High Performance Computing & AI
Practical notes on Python, JupyterHub, Kubernetes and AI for science — from the San Diego Supercomputer Center.
-
Software Carpentry setup for Chromebook
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.
-
Zero based indexing
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.
-
Write unit tests as cells of IPython notebooks
Plugin for py.test to write unit tests as cells in IPython notebooks: Homepage on Github:
-
How to perform code review for scientific software
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, improve readibility and usability. It is used extensively in industry, not much in academia.
-
Create a Github account for your research group with free private repositories
See the updated version at 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 online issue-tracking interface.
-
Thoughts on a career as a computational scientist
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.
-
Machine learning at scale with Python
My talk for the San Diego Data Science meetup: http://www.meetup.com/San-Diego-Data-Science-R-Users-Group/events/170967362/
-
Python on Gordon
Gordon has already a python environment setup which can be activated by loading the python module: module load python add this to .bashrc to load it at every login
-
Build Software Carpentry lessons with Pelican
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 Creative Commons.
-
openproceedings - Github/FigShare based publishing platform for conference proceedings
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 HTML or PDF form or both. The Scipy conference is at the forefront on this and did great work in peer reviewing on Github, see: .
-
wget file from google drive
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.
-
Run IPython Notebook on a HPC cluster via PBS
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 of a HPC cluster and visualize it in a browser that runs on a local machine.
-
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 20% on Planck.
-
Published paper on destriping Cosmic Microwave Background polarimeter data
TL;DR version: Preprint on arxiv: Destriping Cosmic Microwave Background Polarimeter data
-
Jiffylab multiuser IPython notebooks
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: