Difference: UsingNevisT3 (1 vs. 18)

If you need a complete enviroment setup example view:

~kiord/.zshrc

To setup the grid enviroment source:

source ${ATLAS_LOCAL_ROOT_BASE}/packageSetups/atlasLocalPandaClientSetup.sh currentJedi --noAthenaCheck    
source ${ATLAS_LOCAL_ROOT_BASE}/packageSetups/atlasLocalRucioClientsSetup.sh 
voms-proxy-init --voms atlas 

To be able to use the grid dataset replication ask to be included to the grid map. To replicate datasets to xenia use the command (after setting up the grid enviroment):

rucio add-rule mc14_13TeV:mc14_13TeV.samplename --grouping DATASET 1 "NEVIS_GRIDFTP"

You can check the status of replication from this website (replace the username by your username):

https://rucio-ui.cern.ch/list_rules?account=username

or with the command (replace the rule):

rucio rule-info 4f935bec5e3644fabbc7aaee4e1499b3

Once the replication has finished you can find the exact location of the files using the command:

rucio list-file-replicas datasetname

Examples how to allocate and run on data can be found at :

~kiord/scripts

rucio add-rule mc14_13TeV:mc14_13TeV.203989.ProtosPythia_AUET2B_MSTW2008LO_TTS_M900.merge.DAOD_TOPQ1.e3397_s1982_s2008_r5787_r5853_p1852 --grouping DATASET 1 "NEVIS_GRIDFTP"

% ls /xrootdfs/atlas/dq2/...

/sbin/service globus-gridftp-server start/stop/restart

The instructions below can (?) still be used, but data subscriptions are now recommended. There is a webpage to subscribe to datasets.

Note 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 <script type="text/javascript" src="http://www.nevis.columbia.edu/twiki/pub/TWiki/TinyMCEPlugin/tinymce/jscripts/tiny_mce/themes/advanced/langs/en.js"></script><script type="text/javascript" src="http://www.nevis.columbia.edu/twiki/pub/TWiki/TinyMCEPlugin/tinymce/jscripts/tiny_mce/plugins/twikibuttons/langs/en.js"></script><script type="text/javascript" src="http://www.nevis.columbia.edu/twiki/pub/TWiki/TinyMCEPlugin/tinymce/jscripts/tiny_mce/plugins/twikiimage/langs/en.js"></script>get distributed over the nodes that way - they're not all on xenia! To find out what's available and where:

/etc/xrootd-dsi/gridftp-xrootd.conf

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

/sbin/service globus-gridftp-server start/stop/restart

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

/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

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

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 

export ATLAS_LOCAL_ROOT_BASE=/a/data/xenia/share/atlas/ATLASLocalRootBase

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

The database is updated every 4 hours. You can then use Arcond on top of condor to run jobs over the files. The instructions for that are at

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

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

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

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

and this is generally a good idea I think.)

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:

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

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

Arcond User Guide

Unfortunately, there is no way to directly move data into xrootd from dq2-get yet. dq2-get does work, but it's probably good to specify a US site when possible: dq2-get SITE DATASET.

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. Instructions are on the T3 users site (link below), although it is missing the very useful line

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

which also 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. Unfortunately, there is no way to directly move data into xrootdfrom dq2-get yet. dq2-get does work, but it's probably good to specify a US site when possible: dq2-get SITE DATASET.

xenia currently has 7 TB of generally available storage under /data (shared between users and xrootd), and each batch node has 1.7 TB. We will evolve this as we develop understanding of the needs.

Athena is installed in

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

Releases can be added easily.

Otherwise, most of the instructions at

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

should work. We do not have a squid server yet.

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

-- GustaafBrooijmans - 16 Apr 2010