VL-e Resource Guide

This document focuses on listing the grid resources that are available for VL-e project members. It does not explain how to use these resources; for that, you should consult the Grid Tutorial documentation. It is recommended that new users come to the Grid Tuturial, which is held every year.

The grid resources for VL-e are provided jointly by Nikhef and Sara, who participate in a larger framework for grid computing worldwide, in particular for the high energy physics experiments of the LHC. The grid middleware is provided by the European EGEE project. As a national project, VL-e has to share the resources with other applications.

Nikhef and Sara play a somewhat different role: Nikhef focuses mainly on computational clusters, while Sara has a tape storage facility for long-term data storage.

Computing

The clusters are accessible through the gLite stack of software developed by the EGEE project, based largely on Globus. You can use the command-line tools, as explained in the Grid Tutorial. If you require the VL-e Proof of Concept software distribution, you should add a requirement to your JDL file that says:

Requirements = Member("nl.vl-e.poc-release-2", other.GlueHostApplicationSoftwareRunTimeEnvironment);

The following list shows the compute elements that are available to VL-e VOs. This information can be retrieved with

lcg-infosites --vo pvier.

and will vary according to per-VO configurations at the sites. The information system can be publicly queried by standard ldap tools, such as ldapsearch:

ldapsearch -x -H ldap://bdii03.nikhef.nl:2170/ -b 'mds-vo-name=NIKHEF-ELPROD,mds-vo-name=local,o=grid'  

An excellent ldap browser (written in Java) is found here[1]. To browse the information system, connect to bdii03.nikhef.nl on port 2170 and enter 'o=grid' as the base dn.

List of available queues

Resource name	maximum wall time	comments
tbn20.nikhef.nl:2119/jobmanager-pbs-qlong	30 hours	The Nikhef cluster has 390 CPUs
tbn20.nikhef.nl:2119/jobmanager-pbs-qshort	5 hours
ce.gina.sara.nl:2119/jobmanager-pbs-short	4 hours	GINA (Grid In Almere) has 160 CPUs
ce.gina.sara.nl:2119/jobmanager-pbs-medium	33 hours

Your VO affiliation greatly affects your ability to run jobs. While the dutch sites support the VL-e VOs, they also support many other VOs on the same infrastructure. This leads to competition for cycles. The mechanism to address this issue is to allow a fair share of the cycles to be used by a VO, and to give higher priority to VOs who have used little of their fair share in the last period.

Scheduling on the cluster is straightforward, but from a user perspective it is less straightforward to predict how quickly your job will run. The parameter that is of most interest is the estimated response time, which expresses the expected time it will take for a job that is submitted right now to start running on a cluster. See for instance this graph.

Running tests and debugging

If your grid jobs are not behaving as expected, debugging can be a really frustrating ordeal. You have no way to inspect a running job up close, and the turnaround for each modification to your job is high.

To shorten the turnaround, you may request (from mailto:grid.support@sara.nl) the privilege to use the express queues on the GINA an Matrix clusters. The restriction is that jobs may last no longer than a couple of minutes.

If this is still not enough, and an application requires serious testing and debugging, you may request the use of the VL-e P4 Certification Test Bed. Contact mailto:vle-pfour-team@lists.vl-e.nl for support.

Storage

Grid Storage Elements can be discovered with the command

lcg-infosites --vo pvier se

(where you should replace pvier by the name of your own VO).

storage elements reported on August 22, 2007 for pvier

Avail Space(Kb)	Used Space(Kb)	SEs	Remarks
482906560	1587920944	tbn15.nikhef.nl	classic SE; don't use this old one.
1710000000	137730	tbn18.nikhef.nl	Modern DPM system with SRM interface; use this one.
317044396	539916244	mu2.matrix.sara.nl	DCache system with SRM interface

Note that the numbers may be different for other VOs, and there may actually be fewer SEs showing up. If you need more disk quota, please contact grid support (mailto:grid.support@nikhef.nl or mailto:grid.support@sara.nl).

