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Linux

Find the code of a process

You can add filters to top while it is running: press the o key and then type in a filter expression. For example, to monitor all java processes use the filter expression COMMAND=java. Multiple filters by pressing the key again, filter by user with the u key, clear all filters with the = key.

Converting images

convert <image.jpg> <image.png>

convert <image*.png> <filename.pdf>

Merge pdf files

pdfunite file1.pdf file2.pdf merged_output.pdf

Extract pages from a pdf file

pdftk full-pdf.pdf cat 12-15 output outfile_p12-15.pdf

Printers

Web CUPS

http://localhost:631/printers/Dell_C3765dnf_Color_MFP

Audio

arecord -f cdr /tmp/test

arecord  /tmp/test

aplay  /tmp/test

speaker-test

speaker-test -twav

pgrep -a speaker

Hostname

nslookup <ip-address>

View last lines of a file updating "live"

tail -f <filename>

Search for text in files

grep -rli 'some_text' .

r = recursive, i = case insensitive, l = list file names

LaTex

Avoid big vertical space before the last item of a list:

\item some text\par

Remove bullet from a list of items:

\item[]

Custom font size:

\usepackage{anyfontsize}
...
{\fontsize{50}{60}\selectfont Foo}{\fontsize{5}{6}\selectfont bar!}

Installing biblatex and biber packages:

sudo apt-get install texlive-bibtex-extra
sudo apt-get install texlive-bibtex-extra biber

ATHENA

Tutorial Release setup

bash
mkdir workArea
setupATLAS
export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'
mkdir source
mkdir build
mkdir run
cd source

COOL

setupATLAS
asetup 21.0.39,Athena
(asetup 21.2.93,AthAnalysis)

GIT

General

Git global setup

git config --global user.name "Name Surname"
git config --global user.email "mail@somewhere.de"

Create a new repository

git clone https://:@gitlab.cern.ch:8443/<user>/<project-name>.git
cd <project-name>
touch README.md
git add README.md
git commit -m "add README"
git push -u origin master

Push an existing folder

cd existing_folder
git init
git remote add origin https://:@gitlab.cern.ch:8443/<user>/<project-name>.git
git add .
git commit -m "Initial commit"
git push -u origin master

Push an existing Git repository

cd existing_repo
git remote rename origin old-origin
git remote add origin https://:@gitlab.cern.ch:8443/<user>/<project-name>.git
git push -u origin --all
git push -u origin --tags

View the branches in a Git repository

git branch [-a]

Delete a local branch

git branch -d <the_local_branch>

Checkout the latest version on the remote repository

(

git fetch origin

)

git checkout -b <branch_name> origin/master

GIT commit

git commit -[a]m "My message"

(use the -a option in your commit command to stage and add the changes to your repository).

Push a new local branch to a remote git repository link

1. create a new branch:

   git checkout -b feature_branch_name

2. edit, add and commit your files
3. push your branch to the remote repository:

   git push -u origin feature_branch_name

Data quality

Release 22 - MT

A collection of the basic DQ algorithms that have been already implemented and where they reside: https://twiki.cern.ch/twiki/bin/view/Atlas/Run3DQCodeInGit.

AFP DQ code:

mkdir testAFP
cd testAFP/
setupATLAS 
lsetup git
git atlas init-config --apply
git atlas init-workdir https://:@gitlab.cern.ch:8443/atlas/athena.git [:@gitlab.cern.ch:8443] -b 21.0
cd athena/
git checkout -b 21.0-AFP-DQM upstream/21.0 --no-track
git atlas addpkg AFP_Monitoring
ls ForwardDetectors/AFP/AFP_Monitoring/
cd ..
mkdir Build
cd Build/
asetup Athena,21.0,latest,slc6
cmake ../athena/Projects/WorkDir/
make
source ./x86_64-centos7-gcc62-opt/setup.sh 

AFP DQ strategy (as of 13.08.2019):

1. Get some first code running. Song-Ming pointed you to https://twiki.cern.ch/twiki/bin/view/Atlas/DataQuality where this is also roughly described (right hand side): Suggested workflow:
   1. read through the instructions in the example job option
   2. write an algorithm (subclass AthMonitorAlgorithm) that follows the form of the ExampleMonitorAlgorithm to retrieve a quantity (just port over a calculation from your subsystem’s Run II monitoring code) related to your subsystem from a data file (AOD/ESD/etc)
   3. write a configuration file that defines a histogram for this quantity and writes it to the output histogram file
   4. run athena with the JobOption you have created and check the out put file for your histogram
   5. test your ability to change the python configuration. (e.g. try changing the output TDirectory structure)
   6. test your ability to calculate other quantities and use filters in the algorithm
   7. record what percentage of your histograms is migrated
2. for how to get this template code running, the best is to look at: https://twiki.cern.ch/twiki/bin/view/Atlas/DQRun3FrameworkTutorial (which I understand, you have already looked at - though I understand you tried to indeed understand all references, which is very admirable, but not possibly very difficult without having too much practical experience of the ATLAS computing framework).

