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WORKSHOP PENGGUNAAN FASILITAS HPC
UNTUK PENELITIAN
Bale Rucita5 April 2018
Apa itu HPC?
Sekumpulan komputer yang saling terhubung melalui sistem jaringan
Komputer-komputer didisain khusus untuk melakukan pekerjaan berat
Sistem operasi yang dipergunakan: Unix/Linux
process priority
usability
Perangkat lunak yang dipergunakan
GNU
Perangkat-perangkat lunak komersial/proprietary yang didesain khusus untuk HPC
shell: bash, cshell, kshell, etc. scripting: python, perl, awk, tcl, R, etc.
programming: C/C++, Fortran, etc. graphics: gnuplot, matplotlib
1.2 What is the UGent-HPC?
1.2 What is the UGent-HPC?
The HPC is a collection of computers with Intel CPUs, running a Linux operating system, shapedlike pizza boxes and stored above and next to each other in racks, interconnected with copperand fiber cables. Their number crunching power is (presently) measured in hundreds of billionsof floating point operations (gigaflops) and even in teraflops.
The UGent-HPC relies on parallel-processing technology to offer UGent researchers an extremelyfast solution for all their data processing needs.
The HPC currently consists of:
a set of different compute clusters. For an up to date list of all clusters and their hardware, seehttps://www.vscentrum.be/infrastructure/hardware/hardware-ugent.
All the nodes in the HPC run “CentOS 7.2 (phanpy, golett, swalot), Scientific Linux 6.7 (raichu,delcatty)” with cpuset support and BLCR modules.
Two tools perform the job management and job scheduling:
1. TORQUE: a resource manager (based on PBS);
2. Moab: job scheduler and management tools.
1.3 What is the HPC not!
A computer that automatically:
1. runs your PC-applications much faster for bigger problems;
2. develops your applications;
3. solves your bugs;
4. does your thinking;
5. . . .
6. allows you to play games even faster.
The HPC does not replace your desktop computer.
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Tentang pembicara
Yudi Rosandi Staf Geofisika FMIPA, Unpad
Yudi Rosandi
Davenportplatz 10D-67663 KaiserslauternGermany
Date of Birth: August 8, 1971Nationality: IndonesianMarried (2 sons)
Current employment:Postdoc at the Physics DepartmentTU-Kaiserslautern
Websitehttp://y.rosandi.com
Phone+62 82121259117
EDUCATION
Dr. rer. nat.Computational Material ScienceDepartment of Physics University of Kaiserslautern, Germany (2008)Thesis: Effect of surface defects on sputtering by grazing ion bombardment
M.Sc.Department of Physics, Institut Teknologi Bandung, Indonesia (2001)
B.Sc.Department of Physics, Universitas Padjadjaran, Indonesia (1997)
EMPLOYMENT HISTORY
1998 - 2006 : Teaching assistantDepartment of Physics, University of Padjadjaran
2006 - 2012 : Wissenschaftlicher-Mitarbeiter, AG-UrbassekDepartment of Physics, University of Kaiserslautern
2006 - now :Lecturer in University of Padjadjaran
LANGUAGE SKILL
English is used in everyday conversation. Writing and reading, as well as creating research reports.German is sufficient for everyday life activity. Basic administration works, sending/receiving emails, short conversation, etc.Indonesian is the mother-tongue.
PROFESIONAL EXPERIENCE
Research on Computation Material Sciences (Specialities)
Molecular-Dynamics simulations⁃ Computer simulation on XUV-laser interaction with metal surfaces⁃ (on going research)
⁃ Computer simulation on ion induced nano-patterning
Computer Administration
2004 - 2012 :Computer administrator in AG-UrbassekDepartment of Physics, TU-KaiserslauternResponsibilities: managing computer servers
2006 - 2012 : Installing, managing and administratingcomputer cluster at Department of Physics TU-Kaiserslautern (52-cores)
2007 : Building a 160-cores computer cluster at AG-Urbassek and AG-RethfeldDepartment of Physics, TU-Kaiserslautern
2007 - 2012 : Installing, managing and administratingComputer cluster at AG-Urbassek (currently 238-cores)
Lectures
1997-2004: Electronics, Computational Physics, ElectromagneticDept. Physics Unpad
SS-2012: High-performance Computing for PhysicsFB-Physics TU-Kaiserslautern
2010-2013: Computational Physics, Numerical Methods, Elementary Physics, ElectromagneticDept. Physics Unpad
COMPUTER SKILLS
Programming Languages
C/C++ is the most often used computer language. The largest project up to now is the molecular-dynamics simulation program (ObjectMD) can be found at http://merapi.physik.uni-kl.de/objectmd.Scripting languages (bash, awk, php, etc.) are used for research data post processing purpose. Some programs are written also completely in script. An example can be found at http://code.google.com/p/renderball.MPI library is used in parallel programming works.
Published Programming and Computer Administration Tool Projects
ObjectMD, Parallel Object Oriented Molecular-Dynamics Class Library, http://merapi.physik.uni-kl.de/objectmd.
RenderBall, rendering and movie creation tool for MD simulation, http://code.google.com/p/renderball.
Xlider, swf presentation slide creatorhttp://code.google.com/p/text-slider.
Corvix, Linux-cluster distribution and installation toolshttp://corvix.eu.
Gpurun, tool to run code written in OpenCL gpu program.http://code.google.com/p/gpurun/
E-Drift, Parallel electron diffusion simulation program.http://code.google.com/p/edrift/
HPC TOP 500
https://www.top500.org/lists/2017/11/slides/
GURIANG Fasilitas Komputasi Performa Tinggi
Universitas Padjadjaran
sun 2x8 Cores 2x 16 Gb
zwoelfkerne 5x12 Cores
5x32 Gb
gpu 2x4 Cores
4x3500 CUDA Cores
blades 28x4 Cores
28x4 Gb
2013: hibah PGS
Computational ……
• Meningkatkan kualitas publikasi
• Memiliki peluang untuk menghasilkan publikasi cepat
• High rating journals
• Penghubung antara teori dan eksperimen
Isi manuskrip untuk jurnal reputasi baik:
• Teori/hipotesa
• Model/simulasi
• Data eksperimen/survey
• Perbandingan (agreement/contradiction) antara teori — model — eksperimen
c.f. scimago
Cara penggunaan HPC• Transfer file ke sistem HPC
• Koneksi remote ke HPC (ssh)
• Lakukan kompilasi dan uji
• Buat job-script
• Kirim job-script ke antrian
• Tunggu hingga program selesai
• Salin/pindahkan hasil simulasi
Perangkat lunak yang diperlukan (Pengguna Windows)
• Putty
• WinSCP
• Alternatif
Cygwin
bash untuk windows
demo langsung di console
