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Super Computing 2016
In November 2016 members of the ACI-REF consortium had the opportunity to attend Super Computing 2016 (SC16). Below are some of their experiences.
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Three Ways to Productivity
As someone with a lot to do at work (tickets! meetings! reports! documentation! workshops! community-building!), I often consider how I can optimize my work time. Like a good scientist, I try lots of approaches and some of my experiments are more successful than others. This post describes three “success stories” — using a simple technology,…
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How to gain hybrid MPI-OpenMP code performance without changing a line of code a.k.a. dealing with task affinity
Need for hybrid MPI-OpenMP programs The multi-core era is here and our programming habits need to adjust to it. Most people by now have their codes parallelized using MPI for distributed memory machines, as that era has been upon us for 20 years now. MPI codes can work well on multi-core machines, but, with the…
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Island Facilitation
Foster’s rule (also known as the island rule or the island effect) is an ecogeographical rule in evolutionary biology stating that members of a species get smaller or bigger depending on the resources available in the environment. Source: https://en.wikipedia.org/wiki/Foster’s_rule Cyberinfrastructure at the University of Hawaii is relatively new and small compared to the other organizations…
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On Equity and the Long Tail
One of our most common roles as a facilitator is as “teacher” to the researchers whose work we facilitate. It’s a role that not only requires a good set of communication skills, but also a knowledge of what our learners (researchers) already know, what they need to know, and what learning steps are necessary along…
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On Building a fast R environment
In this article we will describe how to build an R distribution from source using the Intel Compiler Suite. Why? The execution of R code can be significantly sped up when it is built with a decent compiler and relies on fast mathematical libraries (mainly linear algebra). Requirements The installation (vide infra) was performed on…
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Software Installation for Researchers at USC
I recently attended the ACI-REF Virtual Residency 2016 workshop where we discussed, among other things, how and when different computing centers should install software for their researchers. The conversation was surprisingly lively because installing software is a topic that touches on many regimes of facilitation. Since every institution has its own perspective, I thought it…
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When a lot of little things add up to a lot of time; HTCondor to the rescue
A student sits at his desk, fretting. The clock is ticking, the deadline is looming, and the giant mound of data he desperately needs processed remains, stubbornly and unabashedly, unaltered. He’s tried many things, but it’s only him and his workstation against the monstrosity of information he’s attempting to subdue. His PC, by itself, is…
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A short note on the Python Virtual Environment
In this post we will discuss the concept of a Virtual Environment in Python. We will discuss the following topics: What is a Virtual Environment (VE) Setting up a VE Activation of a VE Installation of packages within the VE Deactivation of a VE Removal of a VE What is a virtual environment? A Python…
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The Agave Platform
A common task for ACI facilitators is assisting researchers with deploying or getting their software packages to run on the local or national resources and working with the job scheduler. For the most part the reality of using HPC and HTC resources requires getting into the command line, which many new graduate students and post-docs…