LFC

The Logical File Catalog (LFC) is a way to have easy to remember aliases for grid storage files. Think symbolic links. To use the lfc-* tools, set

LFC_HOST=lfc.grid.sara.nl
export LFC_HOST

and of course you need a valid proxy. Now you can do, e.g.

lfc-ls /grid/vlemed/

SRB

Besides these SRM enabled systems, there is a SRB system provided by Sara. Unfortunately it cannot be used with the standard grid tools for logical file names, replicas, etc.; however, there is a gridftp front end. You need to obtain an SRB account by contacting mailto:grid.support@sara.nl (see the quickstart guide).

To use Srb, create a directory called .srb in your home directory and create a dummy file .MdasAuth (contents are irrelevant) and a file .MdasEnv:

mdasCollectionName '/VLENL/home/your.name.vlenl'
mdasCollectionHome '/VLENL/home/your.name.vlenl'
mdasDomainName 'vlenl'
mdasDomainHome 'vlenl'
srbUser 'your.name'
srbHost 'srb.grid.sara.nl'
srbPort '50000'
defaultResource 'vleGridStore'
AUTH_SCHEME 'GSI_AUTH'
SERVER_DN '/O=dutchgrid/O=hosts/OU=sara.nl/CN=srb.grid.sara.nl'

Replace your.name with your SRB account name.

The web-interface to SRB can be reached here [2].

There is a grid-ftp frontend to SRB on the same server on port 50097. This can be accessed (for example) with uberftp :

(create proxy as usual)
uberftp -P 50097 srb.grid.sara.nl

Tape storage

There is no default storage to tape. If you need tape storage, you have to explicitly request it. Sara can provide tape storage with various regimes, such as automatic disk-to-tape migration. Contact mailto:grid.support@sara.nl for more information.

about data replication

The Grid Tutorial explains how you can replicate your data to multiple storage elements, so that when you submit a job that needs this data, the resource broker may find a compute element 'close' to one of your copies. The current situation for VL-e members is such that all clusters on which a job may land are within the Netherlands. Thus, there is no gain in having more than one replica of your data around to improve the transfer efficiency.

Grid Access

Accessing the Grid means using grid tool; installing these tools can be tricky. Currently, there are a number of choices:

• ui.grid.sara.nl, a centrally provided machine at Sara. Contact mailto:grid.support@sara.nl to obtain a local account.
• install the VL-e PoC distribution (See the VL-e PoC distribution page.)
• install the VMWare image of the VL-e PoC distribution.

Monitoring

There are various ways to get information about the current state of the Grid and your grid jobs.

Sara uses Ganglia:

• GINA cluster load for last hour
• GINA joblist report

Nikhef shows some useful statistics:

• Nikhef production facility statistics

External monitoring tools

• gStat
• GridPP Real Time Monitor

VO specific monitoring

• VLemed dashboard

Documentation

Links

• Fokke Dijkstra, Jeroen Engelberts, Sjors Grijpink, David Groep, Arnold Meijster, Jeff Templon@nikhef.nl. The Grid Tutorial handouts 2007. This is the must read beginner's guide to the grid for VL-e users; it covers topics like
  • Grid security; getting a certificate, registering with a VO,
  • Job submission, and
  • Data Management.
• Stephen Burke, Simone Campana, Antonio Delgado Peris, Flavia Donno, Patricia Méndez Lorenzo, Roberto Santinelli, Andrea Sciabà, gLite 3 User Guide
• Nikhef Grid information
• NDPF Node Functions
• Sara system status
• NDPF News Nikhef Data Processing Facility news
• the DutchGrid and Nikhef Certification Authority
• HOWTO: Start using the grid, a quickstart tutorial This quickstart guide is aimed at vlemed users, but it has lots of good stuff for other users, too.
• VLeMed fMRI presentation by Silvia D. Olabarriaga, presented on the Grid Tutorial 26-9-2007, Surfnet, Utrecht