Hiding the complexity: building a distributed ATLAS Tier-2 with a single resource interface using ARC middleware

Since their inception, Grids for high energy physics have found management of data to be the most challenging aspect of operations. This problem has generally been tackled by the experiment's data management framework controlling in fine detail the distribution of data around the grid and the careful brokering of jobs to sites with co-located data. This approach, however, presents experiments with a difficult and complex system to manage as well as introducing a rigidity into the framework which is very far from the original conception of the grid.<p></p> In this paper we describe how the ScotGrid distributed Tier-2, which has sites in Glasgow, Edinburgh and Durham, was presented to ATLAS as a single, unified resource using the ARC middleware stack. In this model the ScotGrid 'data store' is hosted at Glasgow and presented as a single ATLAS storage resource. As jobs are taken from the ATLAS PanDA framework, they are dispatched to the computing cluster with the fastest response time. An ARC compute element at each site then asynchronously stages the data from the data store into a local cache hosted at each site. The job is then launched in the batch system and accesses data locally.<p></p> We discuss the merits of this system compared to other operational models and consider, from the point of view of the resource providers (sites), and from the resource consumers (experiments); and consider issues involved in transitions to this model

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.Comment: 10 pages, 4 figures. To appear in the HealthGrid 2012 con

Distributed Data Analysis in ATLAS

Data analysis using grid resources is one of the fundamental challenges to be addressed before the start of LHC data taking. The ATLAS detector will produce petabytes of data per year, and roughly one thousand users will need to run physics analyses on this data. Appropriate user interfaces and helper applications have been made available to ensure that the grid resources can be used without requiring expertise in grid technology. These tools enlarge the number of grid users from a few production administrators to potentially all participating physicists. ATLAS makes use of three grid infrastructures for the distributed analysis: the EGEE sites, the Open Science Grid, and NorduGrid. These grids are managed by the gLite workload management system, the PanDA workload management system, and ARC middleware; many sites can be accessed via both the gLite WMS and PanDA. Users can choose between two front-end tools to access the distributed resources. Ganga is a tool co-developed with LHCb to provide a common interface to the multitude of execution backends (local, batch, and grid). The PanDA workload management system provides a set of utilities called PanDA Client; with these tools users can easily submit Athena analysis jobs to the PanDA-managed resources. Distributed data is managed by Don Quixote 2, a system developed by ATLAS; DQ2 is used to replicate datasets according to the data distribution policies and maintains a central ca talog of file locations. The operation of the grid resources is continually monitored by the GangaRobot functional testing system, and infrequent site stress tests are performed using the HammerCloud system. In addition, the DAST shift team is a group of power users who take shifts to provide distributed analysis user support; this team has effectively relieved the burden of support from the developers

Організація центрального кешуючого каталогу ресурсів в українській національній грід-інфраструктурі

Проведено аналіз існуючих проблем швидкості роботи інформаційної системи при роботі з грід-порталами у інфраструктурах на базі програмного забезпечення Nordugrid ARC. Розроблено методики кешвідомостей локальних інформаційних служб грід-ресурсів для зменшення часу відгуку при опитуванні стану запущених грід-завдань. Відповідно до представленої методики реалізовано службу кешуючого каталогу ресурсів. Розроблену програмну бібліотеку для взаємодії зі службою впроваджено в грід-порталах віртуальних організацій MolDynGrid та NetworkDynamics в українській національній грід-інфраструктурі.Analysis of existing responsiveness problems of grid information system focused on implementation of grid-portals employing Nordugrid ARC middleware is conducted. Techniques for centralized caching of data from local grid-resource information services were developed. Proposed techniques were implemented in the caching information index service. A software library developed for accessing the cache is incorporated into the grid-portals of MolDynGrid and NetworkDynamics virtual organizations of Ukrainian national grid-infrastructure

Building high availability central data catalog service powered by IBM Mainframe technology in the ukrainian national grid-infrastructure

Проведено аналіз особливостей застосування служб рівня кооперації української національної грід-інфраструктури, зокрема служби центрального каталогу даних LFC. Сформовано вимоги до реалізації високодоступного центрального каталога даних із використанням високонадійного обчислювального комплексу IBM Mainframe Z800. Показано особливості апаратної архітектури z/Architecture та програмного забезпечення проміжного рівня Nordugrid ARC, що були враховані при розробленні методики формування високодоступної служби LFC. Методику впроваджено для побудови системи з використанням мейнфрейму та обчислювального кластеру Київського національного університету імені Тараса Шевченка. Техніку формування опису грід-завдання для використання конфігурації високонадійної служби запроваджено до реалізації грід-порталу віртуальної лабораторії MolDynGrid в українській національній грід-інфраструктурі.Analysis of cooperation level service applications in Ukrainian national grid-infrastructure is conducted focusing on LFC central data catalog services. Methods for building high available central data catalog service employing IBM Z800 Mainframe installation are presented. Specialities of zSeries hardware architecture and Nordugrid ARC middleware software were taken into account for service implementation on top of the mainframe and HPC cluster of Taras Shevchenko National University of Kyiv. Grid job description generation technique for accessing high available LFC service was applied to the implementation of MolDynGrid Virtual Laboratory grid-portal in the Ukrainian national grid-infrastructure