Inside the section: https://twiki.cern.ch/twiki/bin/view/Atlas/DQRun3FrameworkTutorial#New_Monitoring_Framework (which roughly explains some of the algorithms) you find a reference to https://gitlab.cern.ch/atlas/athena/tree/master/Control/AthenaMonitoring where you find in the folders: src / AthenaMonitoring / python the following files:

• ExampleMonitorAlgorithm.cxx
• ExampleMonitorAlgorithm.h
• ExampleMonitorAlgorithm.py

which you would want to rename to AFP DQMonitoring and include it in a relevant package in your project folder: https://gitlab.cern.ch/atlas/athena/tree/master/ForwardDetectors/AFP (Betty's old code there?).

Instructions to run: https://twiki.cern.ch/twiki/bin/view/Atlas/DQRun3FrameworkTutorial#Getting_started_with_the_new_mon.

JIRA tickets: https://its.cern.ch/jira/browse/ATLASDQ-662.

Release 20.7

Run the ATLAS test web display

Get the DQM tools:

mkdir dq_devel
cd dq_devel
setupATLAS
lsetup git
git atlas init-workdir https://:@gitlab.cern.ch:8443/atlas/athena.git
cd athena
git atlas addpkg DataQualityConfigurations
git fetch upstream
git checkout -b 21.0-my-dq-development upstream/21.0 –no-track

TWiki

• https://twiki.cern.ch/twiki/bin/view/Atlas/DQOperationalRecipes

AFP

M. Trzebinski (12.06.2019): list of defects and descriptions created, to be uploaded in the DQDefects DB, a specific GRL (AFP special runs) will be created

Open Call for Tasks in the Data Quality area

https://twiki.cern.ch/twiki/bin/view/Atlas/DQOpenCalls#Finalization_of_the_AFP_DQ_histo

https://its.cern.ch/jira/browse/ATLASDQ-674

Talks

• https://indico.cern.ch/event/675482/contributions/2767773/attachments/1547295/2428923/calpas_atlas_dqm_25102017.pdf

25/10/2017 Data Quality weekly

• https://indico.cern.ch/event/675745/contributions/2765936/attachments/1546490/2427513/calpas_afp_dqm_24102017.pdf

24/10/2017 technical AFP meeting (AFP detector, test AFP in ATLAS web display, which histograms to use and how)

• https://indico.cern.ch/event/671946/contributions/2748538/attachments/1538276/2411072/calpas_afp_dqm_10102017.pdf

10/10/2017 technical AFP meeting (grouping and convention name in COOL, BPM, AFP in ATLAS test web display)

• https://indico.cern.ch/event/670247/contributions/2741588/attachments/1534352/2403011/calpas_afp_dqm_03102017.pdf

03/10/2017 technical AFP meeting (AFP in general DQ meeting, AFP into ATLAS test web display, COOL update)

• https://indico.cern.ch/event/668338/contributions/2732712/attachments/1530324/2395002/calpas_afp_dqm_26092017.pdf

09/26/2017 technical AFP meeting (Monitoring status, COOL parameters, AFP runs list, analysis of runs)

• https://indico.cern.ch/event/668310/contributions/2732588/attachments/1529439/2393167/calpas_afp_dqm_cool_25092017.pdf

09/25/2017 AFP Condition Database meeting (A : variabls for COOL, B: data structure)

• https://indico.cern.ch/event/644125/contributions/2713532/attachments/1522344/2378850/calpas_afp_dqm_Bergen13092017.pdf

09/13/2017 ATLAS ALFA/AFP meeting (A: Online and Offline tools, defects, histo and ref histo, remaining steps. B: TPX-3)

• https://indico.cern.ch/event/662347/contributions/2704608/attachments/1515238/2364441/calpas_afp_dqm_29082017.pdf

08/29/2017 technical AFP meeting (Analysis of run 332303, SiT hit versus luminosity block)

• https://indico.cern.ch/event/661072/contributions/2697715/attachments/1511130/2356620/calpas_afp_dqm_22082017.pdf

08/22/2017 technical AFP meeting (Online and offline monitoring histograms, analysis of run 332303)

• https://indico.cern.ch/event/659927/contributions/2691865/attachments/1508525/2351914/calpas_afp_dqm_15082017.pdf

08/15/2017 technical AFP meeting (Online and offline monitoring histograms and analysis status)

• https://indico.cern.ch/event/658583/contributions/2685037/attachments/1505547/2346132/calpas_afp_dqm_08082017.pdf

