Campus school 2014 at University of Ljubljana

Jul 7, 2014, 9:00 AM → Jul 11, 2014, 7:00 PM CET

II/5, IV/2 and P2 (Fakulteta za strojništvo and FIŠ Novo mesto)

Summer HPC week organized for undergraduate and graduate students at two locations simultaneously:

1. University of Ljubljana,  Faculty of Mechanical Engineering, Aškerčeva 6, Ljubljana (ULFME)
2. Faculty of Information studies, Ulica talcev 3, Novo Mesto (FIS)

Morning lectures and live demonstrations on HPC are prepared by ULFME and FIS and broadcasted from one site to other. In the afternoon hands-on trainings in computing classrooms are conveyed at each site with different excercises on HPCFS supercomputer. On Thursday there will be organized transport from Novo mesto to Ljubljana and back. See attached programme for details.
Participants will receive accounts on supercomputer HPCFS for hands-on from both sites.

Important notices for participants will be published on local WEB page (http://hpc.fs.uni-lj.si/cs14).

agenda campus-sola-HPC2014.pdf

Lab photo cs14lab.jpg

photo cs14ff.jpg

Monday, July 7

Linux

• Introduction to Campus school and visit to HPC center,
• Introduction to GNU/Linux, GUI environments
  Bash, AWK scripts, Modules, Introduction to compiling
  Programming languages in and devel environments in Linuxu

Intro to HPC, HPC usage and NxClient remote desktop connection to HPCFS, Batch and job scheduler LSF and interactive usage of nodes,
Presentation of possible solutions of parallel programs by using OpenMP in MPI, Hello World parallel in C with OpenMP, Hello World with OpenMPI and running on HPCFS.

Conveners: Dr Leon Kos (University of Ljubljana), Matjaž Šubelj (FS)

slides gnulinux.pdf PRACE-Autumn-School-2013-Kos-UL-Using-HPCFS.pdf

Unix shell http://software-carpentry.org/v5/novice/shell/index.html

1:00 PM Lunch

10:45 AM Coffe break each day

Coffee, water and cookies will be self served in Room II/4

Introduction to LINUX

Introduction to linux, programming, programming environments, Hands-on on HPCFS

Convener: Dr Biljana Mileva Boshkoska (FIS)

slides HPCWS.pdf

3:45 PM Tea break each day

Coffee, tea, water and cookies self served

Tuesday, July 8

Introduction to HPC: Video from NM to LJ

HPC introduction and basics in C language.
Introduction to MPI on HPCFS

Predstavitev HPC:
- kaj je HPC in zakaj se uporablja
- kaj sestavlja superračunalnik
Osnove MPI:
- kaj je MPI in zakaj se uporablja
- pošiljanje sporočil med procesi
- tipi komunikacije
- osnovne MPI v jeziku C

Convener: Dr Matjaž Depolli (IJS)

slides HPC.pdf MPI.pdf

1:00 PM Lunch

HPC introduction: MPI tutorials on HPCFS

Convener: Dr Leon Kos (University of Ljubljana)

slides

• MPI.pdf
• OpenMPIntro_01.pdf
• PRACE-Autumn-School-2013-Kos-UL-Introduction-to-MPI.pdf

Hands-on HPC

• spoznavanje z MPI
• merjenje zmogljivosti
• sinhrona komunikacija
• skupinska komunikacija

Convener: Dr Matjaž Depolli (IJS)

slides vaje.pdf

Wednesday, July 9

HPC for applications (NM video to FS)

• GPU applications (Abellium),
• Analysis of monoamin oksidaze (Kemijski inštitut),
• Problem MAX-Klike (IJS, Depolli)

Convener: Dr Tadej Kanduč

1 Uporaba GPU

- Predstavitev osnov programiranja grafičnih procesorjev s pomočjo tehnologije OpenCL - Demonstracija izbranih primerov uporabe

Speaker: Alen Orbanić (Abelium)

Slides GPU-2.pdf

2 Max Klika

- O NP-polnem problemu iskanja največje klike v grafu - Dve vzporednosti v algoritmu - Implementacija za večjedrne računalnike

Speaker: Dr Matjaž Depolli (JSI)

Slides MaxClique.pdf

3 Molekularne simulacije

- molekularne simulacije hidratiranih proteinov - obravnava daljnosežne elektrostatike - razgradnja serotonina in dopamina V predavanju bom predstavil molekularne simulacije hidratiranih proteinov. Klasične molekulske simulacije so numerično reševanje enačb gibanja za atomska jedra. Seznanili se bomo z upoštevanjem efektov topila, začetnim pogojem, uravnoteženjem in analizo trajektorije. Posebno pozornost bomo posvetili obravnavi daljnosežne elektrostatike. Za nekatere aplikacije je potrebo kvantizirati enačbe gibanja z metodo integracije po poti, za obravnavo kemijske reaktivnosti pa je treba uporabiti multiskalni pristop QM/MM. Encimska reakcija je tipičen primer, ki zahteva multiskalno obravnavo. Kot primer bom prikazal razgradnjo serotonina in dopamina z encimoma monoamino oksidaza A in B. Diskutirali bomo relevanco biomolekularnih simulacij za načrtovanje zdravil.)

