Research Readings (HHMI) - Summer 2004
Last updated: Wednesday, 15-Sep-2004 18:45:42 EDT
The List
- AltiVec1 - everyone; May 21, 2004
- AltiVec2 - everyone; May 21, 2004
- HPC - John and Dawit; May 24, 2004
- DDJ 1, 2, 3 - John and Dawit; July 4, 2004
- PMDG - everyone; July 25, 2004
- POCO - John and Dawit; July 25, 2004
- NASA -
Checkout Roster
- MPI1 - JoshH
- MPI2 - JoshH
- Leach - Charlie
- HPC - Dawit
Books
- HPC - High Performance Computing 2e, Dowd and Severance.
- Chapters 1, 2, 3, 4, 5, 6, 12, 14, 15, and 16
- CMPCB - Computational Methods in Physics, Chemistry and
Biology, Harrison.
- MPI1 - MPI hummannahumma volume 1.
- MPI2 - MPI hummannahumma volume 2.
- POCO - Structured Computer Organization - Tannenbaum.
- Portions relevant to x86 assembly language.
- Molecular Dynamics - Leach.
Journal Articles
- DDJ 1 - Optimization Techniques, Tim Kientzle, Dr Dobbs, May, 2004
- DDJ 2 - Optimizing for Intel Architecture CPUs, Victor Duvanenko, Dr Dobbs, May, 2004
- DDJ 3 - To Inline or Not to Inline, Richard Vaughan, Dr Dobbs, May, 2004
- NASA - An Evaluation of PowerMac G4 Systems for FORTRAN-based Scientific Computing..., Craig Hunter, NASA.
The paper is here.
- PMDG - Parallel Molecular Dynamics: GROMACS, Erik Lindahl, ClusterWorld, v2 n8
Manuals, etc
- AltiVec1 -
AltiVec White Paper
- AltiVec2 -
AltiVec Glance
- CMDO - Computational molecular dynamics overview. There are two
of these, they need to be re-named and re-organized. Both are in
/cluster/project/gromacs-overview.
- GCC - GCC 3.3 manual, the sections on x86 and AltiVec in "Built-in Functions Specific to Particular Target Machines".
Links