Jonathan Dursi

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Spark, Chapel, TensorFlow: Workshop at UMich

The kind folks at the University of Michigan’s Center for Computational Discovery and Engineering (MICDE), which is just part of the very impressive Advanced Research Computing division, invited me to give a workshop there a couple of months ago about the rapidly-evolving large-scale numerical computing ecosystem. There’s lots that I want to do to extend this to a half-day length, but the workshop materials — including a VM that can be used to play with Spark, Chapel and TensorFlow, along with Jupyter notebooks for each...

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Approximate Mapping of Nanopore Squiggle Data with Spatial Indexing

Over at the Simpson Lab blog, I have an post describing a novel method for Directly Mapping Squiggle Data, using k-d trees to map segmented kmers; a simple proof of concept is available on github.

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On Random vs. Streaming I/O Performance; Or seek(), and You Shall Find --- Eventually.

At the Simpson Lab blog, I’ve written a post on streaming vs random access I/O performance, an important topic in bioinformatics. Using a very simple problem (randomly choosing lines in a non-indexed text file) I give a quick overview of the file system stack and what it means for streaming performance, and reservoir sampling for uniform random online sampling.

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Understanding Partial Order Alignment for Multiple Sequence Alignment

Over at the Simpson Lab blog, I have an explainer on Understanding Partial Order Alignment, an under-appreciated method for multiple sequence alignment; I hope the explanation there (and explanatory implementation) is useful to those exploring graph-based approaches to alignment.

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HPC+MPI on RCE Podcast

In the latest episode of the RCE podcast, Jeff Squyres, Brock Palen, and I spoke about the HPC and MPI series of blogposts and the community reaction. It was a really interesting discussion; Brock has worked closely with an enormous variety of researchers and helps run an HPC centre, while Jeff deeply understands HPC networking, from the getting ones and zeros onto the wires at the lowest-level of hardware up to being an extremely active member of the MPI forum. I was really pleased that...

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Coarray Fortran Goes Mainstream: GCC 5.1

This past week’s release of GCC 5.1 contains at least two new features that are important to the big technical computing community: OpenMP4/OpenACC offloading to Intel Phi/NVIDIA accellerators, and compiler support for Coarray Fortran, with the communications layer provided by the OpenCoarrays Project. While I don’t want to downplay the importance or technical accomplishment of the OpenMP 4 offloading now being available, I think it’s important to highlight the widespread availability for the first time of a tried-and-tested post-MPI programming model for HPC; and one...

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