Lecture Series in Parallel Computing and CUDA-C

A new lecture series in practical aspects of Parallel Computing and CUDA-C will kick off on Tuesday, February 22nd. The series will run twice weekly, on Tuesdays and Fridays from 2:30-3:30 pm in Bassine 251, for a total of 12 lectures over six weeks. Lectures will be given by Gianluca Castellani, Ph.D. Research Computing Specialist and HPC Cluster Administrator (Volen Center, LTS, and Physics) and Francesco Pontiggia, Ph. D., Postdoctoral Fellow, (Volen Center and Biochemistry). The series is jointly sponsored by the Volen Center, MRSEC, Physics Dept., and Library and Technology Services.

Tentative Schdule

Lecture 1 :  Why Parallel Programming? Parallel Architectures and Programming Models.
Lecture 2 :  Parallelization Techniques
Lectures 3 – 4 : Programming in a Shared Memory Environment — Introduction to OpenMP
Lecture 5 : CUDA-C fundamentals. Compiler, kernels, host-device data transfer
Lecture 6 : Time execution tuning, catching error and hardware evaluation
Lectures 7 – 8 : GPU memory types
Lectures 9 – 11 : Distributed Memory — MPI Paradigm
Lecture 12 : Using High Performance Parallel Libraries : An Example — Parallel Matrix Inversion.

Notes and Examples will be posted on the HPCC Wiki

More “Noted in Press”

Brandeis authors noted in boldface.

New route to lycopodium alkaloids

The lycopodium alkaloids are a large and extensively studied alkaloid family. Huperzine A (1), the medicinally most significant lycopodine alkaloid as a potential treatment for Alzheimer’s disease, functions as an acetylcholinesterase inhibitor but may have other roles as has been addressed in several recent reviews.  Sauroine (2, 7,8-dihydroxylycopodine), from Huperzia saururus, was reported in 2004 and shown in 2009 to improve memory retention in the step-down test in male Wistar rats, significantly increasing hippocampal plasticity. 7-Hydroxylycopodine (3), from Huperzia serrata, was also reported in 2004 and may have related biological activity.

In their recent Organic Letters paper entitled the Synthesis of (±)-7-Hydroxylycopodine, the Snider lab at Brandeis developed a new general route to these bridgehead hydroxylated lycopodines. They reported a practical six-step synthesis of 7-hydroxylycopodine which makes it readily available for further biological evaluation. The key step of the synthesis is the treatment of bicyclic enol ether 4 with 60% sulfuric acid that affords tricyclic amino alcohol 5, which is further elaborated to 7-hydroxylycopodine (3) in three steps. The application of this route to the synthesis of sauroine (2) is now under investigation.

Snow

Waltham is enjoying snowfall amounts like we haven’t seen since 1995-96. The students built a mogul on the hill between the science buildings and South St and have been practicing tricks.

KC Hayes contributes this e-card from earlier in the winter:

Learning from unexpected events

Have you ever heard the phrase ‘the eyes are a window to the soul’? New research from Dr. Robert Sekuler’s Vision Lab suggests that the eyes may be a window to the brain as well. In an article published in this month’s issue of the Journal of Vision, Neuroscience grad student Jessica Maryott (PhD ’09) and Psychology grad student Abigail Noyce showed that as participants learn, their eye movements change in a way that lets scientists investigate how that learning takes place, specifically in response to unexpected events.

Participants in the study watched as a disk moved on a computer screen in a zig-zag path; they then reproduced its trajectory from memory. Each path was repeated several times, allowing the researchers to examine the learning process as participants became familiar with the pattern and more accurate at reproducing it. Researchers also measured participants’ eye movements as they watched the disk move, and examined learning-related changes in those as well. The results suggest that eye movements reflect the participant’s level of learning by actually predicting where the disk will be going next.

