Using the T3 Cluster at Nevis

Our installation is very similar to the standard US T3 installation but not exactly the same. Start by adding the following to your .bashrc file (or corresponding file if you use a different shell, but I find bash to work rather well with ATLAS software...):

export ATLAS_LOCAL_ROOT_BASE=/a/data/xenia/share/atlas/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'

Log onto xenia (from kolya or karthur) and go to bash if that is not your default shell. You need to do everything on xenia: this is where everything is installed, and although most of it is accessible by NFS from the rest of the cluster, most Nevis machines still run an incompatible 32-bit OS.

There is a batch queue managed by condor, and storage is available under /data/user (create your own subdirectory). However, please start using xrootd as soon as possible to manage storage. As of Sept 4, 2010 there is 8.8 TB of storage on xenia:/data (with 6.2 TB used) and 11 TB in xrootd. Instructions are on the T3 users site (link below), although it is missing the very useful line

xrdcp <myfile> xroot://xenia.nevis.columbia.edu:1094//data/xrootd/<dataset>/<myfile>

There are also scripts on /data/users/common to help adding files. They use /data/users/common/fileCatalog which is meant to keep track of the files on xrootd.

This is an example command:

xrootadd.sh data11_7TeV.00178109.physics_Muons.merge.NTUP_SMWZ /data/xrootd/data/skims/test

where data11_7TeV.00178109.physics_Muons.merge.NTUP_SMWZ is a folder containing root files and /data/xrootd/data/skims/test is an existing folder on xrootd

The command will create a sub-folder /data/xrootd/data/skims/test/data11_7TeV.00178109.physics_Muons.merge.NTUP_SMWZ containing root files renamed to NTUP.0001.root etc. To avoid renaming use /data/users/common/xrootadd.dont_rename.sh

The xrootadd.sh scripts check that the folder exists in the /data/users/common/fileCatalog before adding to xrootd. You can add the folder there with mkdir or:

/data/users/common/xrootmkdir.sh /data/xrootd/data/skims/test 

Note that this requires the setups under "Data storage for your batch cluster". If people copy files to xrootd that way, they will be accessible to all and will gradually also get distributed over the batch nodes. (Please only copy data files, not log files!!!). Note that files get distributed over the nodes that way - they're not all on xenia! To find out what's available and where:

source /a/data/xenia/share/atlasadmin/condor/Arcond/etc/arcond/arcond_setup.sh
arc_nevis_ls /data/xrootd

The database is updated every hour. You can then use Arcond on top of condor to run jobs over the files. See ArCondNevis for a tutorial. The general ArCond instructions are at

Arcond User Guide

To directly move data into xrootd from dq2-get, see below. Note that it's probably good to specify a US site when possible: dq2-get SITE DATASET.

Old Athena versions are installed in

/a/data/xenia/share/atlas/ATLASLocalRootBase/Athena/i686_slc5_gcc43_opt/

Modern releases are available through cvmfs. Do

showVersions --show=athena

to see the list.

Proof-on-demand is also available, see instructions at

https://twiki.atlas-canada.ca/bin/view/AtlasCanada/ATLASLocalRootBase#Using_PROOF_on_Demand_PoD

Otherwise, most of the instructions at

https://atlaswww.hep.anl.gov/twiki/bin/view/UsAtlasTier3/Tier3gUsersGuide

should work.

That's most of it. Of course, only basic tests have been made.

-- GustaafBrooijmans - 16 Apr 2010

DQ2 to XROOTD

Using DQ2 to XrootD Directly

On xenia it is now possible to transfer files directly to the xrootd using dq2-get. The command to use is:

dq2-get -Y -L  -q FTS -o https://fts.usatlas.bnl.gov:8442/glite-data-transfer-fts/services/FileTransfer -S gsiftp://xenia.nevis.columbia.edu/xrootd

For example I copied the dataset:

user.chapleau.valid1.105592.Pythia_Zprime_tt1000.recon.AOD.e574_s933_s946_r2759.NTUP_TOPBOOST.v1.111015001105  

[tandeen@xenia]~% dq2-get -d -Y -L UKI-SCOTGRID-GLASGOW_LOCALGROUPDISK -q FTS -o https://fts.usatlas.bnl.gov:8443/glite-data-transfer-fts/services/FileTransfer -S gsiftp://xenia.nevis.columbia.edu/xrootd user.chapleau.valid1.105592.Pythia_Zprime_tt1000.recon.AOD.e574_s933_s946_r2759.NTUP_TOPBOOST.v1.111015001105

and on xenia the files can now be seen here:

[tandeen@xenia]~% ls /xrootdfs/xrootd/dq2/user/chapleau/valid1/user.chapleau.valid1.105592.Pythia_Zprime_tt1000.recon.AOD.e574_s933_s946_r2759.NTUP_TOPBOOST.v1.111015001105

Further automation of the process is coming...

Reference for installation (not for users)

To make this work I made the changes below which were different from the basic instructions here: https://twiki.cern.ch/twiki/bin/view/Atlas/Tier3gGridftpSetup I had to add myself to

/etc/grid-security/grid-mapfile

In the xrootd config file:

/etc/xrootd/xrootd-clustered.cfg

I added the line

all.manager meta glrd.usatlas.org:1095

And in

/opt/osg-v1.2/vdt/services/vdt-run-gsiftp.sh.env

I changed the last line to:

export XROOTD_VMP="xenia.nevis.columbia.edu:1094:/xrootd=/xrootd"

Make sure all these config files are readable by everyone (not just root).

To start and stop the server as root do:

source /opt/osg-v1.2/setup.sh 
vdt-control --disable gsiftp  
vdt-control --off gsiftp  
vdt-control --enable gsiftp  
vdt-control --on gsiftp

(some of this may be superfluous).

-- TimothyAndeen - 21 Dec 2011