# Difference between revisions of "HPC - Algorithms and Applications - Winter 13"

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Slides and exercise sheets/solutions will be made available during the lecture. | Slides and exercise sheets/solutions will be made available during the lecture. | ||

− | See the [[HPC - Algorithms and Applications - Winter 12|lecture from winter term 2012/13]] | + | |

+ | Lecture slides will be published here after the lessons: | ||

+ | See also the [[HPC - Algorithms and Applications - Winter 12|lecture from winter term 2012/13]]. | ||

+ | * Oct 21: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS13/intro.pdf Intro] | ||

+ | * Oct 21, Oct 28: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/fundamentals.pdf Fundamentals - Parallel Architectures, Models, and Languages] | ||

+ | <!-- | ||

+ | * Oct 29, Nov 5, Nov 12: Dwarf No. 1 - [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/denseLA.pdf Dense Linear Algebra]; | ||

+ | ** additional material: [http://epubs.siam.org/sirev/resource/1/siread/v46/i1/p3_s1 article by Elmroth et al.] in [http://epubs.siam.org/sirev/ SIAM Review] | ||

+ | ** chapter [http://netlib.org/scalapack/slug/node74.html In-core dense matrices] of the [http://netlib.org/scalapack/slug/scalapack_slug.html ScaLAPACK User's Guide] | ||

+ | * Nov 19, Nov 26: Dwarf No. 5 - [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/structured.pdf Structured Grids] | ||

+ | ** articles by M. Frigo and V. Strumpen:<br> [http://www.fftw.org/~athena/papers/ics05.pdf Cache oblivious stencil operations] (preprint);<br> [http://link.springer.com/article/10.1007%2Fs11227-007-0111-y The memory behavior of cache oblivious stencil operations] (preprint can be found via Google) | ||

+ | ** [http://epubs.siam.org/doi/abs/10.1137/070693199 article by K. Datta et al.] in [http://epubs.siam.org/sirev/ SIAM Review] ([http://www.cs.berkeley.edu/~kdatta/pubs/sirev09_stencil.pdf preprint]) | ||

+ | * Nov 26, Dec 3: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/sfc.pdf Structured Grids and Space-filling Curves], [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/solving_swe.pdf Solving the Shallow Water Equations] | ||

+ | ** Maple worksheets: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/hilbert_adap.mw hilbert_adap.mw] (also as [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/hilbert_adap.pdf PDF]); | ||

+ | * Dec 10: Dwarf No. 6 - [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/unstructured.pdf Unstructured Grids and Partitioning] | ||

+ | ** additional material: [http://epubs.siam.org/sisc/resource/1/sjoce3/v20/i1/p359_s1 article by Karypis and Kumar: A Fast and High Quality Multilevel Scheme for Partitioning Irregular Graphs] | ||

+ | * Dec 17: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/sfc.pdf Partitioning and Space-filling Curves revisited] | ||

+ | ** Maple worksheets: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/hilbert-arith-part.mw hilbert-arith-part.mw] (also as [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/hilbert-arith-part.pdf PDF]); [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/reftree_hilbert_vertexlab.mw reftree_hilbert_vertexlab.mw] (also as [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/reftree_hilbert_vertexlab.pdf PDF]); | ||

+ | ** related article by Mitchell: [http://www.sciencedirect.com/science/article/pii/S0743731506002309 journal article], [http://math.nist.gov/~WMitchell/papers/reftree.pdf preprint], [http://math.nist.gov/phaml/reftree.html webpage by W. Mitchell on reftree method] | ||

+ | * Jan 7: Dwarf no. 2 - [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/sparseLA.pdf Sparse Linear Algebra]: Application example (page rank) and data structures | ||