Sometimes, part of the disk’s path changed after several repetitions going in the opposite direction (a 180 degree change, shown in the green trace on the figure), without warning to the participant. This caused participants to make a prediction error: the actual motion of the disk no longer matched the pattern they had learned, but their eyes moved in the direction of the expected movement (positive velocity) until they were able to correct the error (this is when the green trace reverses velocity and goes below 0 in the figure). After such a prediction error, when the pattern appeared again, participants’ eye movements showed that the previous prediction error produced fast ‘one-shot’ learning, and participants now expected to see the new version of the path (shown in the blue trace, which goes in the new expected direction, 180 degrees from the old – thus showing a negative velocity). The researchers concluded that unexpected events (like the induced error) have high salience for learning. These results suggest that humans have a cognitive system which monitors how well sensory input matches predictions, and responds to errors with sudden, strong learning about the new situation.

Bacterial phenomics

As a self-confessed prokaryotic chauvinist, I’m always on the lookout for new interesting papers aimed at understanding bacterial metabolism and regulation. A recent paper in Cell, entitled “Phenotypic Landscape of a Bacterial Cell” by a group of authors including Biology Professor Susan Lovett demonstrates the application of high-throughput screening to finding new bacterial phenotypes. Approximately 4000 E.coli mutant strains, representing deletions of individual non-essential genes, were plated on 324 different media representing a total of over 100 different stress conditions, and the growth followed by image analysis. Approximately half of the genes screened had one or more identifiable phenotypic repsonses. This approach allows the identification of genes that are conditionally essential, genes that are involved in multiple resistance, etc. This represents a new automated method for identifying phenotypes (hence “phenomics’) and understanding the roles of genes of as yet unidentified function in bacteria. The data set is publicly available at http://ecoliwiki.net/tools/chemgen/.

The Eccentricities of Darwin

From time to time we will present samples of student writing, in this first case from Professor James Morris‘s first-year seminar on The Origin of Species. Gabriella Feingold, a first-year student intending to major in Theater, kept track of her thoughts on the book over the semester in free flowing form of a blog, entitled The Eccentricities of Darwin. She hopes the blog will both educate readers on intricacies of Darwin’s writing, and allow for humorous discussion of this dense but readable text.

Here’s a sample from Gabriella’s blog:

On to Chapter 1 – Variation Under Domestication! In Chapter 1, Darwin makes an effective comparison between domestic variation and natural variation. In order for Darwin’s theory to work, variations must naturally occur and then certain ones must be naturally selected, causing evolution of species. Here, Darwin argues that people witness variation among their domestic animals, so why can’t variations occur in nature? Sure, domestic animals are actively bred, and there is a “selector” deciding which variations stay and which go, but Darwin is always a proponent of the power of nature. Humans are nothing compared to its forces. (That’s a slight paraphrase.)

My favorite part of Chapter 1 is the pigeons! Yes, Darwin goes on and on about pigeons. He has good reason though – everybody loves pigeons. In Victorian England, pigeons were bred by commoners. The idea of breeding pigeons was a familiar one and a hobby to many. Darwin also appeals to the lower class, and thereby a broad audience, by mentioning the significance of pigeons. Now all of the pigeon breeders feel important and start listening to Darwin’s ideas. At least, that’s one way to look at it.

Darwin is kind to all fellow men as he writes, but he is not afraid to put down the classic Greek philosophers. Part of Aristotle’s view on nature was that every creation has a final cause, or a purpose. Darwin, however, disagrees. On page 37, still comparing natural selection to domestic selection, Darwin writes that gardeners never plan for the final plant they end up with. Along the way, they choose variations that they like, and continually improve the plant. Natural selection works the same way. The creation does not have a final purpose, as the great Aristotle might say, rather, according to Darwin, each variation is selected by nature because it is beneficial to the organism (not because the organism is striving for a goal).

HHMI Professors on changing the culture of science education

13 HHMI Professors, including Brandeis’s Irving Epstein, wrote a recent editorial in the journal Science calling for a reexamination of priorities between research and teaching at research universities. The seven initiatives they call for:

  1. Educate faculty about research on learning.
  2. Create awards and named professorships that provide research support for outstanding teachers.
  3. Require excellence in teaching for promotion.
  4. Create teaching discussion groups.
  5. Create cross-disciplinary programs in college-level learning.
  6. Provide ongoing support for effective science teaching.
  7. Engage chairs, deans, and presidents.

Strong stuff — will we respond to this challenge?

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