08/08/2017 technical AFP meeting (ATLAS monitoring system, Online Histogram Presenter)

• https://indico.cern.ch/event/657202/contributions/2677953/attachments/1501737/2345579/calpas_afp_dqm_01082017.pdf

08/01/2017 technical AFP meeting (Data Quality Monitoring importance, strategy, new email list)

Test setup

• create a root file with AFP reconstructed objects (G. Gach)
  • setup the framework

setupATLAS
mkdir ../build && cd ../build
asetup 21.0.39,Athena
mkdir ../source && mv CMakeLists.txt ../source/
cmake ../source
make -j
source x*/setup.sh
mkdir ../run && cd ../run

• • create the root file

Reco_tf.py --inputBSFile 'raw_AFP_file' --outputAODFile 'output.root' --outputHISTFile 'output_HIST.root' --AFPOn True
--autoConfiguration 'everything' --preExec
'all:rec.doTrigger.set_Value_and_Lock(True);rec.doAlfa.set_Value_and_Lock(False);rec.doForwardDet.set_Value_and_Lock(Tr
ue);rec.doAFP.set_Value_and_Lock(True);DQMonFlags.doAFPMon=True;from InDetRecExample.InDetJobProperties import
InDetFlags;InDetFlags.checkDeadElementsOnTrack.set_Value_and_Lock(True);' 'r2a:from
InDetRecExample.InDetJobProperties import InDetFlags;
InDetFlags.useDynamicAlignFolders.set_Value_and_Lock(True);from InDetPrepRawDataToxAOD.SCTxAODJobProperties
import SCTxAODFlags;SCTxAODFlags.Prescale.set_Value_and_Lock(50);from TrigHLTMonitoring.HLTMonFlags import
HLTMonFlags;HLTMonFlags.doGeneral=False;TriggerFlags.AODEDMSet="AODFULL";' --maxEvents 5000 --conditionsTag
'CONDBR2-BLKPA-2017-11' --geometryVersion 'all:ATLAS-R2-2016-01-00-01' --steering 'doRAWtoALL'

• run the ATLAS test web display (R. Narayan, P. Onyisi)
  • get the DQM tools

mkdir dq_devel ; cd dq_devel
SetupATLAS ; lsetup git
git atlas init-workdir https://:@gitlab.cern.ch:8443/atlas/athena.git
cd athena
git atlas addpkg DataQualityConfigurations
git fetch upstream
git checkout -b 21.0-my-dq-development upstream/21.0 –no-track

• • setup a release

mkdir ../build ; cd ../build
asetup 21.0.38

• • get the AFP configuration file

cd ../athena/DataQuality/DataQualityConfigurations/config/ ; mkdir AFP
cp /afs/cern.ch/user/c/calpas/www/collisions_run.config AFP

• • get the AFP reconstructed root file

cp /PATH/TO/YOUR/NEW/output.HIST.root

• • compile

cd ../../../../build
cmake ../athena/Projects/WorkDir ; make -j ; source x*/setup.sh

• • run the DQM

DQWebDisplay.py ../athena/DataQuality/DataQualityConfigurations/config/output.HIST.root TestDisplay 1

TDAQ

General

https://atlasop.cern.ch/twiki/bin/view/Main/Run2Preparation

Setup environment

source /sw/tdaq/setup/setup_tdaq-07-01-00.sh

DQMD display

dqm_display -p ATLAS

ROOT

ROOT tutorial https://root.cern.ch/root/htmldoc/guides/primer/ROOTPrimer.html#root-macros

ROOT setup on lxplus

setupATLAS

localSetupROOT [options] [version]

localSetupROOT --help

Input/output

ROOT input/output

MakeClass

root -l <file_name>
tree_name->MakeClass("<class_name>")

Peaks in histograms

TSpectrum: search by setting the sigma and the amplitude threshold of the peaks:

Int_t Search(const TH1* hist, Double_t sigma = 2, Option_t* option = "", Double_t threshold = 0.05)

Example

#include "TSpectrum.h"

TSpectrum *s = new TSpectrum();
Int_t peak;
...
peak = s->Search(hist, 2.2, "nobackground", 0.12);
cout << "peak: " << peak << "\n";

TChain

        TChain *chain = new TChain("ntuple");

        chain->Add("//data/scratch/atlas_root_v3/mpx04_20120305_Background_2012_LT_100s_1000.root");

        chain->Add("/data/scratch/atlas_root_v3/mpx04_20120327_Background_2012_LT_50s_1000.root");

        chain->Add("/data/scratch/atlas_root_v3/mpx04_20120412_VdM_scan_LT_8s_1000.root");

dir

TDirectory* topDir

m_outputFile = TFile::Open("out_file.root", "RECREATE");
topDir = m_outputFile->mkdir("test");
topDir->cd("test");

