Grid@Nikhef

Overview

The EGI / WLCG grid infrastructure can be accessed from any Nikhef-managed machine running a variant of Red Hat Enterprise Linux 6 or higher (e.g. CentOS 6 or 7) or from a Grid UI (i.e., bosui.nikhef.nl).

To access the Grid from a Nikhef-managed machine, you need to get the grid middleware tools first:

 source /cvmfs/grid.cern.ch/etc/profile.d/setup-cvmfs-ui.sh        ## bash/ksh/zsh

Csh users will have to first run

 /bin/bash

or perhaps even better, change their login shell to bash or zsh. (If you are accessing the Grid from a UI, you can skip this step.)

Sourcing the setup script will set up all required environment variables for running the middleware commands.

Once you have sourced the grid middleware tools or have logged into the UI, type

 voms-proxy-init --voms <YOUR-VO>

to create a voms proxy. Sample output:

 $ voms-proxy-init -voms pvier
 Enter GRID pass phrase:
 Your identity: /O=dutchgrid/O=users/O=nikhef/CN=Some User
 Creating temporary proxy .......................................... Done
 Contacting  voms.grid.sara.nl:30000
 [/O=dutchgrid/O=hosts/OU=sara.nl/CN=voms.grid.sara.nl] "pvier" Done
 Creating proxy
 ................................................................... Done
 Your proxy is valid until Fri Dec  7 00:08:49 2007

Congratulations! You are now ready to use grid middleware tools.

Submitting your job

After creating a voms proxy, some commands to start running your job can look something like:

# Delegate your proxy to an endpoint (-e) with a string to identify your proxy delegation
glite-ce-delegate-proxy -e [CREAM-CE_SERVER]l:8443 [STRING]

# Submit your job to a resource (-r) queue with the output (-o) going to a directory (jids) 
# using the delegation ID string in the previous command and finally adding the job descritpion file (JDL) for your job.
glite-ce-job-submit -r [CREAM-CE_SERVER]:8443/cream-pbs-[QUEUE] -o jids -D [STRING] [JDL-FILE.JDL]

# Check the status of your job... 
glite-ce-job-status https://[CREAM-CE_SERVER]:8443/[JOBID]

General queues and walltimes available:

Queue Name	Max. Walltime (hh:mm:ss)	Allowed VOs
short	04:00:00	alice atlas dans projects.nl pvier virgo dune lsgrid lofar tutor enmr.eu bbmri.nl xenon.biggrid.nl chem.biggrid.nl drihm.eu
medium	36:00:00	alice atlas dans projects.nl pvier virgo dune lsgrid lofar tutor enmr.eu bbmri.nl xenon.biggrid.nl chem.biggrid.nl drihm.eu
long	96:00:00	alice atlas dans projects.nl pvier virgo dune lsgrid lofar tutor bbmri.nl xenon.biggrid.nl chem.biggrid.nl drihm.eu

For more information or find other queues, use lcg-info or lcg-infosites which will give you more information about what is available to your VO. For example,

lcg-infosites --vo pvier -f NIKHEF-ELPROD all

More information is also available on the SURFsara wiki: http://doc.grid.surfsara.nl/en/latest/Pages/Service/system_specifications/gina_specs.html#queues

Specifying Job Requirements

The default values for memory, nodes, CPUs and local scratch space may not be adequate for your use case. It is possible to specify the requirements for your jobs in the JDL file, which will then be translated into requirements on the local batch system. This will either match suitable resources, or match nothing at all if your requirements exceed what is available. If this is the first time you need to specify additional requirements, please ask the site administrators for advice.

Memory requirements

The amount of main memory (RAM) required for the job can be passed by adding this line to the JDL file.

CERequirements = "other.GlueHostMainMemoryRAMSize >= 8192";

This example requests 8GB of RAM (the unit is Megabytes). Be aware that exceeding the requested amount in the actual job may result in termination of the job by the batch system.

Multi-core jobs

Requesting to run on multiple cores and nodes is done by the standard JDL parameters

SMPgranularity = 4;
CpuNumber = 4;

This example requests 4 cores on 1 node. See also Enabling_multicore_jobs_and_jobs_requesting_large_amounts_of_memory.

Local Scratch Space

The amount of local scratch space for your job can be requested by placing the following statement in the JDL.

CERequirements = "other.GLUE2ComputingShareMaxDiskSpace >= 100";

This example requests 100GB of local disk space.