Astronomy 598 Topics in Theoretical Astrophysics (Scientific Supercomputing)


Autumn 2017: Fri 11:00-12:20 Physics/Astronomy Building A210

Instructor: Pramod Gupta
psgupta *at* astro. washington. edu

Office hours: after class, or email.

Web-site: http://vpl.astro.washington.edu/users/psgupta/astro598supercomputing.html

Pre-requisites:
Students should know a programming language. Students should bring their laptop to class. If you have a windows laptop please install ssh client software on your laptop so that you can connect to hyak. Students should have a hyak account. Any UW student can get a hyak account. Instructions are at below link:
http://students.washington.edu/hpcc/getting-started-on-hyak/

Syllabus:
We will use examples of scientific supercomputing from a wide variety of research areas such as Astrophysics, Biology and Chemistry.

(1) Using Linux (command line, setting up the environment, modules, file permissions, compiling programs, installing open source programs as a regular user)

(2) Using a supercomputer (scheduler, submitting jobs, gnu parallel, sql parallel, backfill queue, checkpointing, interactive use, using GUI tools, storing data)

(3) Parallel programming (OpenMP, MPI, OpenACC, Python multiprocessing, Parallel R, Parallel Matlab)


Grades:

Homework problems (100% of grade) will be assigned every week.


Reference Books:

Classics:
The C programming language 2nd edition
Brian W. Kernighan and Dennis M. Ritchie

The UNIX programming environment
Brian W. Kernighan and Rob Pike

Parallel Programming:
Using MPI : portable parallel programming with the message-passing interface
William Gropp, Ewing Lusk, Anthony Skjellum

Using OpenMP : portable shared memory parallel programming
Barbara Chapman, Gabriele Jost, Ruud van der Pas

Parallel programming in OpenMP
Rohit Chandra et al

MPI--the complete reference
Marc Snir et al

Parallel programming with MPI
Peter S. Pacheco