Rocks cluster : a cluster oriented linux distribution or how to install a computer cluster in a day.

Slides:



Advertisements
Similar presentations
2 Copyright © 2005, Oracle. All rights reserved. Installing the Oracle Database Software.
Advertisements

Beowulf Supercomputer System Lee, Jung won CS843.
Setting up of condor scheduler on computing cluster Raman Sehgal NPD-BARC.
Lecture 2 TTH 03:30AM-04:45PM Dr. Jianjun Hu CSCE569 Parallel Computing University of South Carolina Department of.
Customizing a Cluster. What We’ll Be Doing Discuss how to add new packages to compute nodes Discuss frontend and compute node partitioning Discuss how.
Southgreen HPC system Concepts Cluster : compute farm i.e. a collection of compute servers that can be shared and accessed through a single “portal”
Quick Overview of NPACI Rocks Philip M. Papadopoulos Associate Director, Distributed Computing San Diego Supercomputer Center.
Managing Linux Clusters with Rocks Tim Carlson - PNNL
Introduction to bioknoppix: Linux for the life sciences Carlos M Rodríguez Rivera Humberto Ortiz Zuazaga.
Red Hat Linux Network. Red Hat Network Red Hat Network is the environment for system- level support and management of Red Hat Linux networks. Red Hat.
© UC Regents 2010 Extending Rocks Clusters into Amazon EC2 Using Condor Philip Papadopoulos, Ph.D University of California, San Diego San Diego Supercomputer.
PC Cluster Setup on Linux Fedora Core 5 High Performance Computing Lab Department of Computer Science and Information Engineering Tunghai University, Taichung,
6/2/20071 Grid Computing Sun Grid Engine (SGE) Manoj Katwal.
S oftware T ools for A cademics and R esearchers MASSACHUSETTS INSTITUTE OF TECHNOLOGY Office of Educational Innovation and Technology.
Linux clustering Morris Law, IT Coordinator, Science Faculty, Hong Kong Baptist University.
NPACI: National Partnership for Advanced Computational Infrastructure August 17-21, 1998 NPACI Parallel Computing Institute 1 Cluster Archtectures and.
High Performance Computing (HPC) at Center for Information Communication and Technology in UTM.
Automating Linux Installations at CERN G. Cancio, L. Cons, P. Defert, M. Olive, I. Reguero, C. Rossi IT/PDP, CERN presented by G. Cancio.
Building a High-performance Computing Cluster Using FreeBSD BSDCon '03 September 10, 2003 Brooks Davis, Michael AuYeung, Gary Green, Craig Lee The Aerospace.
Rocks Clusters SUN HPC Consortium November 2004 Federico D. Sacerdoti Advanced CyberInfrastructure Group San Diego Supercomputer Center.
Research Computing with Newton Gerald Ragghianti Newton HPC workshop Sept. 3, 2010.
SSI-OSCAR A Single System Image for OSCAR Clusters Geoffroy Vallée INRIA – PARIS project team COSET-1 June 26th, 2004.
The BioBox Initiative: Bio-ClusterGrid Gilbert Thomas Associate Engineer Sun APSTC – Asia Pacific Science & Technology Center.
The Biopackage Repository and BioBrew Linux Projects O’Reilly Biocon Bioinformatics.Org Track February 5, 2003 Glen Otero, Ph.D. Linux Prophet
DynamicBLAST on SURAgrid: Overview, Update, and Demo John-Paul Robinson Enis Afgan and Purushotham Bangalore University of Alabama at Birmingham SURAgrid.
ISG We build general capability Introduction to Olympus Shawn T. Brown, PhD ISG MISSION 2.0 Lead Director of Public Health Applications Pittsburgh Supercomputing.
So, Jung-ki Distributed Computing System LAB School of Computer Science and Engineering Seoul National University Implementation of Package Management.
Cluster Computing Applications for Bioinformatics Thurs., Aug. 9, 2007 Introduction to cluster computing Working with Linux operating systems Overview.
October, Scientific Linux INFN/Trieste B.Gobbo – Compass R.Gomezel - T.Macorini - L.Strizzolo INFN - Trieste.
Rocks ‘n’ Rolls An Introduction to Programming Clusters using Rocks © 2008 UC Regents Anoop Rajendra.
การติดตั้งและทดสอบการทำคลัสเต อร์เสมือนบน Xen, ROCKS, และไท ยกริด Roll Implementation of Virtualization Clusters based on Xen, ROCKS, and ThaiGrid Roll.