Speaker: Dr Janez Mavri (Kemijski institut)

Slides mavri_protein_md_2014.pdf

11:15 AM Coffee break

Simulations (video from LJ to FIS)

Introduction to open source simulation programs in the area of Computational Fluid Dynamic (CFD - OpenFoam) and Structural Mechanics and Multiphysics (Elmer),

Convener: Dr Leon Kos (University of Ljubljana)

slides http://www.csc.fi/csc/kurssit/arkisto/aineisto/PARA2012Elmer/ElmerIntro

4 OpenFOAM introduction

Speaker: Dr Marijo Telenta (FS)

Slides kampus_school_slo.pdf

5 Elmer introduction

Speaker: Andrej Vihtelič

Slides kampus_sola_HPC_2014-ElmerFEM.pdf

1:00 PM Lunch

Simulations on HPC (LJ): CFD practicals on HPCFS

Elmer and OpenFOAM

Conveners: Andrej Vihtelič, Dr Marijo Telenta (FS)

Elmer tutorials http://hpc.fs.uni-lj.si/elmer

notes openfoam_navodila.txt

Hands-on HPC (NM)

• Different HPC programming examples

• Overview of tasks and second part of assignments for home-work

• asinhrona komunikacija

• spoznavanje z OpenMP
• izziv za vse željne več programiranja
• paralelizacija iskanja praštevil

Conveners: Dr Borut Lužar (FIŠ), Dr Matjaž Depolli (IJS), Dr Tadej Kanduč (FIŠ)

Thursday, July 10

8:00 AM Transfer from NM to FS

Bus transfer will be organized in front of FIŠ to Ljubljana and back

6 HPCFS demos

- Cluster Manament Utility - Lustre on ZFS performance $HOME, $WORK, $SCRATCH - Unified Fabric Manager - Allinea DDT - Mathematica parallel setup

Speaker: Dr Leon Kos (University of Ljubljana)

Python MPI

• Python programming language introduction and parallel programming with MPI4Py library.
• NumPy library and its relevance for HPC.
• Simple MPI4Py message passing examples
• Upgraded MPI4Py examples with problem assignments in groups
• Parallelization suggestions for further development

Convener: Dr Leon Kos (University of Ljubljana)

MPI4Py API reference http://mpi4py.scipy.org/docs/apiref/

MPI4Py User manual http://mpi4py.scipy.org/docs/mpi4py.pdf

NumPy Tutorial http://wiki.scipy.org/Tentative_NumPy_Tutorial

Python in High-Performance Computing Intro-lectures.pdf

Python introduction http:http://hpc.fs.uni-lj.si/python-intro//hpc.fs.uni-lj.si/python-intro

1:00 PM EGPR demos

2:00 PM Lunch

Transfer from FS to NM

Friday, July 11

Parallel algorithms (NM) video to LJ

Introduction to development and analysis of parallel algorithms
Introduction to HiPEAC summer school, Ljubljana

Convener: Dr Matjaž Depolli (IJS)

slides Vzporedni_algoritmi.pdf

10:30 AM Coffe break

HPC, visualization and PRACE (LJ) video to NM

• Introduction to PGAS programming languages X10, Chapel (Jure Pečar, Arctur)
• Cluster management with HPC-PUPPET and EasyBlocks (Jure Pečar, Arctur)
• Latest results from CloudFlow and Fortissimo projects (Tomi Ilijaš, Arctur)
• Introduction to PRACE and access to TIER-1 and TIER-0 supercomputers (Leon Kos, ULFME)

Conveners: Jurij Pečar (Arctur), Dr Leon Kos (University of Ljubljana)

slides

• campus-school-pecar.pdf
• PRACE-Campus-School-2014-Kos-UL-Introduction-to-PRACE.pdf
• PRACE_FS_2014.pdf
• visualization-intro.pdf

1:00 PM Lunch

Hands On (FIS)

Various exercises and analysis of student assignments
- pregled rešenih izzivov
- optimiranje programov

Hands on Visualization tools

• Visualization with GNUplot, Inkscape, LLNL VisIt, ParaView, Inkscape, OpenGL, WebGL, ...

VisIt, Paraview and OpenGL tutorial http://trac.lecad.si/sohpc

4:30 PM Closing ceremony