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 or boslook.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
or you could use the arcproxy tool to generate a proxy:
$ arcproxy --voms <YOUR-VO> Enter Password for PKCS12 certificate: Your identity: /DC=org/DC=terena/DC=tcs/C=NL/O=Nikhef/CN=<Some User> Contacting VOMS server (named pvier): voms.grid.sara.nl on port: 30000 Proxy generation succeeded Your proxy is valid until: 2020-11-18 04:32:41
Congratulations! You are now ready to use grid middleware tools.
Submitting your job
NOTICE: If you submitted jobs using glite-ce-*, you will need to use a new set of commands to submit your jobs to the ARC-CEs.
Therefore, we are asking users to submit job description files that are compatible with ARC-CE
Information about how to create your job description files for an ARC-CE can be found at (http://www.nordugrid.org/arc/arc6/users/xrsl.html)[1]
Please be sure to specify a queue in your job description with
("queue" = "short|medium|long|..." )
After creating a voms or arc proxy and have your job description file ready, some commands to start running your job can look something like:
# Submit your job to an ARC endpoint with your xrsl or adl file specified arcsub -c brug.nikhef.nl [YOUR XRSL OR ADL FILE]
# Check the status of all your jobs. Adding -l will give you a long description of each of your jobs. arcstat -a(l)
# Or you can add the unique ID for your jobs with: arcstat [gsiftp|https]://brug.nikhef.nl:443/[jobs|arex]/[UNIQUE JOB ID]
# Fetch your job output, logs etc with... arcget -a # (or arcget with a single job id)
WARNING! The below commands will no longer work after December 2020!
# 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 XRSL (for ARC jobs), ADL (for ARC jobs), or JDL (for CREAM jobs -- out of support in December 2020!) 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";
or for the XRSL file:
(memory=<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;
or the XRSL parameters:
(count=4) (countpernode=1)
These examples request 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.
