X = np.load(‘/tmp/123.npy’, mmap_mode=‘r’)
Jan 7, 2011
Andrea Zonca

 

force local install of python module

python
python setup.py install –prefix FOLDER


creates lib/python2.6/site-packages, to force a local install you should use:

python setup.py install –install-lib FOLDER
Dec 3, 2010
Andrea Zonca

 

gnome alt f2 popup launcher

linux

gnome-panel-control –run-dialog
Aug 31, 2010
Andrea Zonca

 

switch to interactive backend with ipython -pylab

python
objective:
Aug 21, 2010
Andrea Zonca

 

numpy dtypes and fits keywords

python
bool: ‘L’,
uint8: ‘B’,
int16: ‘I’,
int32: ‘J’,
int64: ‘K’,
float32: ‘E’,
float64: ‘D’,
complex64: ‘C’,
complex128: ‘M’
Aug 4, 2010
Andrea Zonca

 

count hits with numpy

python
I have an array where I record hits
a=np.zeros(5)
and an array with the indices of the hits, for example I have 2 hits on index 2
hits=np.array([2,2])
so I want to…
Jul 23, 2010
Andrea Zonca

 

change column name in a fits with pyfits

python
no way to change it manipulating the dtype of the data array.
a=pyfits.open(‘filename.fits’)
a[1].header.update(‘TTYPE1’,‘newname’)
you need to change the header…
Jun 30, 2010
Andrea Zonca

 

healpix coordinates

astrophysics
Healpix considers latitude theta from 0 on north pole to pi south pole,
so the conversion is:
theta = pi/2 - latitude
longitude and phi instead are consistently…
Jun 23, 2010
Andrea Zonca

 

parallel computing the python way

python
Note: The original showmedo.com video tutorial site is no longer available.
Jun 21, 2010
Andrea Zonca

 

quaternions for python

python
Update: SciPy now includes scipy.spatial.transform.Rotation which provides excellent quaternion support. See the SciPy documentation.
Jun 21, 2010
Andrea Zonca

 

change permission recursively to folders only

linux
find . -type d -exec chmod 777 {} ;
Mar 23, 2010
Andrea Zonca

 

aptitude search ‘and’

linux
this is really something really annoying about aptitude, if you run:
aptitude search linux headers
it will make an ‘or’ search…to perform a ‘and’ search, which I need…
Mar 16, 2010
Andrea Zonca

 

using numpy dtype with loadtxt

linux
python
Let’s say you want to read a text file like this:


Mar 3, 2010
Andrea Zonca

 

Stop ipcluster from a script

python
Ipcluster is easy to start but not trivial to stop from a script, after having finished the processing, here’s the solution:
from IPython.kernel import client
mec =…
Feb 19, 2010
Andrea Zonca

 

Correlation

Expectation value or first moment of a random variable is the probability weighted sum of the possible values (weighted mean).
Expectation value of a 6-dice is…
Jan 28, 2010
Andrea Zonca

 

execute bash script remotely with ssh

linux
a bash script launched remotely via ssh does not load the environment, if this is an issue it is necessary to specify –login when calling bash:

ssh user@remoteserver.com…
Jan 7, 2010
Andrea Zonca

 

lock pin hold a package using apt on ubuntu

linux
set hold:
echo packagename hold | dpkg –set-selections

check, should be hi :
dpkg -l packagename

unset hold:
echo packagename install | dpkg –set-selections
Jan 7, 2010
Andrea Zonca

 

load arrays from a text file with numpy

python
space separated text file with 5 arrays in columns:

[sourcecode language=“python”]
ods,rings,gains,offsets,rparams = np.loadtxt(filename,unpack=True)
[/sourcecode]

qui…
Jan 5, 2010
Andrea Zonca

 

Latest Maxima and WxMaxima for Ubuntu Karmic

linux
Note: The original third-party repository for Maxima packages is no longer available.
Dec 15, 2009
Andrea Zonca

 

number of files in a folder and subfolders

linux
folders are not counted
find . -type f | wc -l
Dec 10, 2009
Andrea Zonca

 

forcefully unmount a disk partition

linux
check which processes are accessing a partition:

[sourcecode language=“python”]lsof | grep ‘/opt’[/sourcecode]

kill all the processes accessing the partition (check…
Sep 17, 2008
Andrea Zonca

 

netcat, quickly send binaries through network

linux
just start nc in server mode on localhost:

[sourcecode language=‘python’] nc -l -p 3333 [/sourcecode]

send a string to localhost on port 3333:

[sourcecode…
Apr 29, 2008
Andrea Zonca

 

Decibels, dB and dBm, in terms of Power and Amplitude

astrophysics
It’s not difficult, just always having some doubts…
Mar 29, 2008
Andrea Zonca

 

Relation between Power density and temperature in an antenna

astrophysics
Considering an antenna placed inside a blackbody enclosure at temperature T, the power received per unit bandwidth is:
\(latex \omega = kT\)

where k is Boltzmann…
Mar 28, 2008
Andrea Zonca

 

Producing PDF from XML files

linux
I need to produce formatted pdf from XML data input file.
The more standard way looks like to use XSL stylesheets.
Associating a XSL sheet to an XML file permits most…
Mar 28, 2008
Andrea Zonca

 

vim costumization

linux
it is about perl but it suggests very useful tricks for programming with vim
http://mamchenkov.net/wordpress/2004/05/10/vim-for-perl-developers/
Oct 17, 2006
Andrea Zonca

 

using gnu find

linux
list all the directories excluding “.”:
Oct 3, 2006
Andrea Zonca

 

beginners bash guide

linux
great guide with many examples:

http://tille.xalasys.com/training/bash/
Oct 3, 2006
Andrea Zonca

 

tar quickref

linux
compress: tar cvzf foo.tgz .cc .h
check inside: tar tzf foo.tgz | grep file.txt
extract: tar xvzf foo.tgz
extract 1 file only: tar xvzf foo.tgz path/to/file.txt
Sep 25, 2006
Andrea Zonca

 

software carpentry

linux
basic software for scientists and engineers:
http://www.swc.scipy.org/
Sep 25, 2006
Andrea Zonca

 

Software libero per il trattamento di dati scientifici

linux
nella ricerca del miglior ambiente per analisi di dati scientifici da leggere questi articoli:

http://www.pluto.it/files/journal/pj0501/swlibero-scie1.html

http://www.pl…
Sep 22, 2006
Andrea Zonca

 

command line processing

linux
Very useful summary of many linux command line processing tools (great perl onliners)

http://grad.physics.sunysb.edu/~leckey/personal/forget/
Sep 22, 2006
Andrea Zonca

 

awk made easy

linux
awk ’/REGEX/ {print NR “ $9” $4”_“\(5 ;}' file.txt </strong> <br/> supports extended REGEX like perl ( e.g. [:blank:] Space or tab characters ) <br/> NR is line…
Sep 22, 2006
Andrea Zonca

 

pillole di astrofisica

astrophysics
curiosita’ ben spiegate da annibale d’ercole, interessante l’idea di avere un livello base e un livello avanzato
http://www.bo.astro.it/sait/spigolature/spigostart.html
Sep 20, 2006
Andrea Zonca
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