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.
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 ce
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. To browse the information system, connect to bdii03.nikhef.nl on port 2170 and enter 'o=grid' as the base dn.
|Resource name||maximum wall time||comments|
|tbn20.nikhef.nl:2119/jobmanager-pbs-qlong||30 hours||The Nikhef cluster has 1156 CPU cores|
|ce.gina.sara.nl:2119/jobmanager-pbs-short||4 hours||GINA (Grid In Almere) has 160 CPU cores|
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:email@example.com) 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:firstname.lastname@example.org for support.
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).
|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:email@example.com or mailto:firstname.lastname@example.org).
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.
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:email@example.com 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.
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:firstname.lastname@example.org 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.
There are various ways to get information about the current state of the Grid and your grid jobs.
If you want to be informed of updates, downtimes, etc. you can subscribe to the infrastructure-announce mailing list.
Sara uses Ganglia:
Nikhef shows some useful statistics:
External monitoring tools
VO specific monitoring
- 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 MÃ©ndez Lorenzo, Roberto Santinelli, Andrea SciabÃ , 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