EmilysHowTo

Commissioning

Shift work

MDT DAQ

View JTAG pc's:

  > rdesktop -a 16 -g 1280x1024 pcatlmdtmdm6 &

MDT Control Panel:

  > /det/muon/MDT/MDTControlPanel/runmdtcp

PVSS

  > /scratch/pvss/bin/viewmdtfsm &
To set up a run, there should already be an alias in shell for
  > standalone

or do something like:

  > source /det/muon/standalone/setup-02-00-03.sh
  > setup_daq -p part_MDT_Ec -d /det/muon/standalone/databases/tdaq-02-00-03/muon/partitions/part_MDT_Ec.data.xml

Login to pc-mu-eb-01(02,03) to compile code

  > export $CMTCONFIG=i686slc4-gcc34-dbg
  > standalone

To check out code:

  > svn co $SVNROOT/packagename/trunk packagename

Scheme editor:

  > oks_scheme_editor <file.xml>

Changing thresholds (from Alberto):

  • in DCS, go into any of the JTAG panels
  • click on tabular view, and get the list of BEEs (for example, you can write BEE* in the search window, and then filter chambers matching string)
  • double-click or right-click on the name of any BEE chamber
  • in the window that opens up, select the CSM-JTAG label, in the bottom list
  • right-click in (almost any) position of the panel that will appear (that panel will look strikingly similar to the usual chamber JTAG panel), you should get a small panel where you can enable the calibration initialization and the AMT threshold
  • click on the box to enable the threshold change, write in the new threshold, close the panel
  • REINITIALIZE all the damn BEEs. The change in any of them will affect all chambers connected to the same pcatlmdtmdm machine
  • change the threshold back to its initial value (= 0, and unchecked box) and REINITIALIZE all the damn BEEs.

To see MROD log files:

  • ssh sbc-mdt-rcc-eca-01 (or ba, bc, ecc)
  • cd /logs/mrod (listed by run)

If MDTs go busy:

  • check that the busy is not from a ROD before attempting this
  • ask DAQ shifter not to remove the MDT crate (press "no")
  • hold the trigger (if not already in hold)
  • Log on the sbc on the crate which triggered the busy
  • source /det/muon/standalone/setup-02_00_03.sh
  • test_tim_qpll_reset -b d000000
  • tell daq shifter the hold trigger can be removed

Distributed Analysis/Batch jobs

Castor

List datasets (or use nsls):

  • rfdir /castor/cern.ch/grid/atlas/tzero/prod1/perm/data09_900GeV/[stream]/[run number]

To work off of castor, this must be set up first:

  • export STAGE_SVCCLASS=atlcal

If it still says "Permission Denied", try this:

  • xrdcp root://castoratlas//castor/cern.ch/....

Grid

To submit a grid job:

  > source setup.sh -tag=AtlasProduction,15.3.0.2
  > export PATHENA_GRID_SETUP_SH=/afs/cern.ch/project/gd/LCG-share/current/etc/profile.d/grid_env.sh
  > source /afs/cern.ch/atlas/offline/external/GRID/DA/panda-client/latest/etc/panda/panda_setup.sh
  > pathena jobO_1.py jobO_2.py jobO_3.py [--inDS inputDataset] --outDS outputDataset

To check jobs:

  > pbook
  >>> show()
  >>> retry(5)
  >>> kill(5)

dq2

To setup:

> source /afs/cern.ch/atlas/offline/external/GRID/ddm/DQ2Clients/setup.sh
> voms-proxy-init -voms atlas

  • dq2-ls -f list all files in data set
  • dq2-ls -r list replicas of files
  • dq2-get -f FILENAME1,!FILENAME2,...!FILENAMEN DATASETNAME get those files in data set

Create PoolFileCatalog:

  • dq2-ls -L CERN-PROD_TZERO -P -R "srm://srm-atlas.cern.ch^rfio:" [dataset]

Batch jobs

On tier2:
> qsub -q analysis queScript_DYmumu_Atlfast.sh
To check jobs:
> qstat -u ethompso

Other useful stuff:

> nohup athena.py -s -c 'EvtMax=10' jobOptios.py >& test.log &

ROOT stuff

To create macros with class MyClass from an ntuple:

  > root -l file.ntuple.root
  [0] CollectionTree->MakeSelector("MyClass")

To run macros from MakeSelector:

  > root -l file.ntuple.root
  [0] CollectionTree->Process("MyClass.C+")

or to link together many ntuples:

  > root -l
  [0] TChain *a_tree = new TChain("CollectionTree")
  [1] a_tree->Add("ntuples/*.root")
  [2] a_tree->Process("MyClass.C+")