March 3rd, 2006 Chen Peng, Lilly System Biology1 Cluster and SGE.
Common Practices for Managing Small HPC Clusters Supercomputing 12
CMAQ Runtime Performance as Affected by Number of Processors and NFS Writes Patricia A. Bresnahan, a * Ahmed Ibrahim b, Jesse Bash a and David Miller a.
Batch Scheduling at LeSC with Sun Grid Engine David McBride Systems Programmer London e-Science Centre Department of Computing, Imperial College.
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
The BioBox Initiative: Bio-ClusterGrid Maddie Wong Technical Marketing Engineer Sun APSTC – Asia Pacific Science & Technology Center.
Deploying a Network of GNU/Linux Clusters with Rocks / Arto Teräs Slide 1(18) Deploying a Network of GNU/Linux Clusters with Rocks Arto Teräs.
Renaissance Computing Institute: An Overview Lavanya Ramakrishnan, John McGee, Alan Blatecky, Daniel A. Reed Renaissance Computing Institute.
CHAPTER 2. Overview 1. Pre-Installation Tasks 2. Installing and Configuring Linux 3. X Server 4. Post Installation Configuration and Tasks.
The iPlant Collaborative Community Cyberinfrastructure for Life Science Tools and Services Workshop Discovery Environment Overview.
1 Development of a High-Throughput Computing Cluster at Florida Tech P. FORD, R. PENA, J. HELSBY, R. HOCH, M. HOHLMANN Physics and Space Sciences Dept,
Status of Florida Tier2 Center A mini tutorial on ROCKS appliances Jorge L. Rodriguez February 2003.
 Load balancing is the process of distributing a workload evenly throughout a group or cluster of computers to maximize throughput.  This means that.
Cluster Software Overview
The LBNL Perceus Cluster Infrastructure Next Generation Cluster Provisioning and Management October 10, 2007 Internet2 Fall Conference Gary Jung, SCS Project.
Cluster Computing Applications for Bioinformatics Thurs., Sept. 20, 2007 process management shell scripting Sun Grid Engine running parallel programs.
Biomedical and Bioscience Gateway to National Cyberinfrastructure John McGee Renaissance Computing Institute
ISG We build general capability Introduction to Olympus Shawn T. Brown, PhD ISG MISSION 2.0 Lead Director of Public Health Applications Pittsburgh Supercomputing.
Building and managing production bioclusters Chris Dagdigian BIOSILICO Vol2, No. 5 September 2004 Ankur Dhanik.
Final Implementation of a High Performance Computing Cluster at Florida Tech P. FORD, X. FAVE, K. GNANVO, R. HOCH, M. HOHLMANN, D. MITRA Physics and Space.
The Hungarian ClusterGRID Project Péter Stefán research associate NIIF/HUNGARNET
15-Feb-02Steve Traylen, RAL WP6 Test Bed Report1 RAL/UK WP6 Test Bed Report Steve Traylen, WP6 PPGRID/RAL, UK
CIP HPC CIP - HPC HPC = High Performance Computer It’s not a regular computer, it’s bigger, faster, more powerful, and more.
2: Operating Systems Networking for Home & Small Business.
3 Copyright © 2006, Oracle. All rights reserved. Installation and Administration Basics.
EGEE-III INFSO-RI Enabling Grids for E-sciencE EGEE and gLite are registered trademarksEGEE-III INFSO-RI MPI on the grid:
© 2007 UC Regents1 Rocks – Present and Future The State of Things Open Source Grids and Clusters Conference Philip Papadopoulos, Greg Bruno Mason Katz,
June 28, 2016 Cluster Management for Non-XSEDE Systems Barbara Hallock, Eric Coulter, Sudhakar Pamidighantam.
Advanced Network Administration Computer Clusters.
Cluster / Grid Status Update
Using Paraguin to Create Parallel Programs
Stallo: First impressions
Integration of Singularity With Makeflow
GRID AND CLOUD COMPUTING
X in [Integration, Delivery, Deployment]
EDUHIPC-18: WORKSHOP ON EDUCATION FOR HIGH-PERFORMANCE COMPUTING, 17 December 2018, Bengaluru, India Parallel & Distributed Computing (PDC) Using Low Cost,
SiCortex Update IDC HPC User Forum
OPS235: Week 1 Installing Linux ( Lab1: Investigations 1-4)
Introduction to Clusters, Rocks, and MPI
Presentation transcript:

