CarolineRiedlSandbox < Sandbox

---+!! Caroline's Pages
%TOC%

---++!! Quicklinks
   * [[http://twiki.npl.illinois.edu/bin/view/COMPASS/WebHome][Illinois COMPASS Twiki]]
   * [[https://twiki.cern.ch/twiki/bin/viewauth/Compass/WebHome][COMPASS Twiki]]
      * [[http://wwwcompass.cern.ch/twiki/bin/view/Drell_Yan/Subgroupmeeting][Drell-Yan Analysis Twiki]] Slides: =/afs/cern.ch/compass/Talks/SubGroups/DY/=
   * [[http://wwwcompass.cern.ch/compass/software/offline/welcome.html#software][COMPASS Sotware]]
      * [[http://wwwcompass.cern.ch/twiki/bin/view/DataReconstruction/CoralSoftware][CORAL]]
      * [[http://ges.web.cern.ch/ges/phast/][PHAST]]
   * [[https://compassshifts.web.cern.ch/compassshifts/2015/][Shifts 2015]]

---++ COMPASS

---+++ DY2015 periods

[[https://twiki.cern.ch/twiki/bin/view/Compass/Drell_Yan/2015DataPeriods][Main Twiki]]

---+++ My online logbook
   * *[[CarolineRiedlSandbox_01][My online logbook 2015 / 2016]]*
*user criedl* 
   * =bash= shell. (To switch to =c= shell, type =csh=)
   * login settings for bash: =~/.bashrc= (for c: =~/.tcshrc=)
   * Working directory: "MYDIR"= =/afs/cern.ch/user/c/criedl/COMPASS/=

---+++ git 2016
Setting it up: [[#CarolineRiedlSandbox_01#June_2016][see here]]

---++++!! Basics
<verbatim>
git config --list
git config user.name
git help <verb>
git <verb> --help
man git-<verb>
git help config
git clone ssh://git@gitlab.cern.ch:7999/illinois-and-friends-group/dy-analysis.git
</verbatim>

---++++ dy-analysis 
   * *SetUpEnvironment.sh* is linked here from =MYDIR= and has to be executed for every new shell (follow instructions printed in shell)
   * *Depends.mk* is the master config & job submission file 
   * *phast* can be compiled from this directory - then the source files (!UserEvents) from =dy-analysis/users= are copied to =phast/user= and everything is compiled. 


---++++ dc05
---++++ straw-chambers

---+++ CORAL and PHAST
_last update: August 8, 2016_

---++++ Compilation

_It is assumed that all steps are executed in the same shell session. If this is not the case, it is necessary to first [[#Setting_up_the_environment][set up the environment]]._ 

0. If indicated, check out fresh version of CORAL (YYYYMMDD is today's date)
<verbatim>
cd MYDIR
mkdir YYYY-MM-DD-coral_svn
rm coral_svn
ln -s YYYY-MM-DD-coral_svn coral_svn
mv <OLD>-coral_svn SoftwareBin
cd YYYY-MM-DD-coral_svn
svn co https://svn.cern.ch/reps/coral/trunk
cd trunk
ln -s ../../PreExeCoral.sh .
ln -s ../../PreCompilation.sh .
. PreCompilation.sh
. setup.sh
. /afs/cern.ch/sw/lcg/contrib/gcc/4.7/x86_64-slc6-gcc47-opt/setup.sh
</verbatim>

1. [[#Setting_up_the_environment][Set up environment]] (if not done yet)

2. Compile CORAL
<verbatim>
make clean
make -j
</verbatim>

3. Compile PHAST libraries

*Personal setup*:
<verbatim>
cd MYDIR/phast.A.BBB
make clean
make -j
</verbatim>

or

*With git setup:*
<verbatim>
cd MYDIR/git/dy-analysis/
./SetUpEnvironment.sh
make phast
</verbatim>
If successful, it will produce executable =phast= in the phast directory (both methods!).

4. Compile CORAL & PHAST
<verbatim>
cd coral
make clean
make
</verbatim>
If successful, it will produce executable =coral.exe= in the coral directory.

---++++ Setting up the environment
There are currently three scripts in =MYDIR= that have to be sourced:
   * =PreCompilation.sh=: before compiling (personal setup)
   * =PreExeCoral.sh=: before executing coral (personal setup). 
   * %N% =SetUpEnvironment.sh=: before working with git 

Notes:
   * The scripts are to be linked to the directories in that there are to be executed. After execution, follow the instructions printed into the shell. 
   * =setup.sh= sets the environment =$COMPASS_FILES= to =/afs/cern.ch/compass/detector=.

---+++++ Before a new analysis session
<verbatim>
cd MYDIR/coral_svn/trunk
. setup.sh 
cd ../../MyRun/mDSTs
. PreExeCoral.sh
</verbatim>  

---+++++ Before compiling =coral=
<verbatim>
cd MYDIR/coral_svn/trunk
. PreCompilation.sh
. setup.sh
. /afs/cern.ch/sw/lcg/contrib/gcc/4.7/x86_64-slc6-gcc47-opt/setup.sh
</verbatim>


---++++ ManyRDs.csh
Submit several (many) coral jobs to the batch with [[https://twiki.cern.ch/twiki/bin/view/Compass/DataReconstruction/CoralBatch][ManyRDs.csh]]
<verbatim>
cd /afs/cern.ch/user/c/criedl/COMPASS/MyRun/mDSTs
./ManyRDs.csh -H
</verbatim>
prints out some help. See also Jose's or Mathieu's writeups. 

