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HPC @ Uni.lu

High Performance Computing in Luxembourg

All sessions will take place at the Kirchberg Campus, mainly in the Paul Feidert Room.

Important You are expected to bring your personal laptop for all sessions since there will be no workstation available on site.

All tutorials proposed as practical sessions are available on GitHub.
The detailed program is available here.

Agenda - Day 1 (May 6th, 2014)

May 6th By Title Location
9h00-9H10 S. Varrette Opening P. Feidert
9h10-10h15 S. Varrette Keynote: HPC platforms @ UL: Overview and Usage P. Feidert
10h15-10h30   Coffee break P. Feidert
10h30-11h15 S. Varrette PS1: Getting Started (ssh, scp, rsync, oar, modules, builds) P. Feidert
11h15-12h30 H. Cartiaux PS2: HPC workflow with sequential jobs (C,python,java) P. Feidert
12h30-13h30   LUNCH  
13h30-14h30 S. Varrette PS3: HPC workflow with MPI jobs Ex: OSU MB/HPL * P. Feidert
14h30-16h30 S. Grimonet PS4: Direct, Reverse and parallel Memory debugging with TotalView P. Feidert
16h30-17h30   Roguewave Open discussion and Day 1 Closing P. Feidert

PS = Practical Session using your laptop

*this session have been rescheduled on May 7th

Agenda - Day 2 (May 7th, 2014)

May 7th By Title Location
9h30-10h00 S.Varrette Follow-up Keynote: Last HPC challenges P. Feidert
10h00-10h45   Keynote: Experience reports from top users P. Feidert
  J. Berryman HPC usage in the UL Soft Matter Theory Group P. Feidert
  V. Satagopam HPC@Uni.lu: a Bio-Core user experience P. Feidert
  X. Besseron XDEM Research on UL HPC platform P. Feidert
  J.Muszynski P2P Java experiments on the UL HPC Platform P. Feidert
  F. Pinel Uni.lu HPC usage P. Feidert
10h45-11h00   Coffee break P. Feidert
11h00-11h55 V.Plugaru PS5: Using Matlab on the UL HPC Platform P. Feidert
11h55-12h30 J. Emeras PS6: Using R on the UL HPC Platform P. Feidert
12h30-13h30   LUNCH  
13h30-14h30 V.Plugaru PS7: Bio-informatic softwares on the UL HPC Platform P. Feidert
14h30-16h00 P. Wohlschlegel PS8: Unified profiling and debugging with Allinea P. Feidert
16h00-16h30   Allinea Open discussion P. Feidert
16h30-17h00 S.Varrette (Rescheduled) PS3: HPC workflow with MPI jobs Ex: OSU MB/HP P. Feidert
17h00-17h10 S.Varrette Closing P. Feidert




Detailed Program for the practical sessions

Practical Session 1

Getting Started (ssh, scp, rsync, oar, modules, builds, screen), by: S. Varrette

Online Instructions

This tutorial will guide you through your first steps on the UL HPC platform. we will cover the following topics:

  • Platform access via SSH
  • Overview of the working environment
  • Usage of the web monitoring interfaces (monika, ganglia etc.)
  • Reserving resources with OAR and Job management
  • Using modules
  • Advanced job management and Persistent Terminal Sessions using GNU Screen.
    • illustration on Linux kernel compilation

Practical Session 2

HPC workflow with sequential jobs (C,python,java), by H. Cartiaux

Online Instructions

For many users, the typical usage of the HPC facility is to execute 1 (sequential) program with many parameters. On your local machine, you can just start your program 100 times sequentially. However, you will obtain better results if you are able to parallelize the executions, either across many thread and/or many nodes of the HPC platform

During this session, we will cover 3 use cases:

  1. Use the serial launcher (1 node, in sequential and parallel mode) over a C program.
  2. Use the generic launcher, distribute your executions on several nodes over a python program.
  3. A more advanced usage over a complex Java program JCell, a Java library design to work with cellular genetic algorithms (cGAs)

Practical Session 3

HPC workflow with MPI jobs. Ex: OSU MB/HP, by S. Varrette

Online instructions for OSU Microbenchmarks and for HPL

The objective of this session is to compile and run MPI programs over various reference MPI implementations (Intel MPI, OpenMPI or MVAPICH2, all available on the cluster). In practice, this session will focus on the following MPI applications:

Practical Session 4

Direct, Reverse and parallel Memory debugging with TotalView, by S. Grimonet

Online Instructions

The objective of this session is to get a brief overview of the TotalView, a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. The following topics will be covered:

  • Startup and Overview
  • IHM Navigation and process control
  • Action points (TP)
  • Examination and Data Analysis (TP)
  • Debugging Parallel Applications (TP)
  • Memory reports using MemoryScape (TP)
  • Remote Debugging
  • CUDA Debugging
  • Xeon Phi Debugging
  • Memory Debugging with MemoryScape
  • Events and memory errors (TP)
  • Delayed Scripted debugging (non-interactive) (TP)
  • Reverse debugging using ReplayEngine (TP)
  • Asynchronous control of Parallel Applications (TP)
  • Type Transformation (TP)

Practical Session 5

Using Matlab on the UL HPC Platform, by V. Plugaru

Online instructions

The objective of this session is to exemplify the execution of MATLAB - a high-level language and interactive environment for numerical computation, visualization and programming, on top of the UL HPC platform. The following topics will be covered:

  • how to run MATLAB in interactive mode, with either the full graphical interface or the text-mode interface
  • how to run MATLAB in passive (batch) mode, enabling unattended execution on the clusters
  • how to use MATLAB script (.m) files
  • how to plot data, saving the plots to file
  • how to take advantage of some of the parallelization capabilities of MATLAB to speed up your tasks

Practical Session 6

Using R on the UL HPC Platform, by J. Emeras

Through this session you will learn how to use R from your local machine or from one of the resources of the UL HPC platform clusters. We will also use the ggplot library to generate nice graphics and export them as pdf files. Then, we will see how to organize and group data. Finally we will illustrate how R can benefit from multicore and cluster parallelization.

Practical Session 7

Bio-informatic softwares on the UL HPC Platform, by V. Plugaru

The objective of this session is to exemplify the execution of several Bioinformatics packages on top of the UL HPC platform. The targeted applications are:

In particular, the following topics will be covered:

  1. how to load and run pre-configured versions of these applications on the clusters
  2. how to download and use updated versions of Bowtie2/TopHat
  3. discuss the parallelization capabilities of these applications

Practical Session 8

Unified profiling and debugging with Allinea, by P. Wohlschlegel

Developing an HPC application designed for MPI or hybrid environments can be a very challenging task - especially when it comes to fixing bugs, optimizing workload or even resolving both type of issues simultaneously. Those challenges are made easier with Allinea Tools. Using Allinea environment, it is now possible for developers to adopt instantly efficient and scalable development tools and to focus immediately on their core activity : science.

Allinea tools are available for you in University of Luxembourg, and this workshop has been arranged to help you get started with Allinea MAP and Allinea DDT. During this workshop, we will review the capabilities of Allinea tools and see, through hands-on exercises, how this environment can help reduce your time to results to the minimum.