Worker Node Software Management: the VO perspective Mark Santcroos - - PowerPoint PPT Presentation

Worker Node Software Management: the VO perspective

Mark Santcroos Dennis van Dok

Introduction

• e-BioScience group

– Bioinformatics Laboratory – Clinical Epidemiology, Biostatistics and Bioinformatics – Academic Medical Centre, Amsterdam

• Intermediate between medical researchers and

Dutch NGI

• Support a wide range of applications in Next

Generation Sequencing and Medical Imaging

Worker Node Software

• Running on 15 sites in the Netherlands
• Base worker node installation (glite-WN)
• Proof of Concept (PoC) software installation,

heritage of Virtual Laboratory for e-Science (ended 2009)

Perspective

• Dennis van Dok is part of team that developed

and managed the PoC environment at BiG Grid

• Mark is a VO manager for the vlemed VO

Job / Application Scenarios

• Use installed software
• Application in Job Sandbox
• Fetch Application using wrapper
• Upgrade versions in PoC distribution
• Lobby for new versions with Site admins

Limitations

• Sandbox solution has size limits
• Sandbox and wrapper have network overhead
• Installed version out of date / too new
• Responsibility of maintaining applications for end-

user not always preferable

• Site admins have to be in the loop

High Level Goal

• Have a flexible solution to make software

available on the grid for end users that is also manageable from a VO admin perspective.

Packaging Requirements

• Automatic dependency resolution
• Supported on Linux
• Tools for install/update/remove/status
• Running entire in userspace, unprivileged
• Multiple installed versions of the same software

Unsuitable candidates

• rpm/yum
• deb/apt
• portage
• Arch User Repository
• pacman
• …
• Reasons: too OS specific, difficult to manage

unprivileged

Pkgsrc

• Originating in NetBSD
• Supported on Linux
• Self contained
• Actively maintained
• Can be used as a non-privileged user
• Large collection of applications already packaged
• Can make use of system provided dependencies
• Allows maintaining a local set of packages
• Could add packages to the main distribution
• Supports binary and source packages

Creating a package

DISTNAME= vlet-1.3.2 CATEGORIES= local MASTER_SITES= http://orange.ebioscience.amc.nl/pkgsrc/distfiles/ EXTRACT_SUFX= .zip MAINTAINER= m.a.santcroos@amc.uva.nl HOMEPAGE= http://orange.ebioscience.amc.nl/pkgsrc/distfiles/ COMMENT= This is the VL-e Toolkit LICENSE= apache-2.0 NO_CONFIGURE= yes NO_BUILD= yes PKG_DESTDIR_SUPPORT= user-destdir INSTALLATION_DIRS= bin lib post-extract: ${CP} ${FILESDIR}/Makefile ${WRKSRC}/Makefile .include "../../mk/bsd.pkg.mk"

Package Tree Management

• update-tree.sh

– Pull upstream pkgsrc changes – Create tarball – Put on website

Implementation Principles

• $VO_[VONAME]_SW_DIR is a directory shared

between all worker nodes on a site

• Run with a Software (VO) Manager proxy
• Install packages per site / cluster / CE

Architecture

Server (UI) Shared Storage Area Worker Nodes Management Jobs Mount

Managing packages

• site-pkgtool.sh

– Program to manage packages centrally – Initiates grid jobs

• Install, Remove, Update
• Init, Reinit, Check, Dump, Info, Version

Script on the worker node

• pkgsrc-cmd.sh

– Wrapper program that runs on the worker node

• Running as a grid job

Information Management

• list-installed-packages.sh

– Display information about installed packages for sites

• get-site-status.sh

– Gather information from all supported sites

• verify-package.sh

– Check if a certain package is available on a site

• get-tags.sh

– Get all the package tags for the configured sites

Installing a package

• Check if distribution is fresh
• Extract tree in scratch space
• Build package and dependencies
• Install package in shared software area
• Install modulefile

Environment Modules

• “The Environment Modules package provides for

the dynamic modification of a user's environment via modulefiles.”

• Select versions
• Setup environment
• Integrates with system provided setup

Tags

• Software Tags in Information System (BDII)
• Publish installed software versions per CE
• Used for resource selection by adding it to the

“Requirements” of a JDL

• Use lcg-ManageVOTag tool to publish tag
• Structure of tags is VO-${vo}_SW_${package}

Practical issues

• Tags are not omnipresent
• Shared area can become bottleneck
• No intelligent matching on tags

Conclusions

• Flexible software management system
• Relieves burden from user
• Creating packages is still labor intensive work

Discussion

• One size fits all? (Did we reinvent the wheel?)
• Connect to EGI AppDB?
• EMI Community Repositories?
• Usable for data distribution?
• Other mechanism for matching?

Links

• pkgsrc

– http://www.netbsd.org/docs/software/packages.html

• Modules

– http://modules.sourceforge.net/

• BiG Grid

– http://www.biggrid.nl/

• Bioinformatics Laboratory

– http://www.bioinformaticslaboratory.nl/

• Project Code

– http://dvandok.github.com/userspace-package- management/

Acknowledgements

• AMC Bioinformatics Laboratory

– Prof. dr. Antoine van Kampen – Dr. Silvia Delgado Olabarriaga – Barbera van Schaik

• Big Grid / Nikhef

– Jan Just Keijser

Thanks!