Rocks cluster : a cluster oriented linux distribution or how to install a computer cluster in a day

Physical setup

Installing the Frontend

If you have home made rolls or community rolls Now is the time to provide them Installing the Frontend

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: - BIO - Area51 What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: - BIO - Area51 HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. The following software packages are included in the HPC Roll: - MPI over ethernet environments (OpenMPI, MPICH, MPICH2) - PVM - Benchmarks (stream, iperf, IOzone) What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO - Area51 What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO - Area51 SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. Provides: - SGE ready to be used (preconfigured queue, hosts groups, pe, etc. ) - Integrated with HPC roll (no extra configuration is needed to use OpenMPI, MPIC or OpenMPI) What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO: The Bio-informatics Roll is a collection of some of the most common bio- informatics tools that are being used by the community today. - Area51 What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO: The Bio-informatics Roll is a collection of some of the most common bio- informatics tools that are being used by the community today. - Area51 What are “rolls” ? BIO: The Bio-informatics Roll is a collection of some of the most common bio-informatics tools that are being used by the community today. - HMMER - From Janelia Farm research institute - NCBI BLAST - From National Center for Biotechnology Information - MpiBLAST - From Los Alamos National Laboratory - biopython - ClustalW - From the European BioInformatics Institute - MrBayes - From School of Computational Science at the Florida State University - T_Coffee - From Information Genomique et Structurale at Centre National de la Recherche Scientifique - Emboss - From European Molecular Biology Institute - Phylip - From the Dept. of Biology at the University of Washington - fasta - From the University of Virginia - Glimmer - From Center for Bioinformatics and Computational Biology at the University of Maryland - TIGR Assembler - From the J. Craig Venter Institute -All the perl utilities mentioned below are from CPAN perl-bioperl perl-bioperl-ext perl-bioperl-run perl-bioperl-db

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO: The Bio-informatics Roll is a collection of some of the most common bio- informatics tools that are being used by the community today. - Area51: The Rocks Area51 Roll contains utilities and services used to analyze the integrity of the files and the kernel on your cluster. What are “rolls” ?

Rolls are packages of packages designed to integrate themselves in the managing system in the same way as the base software, some of them are provided by the distribution developers. On the other hand, extended documentation on how to create new ones has promoted the appearance of others created by the community. Examples: - HPC: The primary purpose of the HPC Roll is to provide configured software tools that can be used to run parallel applications on your cluster. - SGE: The SGE Roll installs and configures the SUN Grid Engine scheduler. - BIO: The Bio-informatics Roll is a collection of some of the most common bio- informatics tools that are being used by the community today. - Area51: The Rocks Area51 Roll contains utilities and services used to analyze the integrity of the files and the kernel on your cluster. Area51: The Rocks Area51 Roll contains utilities and services used to analyze the integrity of the files and the kernel on your cluster. The following software packages are included in the Area51 Roll: - Tripwire - chkrootkit What are “rolls” ?

Installing the Frontend

Partition NameSize /16 GB Swap1 GB /var4 GB /state/partition1 remainder of root disk Compute node default partitioning Installing the Frontend

DONE!!!

Installing compute nodes ]# insert-ethers

Installing compute nodes

Adding external NFS servers ]# echo " data0 -fstype=nfs4,rsize=32768,wsize=32768,nodev,nosuid,_netdev,intr,noatime,nostrict :/& data1 -fstype=nfs4,rsize=32768,wsize=32768,nodev,nosuid,_netdev,intr,noatime,nostrict :/& data2 -fstype=nfs4,rsize=32768,wsize=32768,nodev,nosuid,_netdev,intr,noatime,nostrict :/& apps -fstype=nfs4,rsize=32768,wsize=32768,nodev,nosuid,_netdev,intr,noatime,nostrict :/& ">>/etc/auto.share ]# rocks sync config ]# cd /var/411 ]# make Adding extra RPMs ]# cp my_new_rpm.el5.x86_64.rpm /export/rocks/install/contrib/5.4/x86_64/RPMS/ ]# vi /export/rocks/install/site-profiles/5.4/nodes/extend-login.xml ]# cd /export/rocks/install/ ]# rocks sync config ]# rocks create distro Now we should reinstall all nodes :( …but we can do this: ]# rocks run host rpm -Uvh /share/rocks/install/contrib/5.4/x86_64/RPMS/ Customization and postconfiguration

Monitoring the cluster

Ganlia Is installed and configured automatically But, most of the times, I prefer to use: #] qstat -f -u \*|less

-Lustre. There Is a lustre roll and lots of “How to install lustre on rocks” - Infiniband. How to configure a fast network for message passing is explained in the basic manual, apart from that, there are infiniband rolls and “Howtos”and I know a company in Barcelona (ANIMA) that installs computer clusters with rocks cluster and infiniband I have not talk about: (…and you are probably going to ask)

- By default it is intended that users access the cluster using the frontend. This can be corrected installing a node with the login appliance - /home and /share/apps are in the frontend node and are exported to all nodes, even to itself, through NFS, this can cause huge “iowait” problems. It can be corrected “never” using those directories and using external file servers to store your data and applications -Compute nodes OS is dependent to frontend OS This can not be corrected :( No todo el monte es orégano