Software

Set up new work area

  • mkdir [release]
  • cp a requirements file to the release
  • source /afs/cern.ch/sw/contrib/CMT/v1r20p20090520/mgr/setup.sh
  • cmt config

For a list of all tags to be used in the requirements file see AtlasLogin

SVN

Creating a new package in my own SVN area:

  • svn import . $SVNUSR/ethompso/JetCommonAnalysis/trunk -m "initial import"
  • Delete the current directory
  • svn co $SVNUSR/ethompso/JetCommonAnalysis/trunk JetCommonAnalysis
  • svn mkdir $SVNUSR/ethompso/JetCommonAnalysis/tags
  • svn cp $SVNUSR/ethompso/JetCommonAnalysis/trunk $SVNUSR/ethompso/JetCommonAnalysis/tags/JetCommonAnalysis-00-00-01 -m "first import"

Checking out code from an institute:

  • svn co $SVNGRP/Institutes/UMass/EWAnalysis/trunk EWAnalysis

The last parameter is the local name of the directory with the package. Similarly, to get a tag, you use:

  • svn co $SVNGRP/Institutes/UMass/EWAnalysis/tags/EWAnalysis-00-00-02 EWAnalysis

TWiki: SVN: Modifying and checking in code

To check in a new version of a package, go to the package directory

  • cd MuonSpectrometer/MuonReconstruction/MuonRecTools/MuonTrackSummaryHelperTool

  • edit the ChangeLog and add your change + the version tag

pico ChangeLog

  • perform a final check of your changes by looking at the diff (important!! you WILL find problems from time to time like remaining cout's ....)

svn diff

  • now check in the package

svn ci -m "MESSAGE HERE"

  • if it says this:

[ethompso@lxatlasumass2]% svn ci -m "implement MuonTrackSummary dump methods"
Sending        ChangeLog
Sending        src/MuonTrackSummaryHelperTool.cxx
Transmitting file data ..svn: Commit failed (details follow):
svn: Commit blocked by pre-commit hook (exit code 1) with output:

ATLAS POLICY: Unable to modify /MuonSpectrometer/MuonReconstruction/MuonRecTools/
                          MuonTrackSummaryHelperTool/tags/MuonTrackSummaryHelperTool-00-12-01 path.

It is within a '/tags' directory and tags are read-only.

Possible reasons:
[1] Maybe you forget to switch the context (svn switch) after check out of a tag?
[2] This tag already exists in repository and you have tried to create it once again?

Contact Atlas librarian ('atlas-svn-managers@cern.ch') for details.

  • then do this:

svn switch $SVNROOT/MuonSpectrometer/MuonReconstruction/MuonRecTools/MuonTrackSummaryHelperTool/trunk

  • and tag it (replace the path with the absolute path of your package

svn cp . $SVNROOT/MuonSpectrometer/MuonReconstruction/MuonRecTools/MuonTrackSummaryHelperTool/tags/MuonTrackSummaryHelperTool-00-12-01  -m "MESSAGE HERE"

Transformatons

  • trf_ls lists transforms

Detailed track summary dump

athena.py -s -c 'EvtMax=-1; PoolESDInput=["/afs/cern.ch/user/e/emoyse/public/ReferenceESD/ESD_15.0.1_ttbar.pool.root"] ;
PoolESDOutput="copy_ESD.15.0.1.pool.root" ;DumpFileName="ReadOut150001"'../share/readTopOptions.py >! read15.0.1.log

dev_area/15.5.3/Tracking/TrkEventCnv/TrkEventTPCnv/src/TrkTrackSummary/

VP1

To run, add at bottom of job options:

   from AthenaCommon.AlgSequence import AlgSequence
   topSequence = AlgSequence()

   from VP1Algs.VP1AlgsConf import VP1Alg
   topSequence += VP1Alg()

Instructions for selecting events and viewing in vp1 (from Niels):

setup athena with source setup.sh -tag=15.5.3.3,AtlasTier0,slc4,gcc34,32,opt,runtime

then run:

athena ESDAnalysis_combined.py >&! out_filter_541MinBias.txt &

add your events to:

events541_MinBias.list

Other

Atlas Run Query:
http://atlas-runquery.cern.ch/query.py?q=find+run+141000%2B+and+events+1000%2B+%2F+show+t+and+lhc+and+mag

Check disk usage:
du -h --max-depth 1 /home

-- EmilyThompson - 2009-08-28

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Topic revision: r20 - 2011-08-25 - EmilyThompson
 
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