+ | * Jan 14: Parallel Sparse Matrix-Vector Multiplication | ||

+ | ** [http://www.staff.science.uu.nl/~bisse101/Education/PA/pa.html lecture material] accompanying the book by R. Bisseling (see esp. the slides [http://www.staff.science.uu.nl/~bisse101/Book/PSC/psc4_3.pdf psc4_3.pdf], [http://www.staff.science.uu.nl/~bisse101/Book/PSC/psc4_4.pdf psc4_4.pdf], [http://www.staff.science.uu.nl/~bisse101/Book/PSC/psc4_5.pdf psc4_5.pdf], and [http://www.staff.science.uu.nl/~bisse101/Book/PSC/psc4_6.pdf psc4_6.pdf]) | ||

+ | * Jan 21: Dwarf no. 4: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/moldyn.pdf N-body methods] and [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/moldyn_impl.pdf implementation] | ||

+ | ** Maple worksheet: [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/twobody.mw twobody.mw] (also as [http://www5.in.tum.de/lehre/vorlesungen/hpc/WS12/twobody.pdf PDF]) | ||

+ | ** [http://epubs.siam.org/doi/abs/10.1137/0913055 article on Fast Multipole methods by C.R. Anderson] | ||

+ | ** [http://www.nature.com/nature/journal/v324/n6096/abs/324446a0.html article by Barnes & Hut in Nature] (both articles can be accessed via TUM ebib-access) | ||

+ | --> | ||

= Literature and Online Material = | = Literature and Online Material = |

## Revision as of 11:14, 21 October 2013

**Term**- Winter 13/14
**Lecturer**- Prof. Dr. Michael Bader
**Time and Place**- Lecture: Monday, 14.15-15.45, MI 02.07.023 (starts Oct 21);

Tutorial: Wednesday, 10-12, MI 02.07.023 (starts Oct 23, roughly bi-weekly) **Audience**- Elective topic in Informatics Bachelor/Master: students in mathematics or in any science or engineering discipline are welcome!
**Tutorials**- Oliver Meister
**Exam**- written or oral exam at end of semester
**Semesterwochenstunden / ECTS Credits**- 3 SWS (2V + 1Ü) / 4 ECTS
**TUMonline**- https://campus.tum.de/tumonline/lv.detail?clvnr=950111465 (lecture)

https://campus.tum.de/tumonline/wbStpModHB.detailPage?&pKnotenNr=705979 (module description)

# Content

The lecture will have a focus on parallel algorithms and implementation techniques in the field of numerical simulation and high performance computing, such as:

- linear algebra problems on dense and sparse matrices
- simulation on structured and unstructured meshes
- particle-based simulations (with long-range and short-range interactions)
- spectral methods (parallel FFT and related algorithms)
- Monte Carlo and statistical methods

(a.k.a. *the seven dwarfs of HPC*).

The accompanying tutorials will include practical assignments, and will concentrate on the programming of GPU and accelerator platforms.

# Lecture Material

Slides and exercise sheets/solutions will be made available during the lecture.

Lecture slides will be published here after the lessons: See also the lecture from winter term 2012/13.

- Oct 21: Intro
- Oct 21, Oct 28: Fundamentals - Parallel Architectures, Models, and Languages

# Literature and Online Material

- R.H. Bisseling: Parallel Scientific Computing - A structured approach using BSP and MPI, Oxford University Press, 2004.
- Course notes on Rob Bisseling's lecture on Parallel Algorithms (based on the text book)

- T.G. Mattson, B.A. Sanders, B.L. Massingill: Patterns for Parallel Programming, Addison-Wesley, 2005
- D.B. Kirk, W.W. Hwu: Programming Massively Parallel Processors - A Hands-on Approach, Morgan-Kaufman, 2010
- J. Sanders, E. Kandrot: CUDA by Example, Addison-Wesley, 2011

# Prerequisites

Helpful, but not strictly required is knowledge in:

- basics of numerical methods (e.g.: lecture
*IN0019 Numerical Programming*or similar) - basics of parallel programming (lecture
*Parallel Programming*,*HPC - Programming Paradigms and Scalability*, or similar)

Most important is a certain interest in problems from scientific computing and numerical simulation!