Note: While the bulk of the system will become available in summer 2012, LRZ is already operating a migration system with a similar architecture.

• Introduction to the x86 Westmere and Sandy Bridge Processor Architecture
• Usage of Intel Compilers: switches, optimization, profiling, OpenMP, advanced features
• Usage of the Intel debugger
• Explicit and compiler-directed vectorization with SSE and AVX

• Programming for NUMA
• Intel Cilk Plus
• Fortran standard support and extensions in Intel Fortran
• Intel Inspector XE (correctness checking for memory and threading)
• Threading Building Blocks, OpenCL and other parallel programming models
• Static Security Analysis
• Performance Libraries (MKL, IPP)
• VTune Amplifier XE (performance analysis)

• Intel Performance Monitoring Unit (PMU) and other performance analysis tools
• Intel Cluster Tools Overview and Usage
• Intel Many Integrated Core (MIC) Architecture
• A case study illustrating the use of the Intel toolchain

Thursday schedule:

• Using LoadLeveler for batch queuing
• IBM's parallel environment
• Performance Tools (High Performance Toolkit, Eclipse User Interface) including a demonstration.

On day 1, an introduction to Totalview including memory debugging and exercises is provided

On day 2, CUDA debugging and the Replay Engine are covered. In the afternoon, the Threadspotter tool for identifying performance issues is presented

To consolidate the lecture material, each day's approximately 4 hours of lecture are complemented by 3 hours of hands-on sessions.

The scalalife winterschool on molecular modelling focuses on the scalalife software packages (www.scalalife.eu) and aims to give an introduction to students in the field of life sciences and HPC. The developers of the software packages Gromacs, Dalton and Discrete give lectures and hands-on tutorials. Additional software packages used in the life scinece community are also explained in lectures and tutorials.

Day 1: Lifescience Suite: Schrodinger Software (http://www.schrodinger.com/)

Day 2: HPC tools and resources for life sciences:

• Introduction to scalalife
• Available lifescience tools with demo and hands-on (Force-feedback device)
• Remote Visualisation (VMD+NAMD, Gromacs)
• 3D Stereo Portable Device
• 3D Screen, (Wall-E)
• Holobench

Day 3: Discussion in small groups and trip to Zugspitze

Day 4: GROMACS

Day 5:

• Morning : DALTON
• Afternoon : DISCRETE and Visiting SuperMUC

Participants should have knowledge in programming and life science software.

RRZE building, University campus Erlangen, Martensstr. 1

LRZ Building, University campus Garching, near Munich: Via video conference if there is sufficient interest, however without hands-on sessions

Day 1

• Introduction to High Performance Computing
• HPC systems at LRZ and in Germany
• Technical aspects of software engineering: development process, usage of libraries, memory management, tools for code documentation, development environments
• Tools: Using Secure Shell, User interfaces, Source code versioning systems and Make

Day 2

• Basic parallel programming with MPI and OpenMP
• Processor Architectures: Register, Cache, Locality, Performance metrics

Day 3

• Principles of code optimization (unrolling, blocking, dependencies, C++ issues, bandwidth issues, performance projections)
• Using performance libraries
• Advanced MPI programming

Day 4

• Parallel algorithms: data parallelism, domain decomposition, task parallelism, master-worker, granularity, load balancing, scalability models
• Advanced OpenMP programming
• Parallel Architectures: multi-core, multi-socket, ccNUMA, cache coherence and affinity, tools for handling memory affinity

Day 5

• Architecture-specific optimization strategies: compiler switches, avoiding cache thrashing, exploiting SIMD capabilities
• MPI exercises

Each day is comprised of approximately 5 hours of lectures and 2 hours of hands-on sessions.

 Day 1

• Intel Tracing Tools: MPI tracing and correctness checking
• Intel Threading tools for OpenMP correctness checking and profiling
• Profiling on SGI Altix systems: histx and lipfpm
• Introduction to Scalasca

 Day 2

• Parallel application performance analysis with Scalasca
• Parallel input/output with MPI-IO

 Day 3

• I/O tuning on high performance file systems
• Portability of binary files, big/little endian issues
• Using I/O libraries (pNetCDF, HDF5)

Day 4

• Introduction to the PGAS languages Coarray Fortran and UPC: Partitioned global address space languages have emerged as an alternative to other parallel programming models, promising a shorter development cycle due to improved programmability while keeping the performance level on par with MPI. This course introduces the parallel  facilities integrated into the Fortran language (coarrays) and the C language (unified parallel C), respectively. A hands-on session allows to experiment with the new concepts, using prototype implementations on LRZ's HPC systems.

• Introduction to Eclipse IDE
• Introduction to CDT
• Hands-on with CDT
• Short introduction and demo of Photran

Different modern Krylov Subspace Methods (CG, GMRES, BiCGSTAB ...) as well as highly efficient preconditioning techniques are presented in the context of real life applications.

Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the

• basic constructs of iterative solvers
• the Message Passing Interface (MPI)
• the shared memory directives of OpenMP.

This course is organized by the University of Kassel, the high performance computing centre of Stuttgart (HLRS) and IAG.

• object oriented features, submodules
• design patterns
• generation and handling of shared libraries
• mixed language programming
• standardized IEEE arithmetic
• I/O extensions from Fortran 2003
• parallel programming with coarrays
• source code versioning system (subversion)

To consolidate the lecture material, each day's approximately 4 hours of lecture are complemented by 3 hours of hands-on sessions.