Ganga: a job management and optimising tool

Ganga, the job-management system (http://cern.ch/ganga), developed as an ATLAS- LHCb common project, offers a simple, effcient and consistent user experience in a variety of heterogeneous environments: from local clusters to global Grid systems. Ganga helps end-users to organise their analysis activities on the Grid by providing automatic persistency of the job's metadata. A user has full access to the job history including their configuration and input/output. It is however important that users can see a single environment for developing and testing algorithms locally and for running on large data samples on the Grid. The tool allows for some basic monitoring and a steadily increasing number of users of more than 300 users have been confirmed, both in HEP, as well as in non-HEP applications. The paper will introduce the Ganga philosophy, the Ganga architecture and current and future strategy

Архітектура побудови віртуального оточення для грід-застосувань

У статті розглянуто проблематику конфігурації грід-ресурсів для виконання прикладних обчислювальних задач у грід-середовищі. Запропоновано технологію автоматизованого налаштування оточення для виконання завдань у грід-середовищі з використанням технології віртуалізації. Представлена архітектура побудови віртуального оточення для грід-застосувань.В статье рассмотрена проблематика конфигурирования грид-ресурсов для выполнения прикладных вычислительных задач в грид-среде. Предложена технология автоматизированной настройки окружения для выполнения задач в грид-среде с использованием технологии виртуализации. Представлена архитектура построения виртуального окружения для грид-применений.The article considers the problems of configuring of grid resources to perform computational tasks in grid environment. Moreover it is suggested the technology of automated configuration environ-ment to perform tasks in grid environment using virtualization technology. The architecture of a virtual environment for grid applications is introduced in the article

Вирішення проблем інтеграції віртуальних організацій на провайдерах ресурсів в українському національному грід-сегменті

В роботі проведено аналіз існуючих проблем інтеграції віртуальних організацій (ВО) в українському національному грід-сегменті (УНГ) та показано ключові обмеження провайдерів ресурсів. Запропоновано методики вирішення проблем масштабованості, гнучкості та цілісності політик, відокремлення ВО. Виконано успішне впровадження методик на трьох кластерах УНГ.Contemporary virtual organizations (VO) integration problems in Ukrainian National Grid (UNG) has been analyzed. Key limitations of UNG resource providers are shown. Techniques for solving the problems of scalability, policy flexibility and integrity as well as VO separation are proposed. Successful deployments of proposed methods are conducted on three UNG member clusters

Virtual organizations internal structure projection methods for grid-infrastructures

Проведено аналіз особливостей внутрішньої структури віртуальних організацій (ВО) та показано їх вплив на ефективне планування ресурсів провайдером грід-інфраструктури. Досліджено методи виділення ресурсів Nordugrid ARC та сформовано методики розмежування доступу за параметрами участі у ВО. Відповідно до методик розроблено програмне забезпечення, яке успішно впроваджено на трьох кластерах українського національного грід (УНГ).Virtual Organizations (VOs) have an internal structure that was not driven by grid-infrastructure. The structure of the VO is influenced by many factors including number of members, resource usage, grid services usage and moreover social cooperation of researchers. Similarly to ordinary organizations that are usually divided into departments, hierarchical structure is also defined for the VOs. Generally, three parameters are used to describe VO structure: groups, roles and attributes. Grid-infrastructure resource provider's scheduler efficiency relies on VO internal structure recognition. Internal structure development process starts with VO particularity analysis. Virtual laboratory MolDynGrid that was established to conduct researches in structural biology and bioinformatics has been chosen as an example to demonstrate such analysis. Different requirements for several laboratory researches (molecular dynamics simulations using GROMACS software, molecular structure modeling using Modeller software, docking using AutoDock software) were described. Production versus testing computation properties were discussed. Based on performed analysis an internal structure for MolDynGrid VO has been settled. Methods of resource allocation employed by Nordugrid ARC were investigated. Necessity of binding different tasks to distinct queues of local resource management system has been shown. Lack of mechanisms for VO internal structure mapping to scheduler queues was pointed out. Analysis of the job processing algorithm in Nordugrid ARC computing element (A-REX) has shown that per-queue access control based on VO internal structure defined via Virtual Organization Membership Service (VOMS) attributes can be implemented as plug-in called out of A-REX when job gets moved to ACCEPTED state. Access separation algorithm has been developed and implemented in software. Plug-in introduces additional configuration options in Nordugrid ARC common configuration file that allow to specify access policy in terms of Fully Qualified Attribute Names (FQAN) representing internal structure developed for a VO. Software implementation of the methods presented has been successfully deployed on three Ukrainian National Grid clusters: Institute of Molecular Biology and Genetics NAS of Ukraine, Taras Shevchenko National University of Kyiv, National Scientific Centre for Medical and Biotechnical Research at the Presidium of NAS of Ukraine. Example of plug-in configuration considering particularities of Institute of Molecular Biology and Genetics NAS of Ukraine cluster has been shown. Methods are applicable to the other grid-enabled clusters