  * %I% Sending more than one chunk at the same time: =./ManyRDs.csh -d <Outputdir>  -s <start-chunk> <trafdic-file> <number-of-chunks>= <br>
     Coral then runs over <number-of-chunks> chunks starting with <start-chunk>. Note that it will only consider chunks in this grid engine (like cdr11001, cdr 12001, ...)
   * %I% Correct !TraF !SmoothPos is done automatically, don't need to put in values by hand!  

---++++ Check status of your running jobs 
=bjobs= 

---+++ DC5 analysis
---++++ Documentation
<verbatim>
ssh pccogw01 
cd /online/detector/dc05
</verbatim>

My laptop:
=/Users/criedl/Box\ Sync/COMPASS/DC56/DocumentationAndManuals=

---++++ Required software resources
Last update: October 19, 2015

   * In =coral_svn/trunk/src/geom/CsDriftChamber.cc=, the string =DC5= has to appear in two places (not counting appearances in comments) 
   * *RT-relation*
      * Sep 30 (>=263154): DC5 RT relation in MySQL not suitable any more because T0 shifted by -20-30ns (longer optical cable). _Use private one with this modification applied fttb_
      * Sep 23: DC5 RT relation submitted to MySQL (new fit and proper T0)
   * *detectors.dat* 
      * detectors.dat produced before October have likely a wrong z-position for DC5. 

| file | period (week) | latest release date |
| detectors.259361.transv.dat | P1 | Sep 2 |
| detectors.260073.transv.dat | P2 | Sep 2 | 
| detectors.260626.transv.dat | P3a | Sep 2| 
| detectors.260876.transv.dat | P3b | Sep 2 |
| detectors.261513.transv.dat | P4a (W10) | Sep 23 |
| detectors.261974.transv.dat | P4b | Sep 21 |

_This needs to be updated. As of June 4, 2016, there exist the following 2015 detectors.dat in the official location:_
<verbatim>
detectors.257625.transv.dat
detectors.258106.transv.dat
detectors.258722.transv.dat
detectors.259022.transv.dat
detectors.259361.transv.dat
detectors.260073.transv.dat
detectors.260626.transv.dat
detectors.260876.transv.dat
detectors.261513.transv.dat
detectors.261970.transv.dat
detectors.262425.transv.dat
detectors.263140.transv.dat
detectors.263637.transv.dat
detectors.264163.transv.dat
detectors.264722.transv.dat
</verbatim>

---+++ Alignment
   * [[http://wwwcompass.cern.ch/twiki/bin/view/DataReconstruction/Alignment][Alignment Twiki]]
   * [[http://wwwcompass.cern.ch/compass/notes/2003-4/2003-4.ps][Note (2003)]]
   * [[http://wwwcompass.cern.ch/runLogbook/dirphp/list_runs.php?wherereq=+%28tb_run.runtypeid+%3D+2%29][Alignment runs]]
      * If this link does not work,  go to [[http://wwwcompass.cern.ch/runLogbook/dirphp/select_runs.php][this link]] and search logbook for alignment (bullet 7, "Run type equal to: (2) alignment)".
      * Example run: =/castor/cern.ch/compass/data/2015/raw/tmp/cdr11001-258106.raw=
---++++ detectors.dat

=/afs/cern.ch/compass/detector/geometry/2015/detectors.*.dat=

---++++!! CORAL code

After having checked out a new version of CORAL, compile also the alignment:
<verbatim>
cd coral_svn/trunk/src/alignment
make 
</verbatim>

---++++!! Scripts
[[#Setting_up_the_environment][First set up environment.]]

*From Marica:*
   * =base= - contains all the options files (to run traf, to run align and to run checkTracks)
   * =plots_control= - contains options files to run =checkTracks= for each detector, in my opinion these plots are better than the ones created using checkTracks options from base which are the ones by default if we use the script inside folder /run
   * =run= 
      * =alignalll= is the main script where you specify the files you want to use, the runs, the number of chunks, the number of iterations (how many times to run all the procedure for alignment)...
      * =run_align.sh= is just to run alignalll in the batch system and redirection the outputs.

   * *Run CORAL* using specific alignment options (example):
<verbatim>
cd coral_svn/trunk/src/alignment
Linux/traf traf.fieldoff.opt
</verbatim>
This produces a *root tree* (in  this example, =traf.fieldoff.root=) with all the informations on the hits/tracks/detectors needed for alignment itself and also to produce the quality control plots with residuals (below).

   * *Run alignment* using this *root tree*:
<verbatim>
Linux/align align.FIELDOFF.opt
</verbatim>
This produces a text file =align.fieldoff.out= with all the shifts to apply to the =detectors.dat= used up to now:
<verbatim>
Linux/updateFromAlign align.fieldoff.out
$COMPASS_FILES/geometry/2006/FIELDOFF/detectors.dat new.detectors.dat
</verbatim>

   * *Re-run CORAL* using =new.detectors.dat=, which produces a new *root tree*. 

   * *Check new residuals for improvement.*
<verbatim>
Linux/checkTracks checkTracks.FIELDOFF.opt
</verbatim>

---+++ DAQ machines from outside
<verbatim>
ssh -X lxplus.cern.ch
ssh pccogw01 -CX
ssh pccorc31
</verbatim>

Then =run_manager=, =add_comment= etc. should work.

---+++ DCS
   * [[https://compass-dcs.web.cern.ch/compass-dcs/scripts/welcome.asp][DCS www page]]
   * [[http://wwwcompass.cern.ch/twiki/bin/view/SlowControl/WebHome][DCS Twiki]]

How to access the *DCS panel*: first login to COMPASS gateway  =pccogw01=
   <verbatim>  
   ssh -X criedl@lxplus.cern.ch
   ssh criedl@pccogw01 -CX 
   ssh -l dcs pccompass07 -CX
   dcsUI
   </verbatim>
(username: operator; no password needed)

---++ General computing
---+++ emacs
in-line emacs: =emacs -nw=

exit with =C-x C-c=
---+++ svn
<verbatim>
svn co https://svn.cern.ch/reps/coral/trunk
svn info
svn log
svn update 
</verbatim>


---++ CERN
   * [[http://public.web.cern.ch/public/][CERN www]]
   * [[https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBook][WorkBook]]
   * [[https://twiki.cern.ch/twiki/bin/view/CMSPublic/WorkBookComingToCERN?redirectedfrom=CMS.WorkBookComingToCERN][Coming to CERN]]
   * [[http://www.tpg.ch/fr/index.php][Geneva public transportation]]
   * [[https://edh.cern.ch/Hostel/Home][CERN hostel]]
   * [[https://espace.cern.ch/cern-market/default.aspx][Other accommodation]]
   * [[http://consult.cern.ch/xwho/people][CERN phone book]]

---++ CMS
   * [[https://cms.web.cern.ch/org/cms-calendar][CMS calendar]]
   * [[http://cms.web.cern.ch/][CMS main www]]
   * [[http://cms.cern.ch/iCMS/][iCMS]] 
      * [[http://cms.cern.ch/iCMS/analysisadmin/analysismanagement][CMS PAS]]
      * [[http://cms.cern.ch:80/iCMS/jsp/db_notes/notestable.jsp?typeid=AN][CMS AN]]
      * [[http://cms.cern.ch:80/iCMS/jsp/iCMS.jsp?mode=single&part=publications][CMS info server]]  
   * [[https://hypernews.cern.ch/HyperNews/CMS/cindex][HyperNews]] 
   * [[https://indico.cern.ch/categoryDisplay.py?categId=26][Indico: CMS Higgs meetings]]
   * [[https://indico.cern.ch/categOverview.py?categId=2l76][Indico: all CMS meetings of today]]
   * [[http://cms.web.cern.ch/org/cms-detector][CMS detector]]

---++ MyCMS
   * [[Sandbox.CarolineRiedlSandbox10][Physics]] - Notes and links about Higgs and other LHC physics
      * [[https://twiki.cern.ch/twiki/bin/view/Sandbox/CarolineRiedlSandbox11][My analysis]]
      * [[https://twiki.cern.ch/twiki/bin/view/CMS/Higgs2Tau2MuMu][German HTauTauMuMu Twiki]]
      * [[https://twiki.cern.ch/twiki/bin/view/CMS/Higgs2Tau2ElEl][German HTauTauEE Twiki]]
      * %I% [[https://twiki.cern.ch/twiki/bin/view/CMS/Higgs2Tau2MuMuatCERN][German HTauTau coordination]]

   * [[https://twiki.cern.ch/twiki/bin/view/CMS/DataCertificationatDQMGroup][Data Certification at DQM Group]]
      * [[https://twiki.cern.ch/twiki/bin/view/CMS/CertificationResults][JSONs and Lumi 2011]]
      * [[https://twiki.cern.ch/twiki/bin/view/CMS/CertificationCollisions11][Data Certification Logbook 2011]]

---++ CMS@DESY
   * [[http://cms.desy.de/][CMS-DESY]]
   * [[https://indico.desy.de/categoryDisplay.py?categId=209][Higgs Group Meetings]] (Wednesday 10:00)
   * [[https://indico.desy.de/categoryDisplay.py?categId=239][KA-HH Tau Group Meetings]] (Tuesday 13:15)
   * [[http://indico.desy.de/][DESY indico]]
   * [[https://twiki.cern.ch/twiki/bin/view/CMS/HamburgWiki][Hamburg CMS Twiki]]
      * [[https://twiki.cern.ch/twiki/bin/view/CMS/DesyPhysics][DESY physics contributions]]
   
-- Main.CarolineRiedl - 2015-06-11
-- Main.CarolineRiedl - 10-May-2011
Topic revision: r105 - 2016-09-09 - CarolineRiedl
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