...Save_Hists...

 m_outputFile->Write();
 m_outputFile->Close();

Root dir

Draw

In an online session:

tree->Draw("variable_name");

Vectors

std::vector<double> *myvector = new std::vector<double>;

Loop over vectors

vector<int> vi;
...
for ( int i : vi ) cout << "i = " << i << endl;

External variables

In header global.h:

  // Global variables
  #ifndef GLOBAL_H
  #define GLOBAL_H
  extern Bool_t ext_var;
  #endif

In .C macro or .cpp source file;

#include "global.h"

Bool_t ext_var;

void macro()
{
...
   cout << ext_var << "\n";
...
}

Animated GIF

c1->SaveAs("MSet.gif+NN");
Each frame is delayed by NN*10ms.

SSH and SCP stuff

ssh and scp with port specification:

• ssh name@server -p

• scp -P <port> name@server:<path/to/file>

  P capital!

Vydio stuff

sudo dpkg -i ./VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.deb
sudo apt install libqt4-designer libqt4-opengl libqt4-svg libqtgui4 libqtwebkit4
mkdir ../prg
gvim ../prg/videbcontrol
chmod 755 ../prg/videbcontrol
../prg/videbcontrol VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.deb
sudo dpkg -i ./VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.modfied.deb
../prg/videbcontrol VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.deb
rm VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.modfied.deb
../prg/videbcontrol VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.deb
sudo apt install libqt4-designer libqt4-opengl libqt4-svg libqtgui4 libqtwebkit4
sudo apt install libqtgui4 libqtwebkit4
rm VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.modfied.deb
../prg/videbcontrol VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.deb
sudo apt install libqt4-opengl
sudo apt install libqt4-svg
sudo apt install libqt4gui
sudo apt install libqtgui4
sudo apt install libqtwebkit4
sudo apt install libqt4-network
sudo dpkg -i ./VidyoDesktopInstaller-ubuntu64-TAG_VD_3_6_3_017.modfied.deb

LUMI stuff

Good runs

• 2015: 251103-286474, 286475-287983
• 2016: 289496-314199
• 2017: 324320-341649, 341692-342182
• 2018: 348197-367384

Vdm scans - Run-2

• 2015: 277025,277089,280231,280500,280520,286282,287224,287594
• 2016: 299390,300287,301915,301918,309311,309375,310781,312796,313067,313285,313878,313935
• 2017: 324832,324839,325020,329484,330875,335302,336506,339197,340453,340634,340644
• 2018: 354494,365218,365763,365768

LUMI DQ defects

• 2017
  • 338377 LUMI_ONL_DET_ERROR_SEVERE 1−528; LUMI_ONL_OLC2HLT_SEVERE 1−575

ALFA

DCS server at P1

pcatlrpolcs (pcatlfwd01)

source /det/dcs/linuxScripts/set_env.sh

Radmons

/det/dcs/Production/ATLAS_DCS_RPO/scripts/libs/RadMonLib.ctl

https://indico.cern.ch/event/472136/contributions/2165711/attachments/1276882/1894886/Radiation_status_2016.pdf

https://indico.cern.ch/event/484369/contributions/1993893/attachments/1226159/1795122/ALFA_radmons_20160211.pdf

https://indico.cern.ch/event/574904/contributions/2335039/attachments/1353890/2045310/Radiation_Oct_2016.pdf

https://indico.cern.ch/event/612336/contributions/2497687/attachments/1423742/2183127/Radiation_Feb_2017.pdf

https://indico.cern.ch/event/574904/contributions/2335039/attachments/1353890/2045310/Radiation_Oct_2016.pdf

https://indico.cern.ch/event/645856/contributions/2644078/attachments/1487452/2310647/Radiation_Radmons_2017.pdf

https://indico.cern.ch/event/645856/contributions/2644079/attachments/1488568/2313303/new_RadMons.pdf

https://indico.cern.ch/event/644125/contributions/2713542/attachments/1522330/2378815/Radiation_Sept_2017.pdf

https://indico.cern.ch/event/710304/contributions/3007162/attachments/1653516/2645869/Radiation_Jan_2018.pptx

https://atlasop.cern.ch/elisa/display/334932

https://atlasop.cern.ch/elisa/display/348971

HGTD

Open questions

• water cooling (from LAr?) only for DC-DC converters?
• LV: any (hardware) protection against overvoltage?

HV

LV

Temperature

Pressure

Humidity

Presentations about FOS-LPG:

• https://indico.cern.ch/event/781529/contributions/3291145/attachments/1788171/2913700/Discuss_Spec_Review.pdf#search=lpg%20humidity%20sensors
• https://indico.cern.ch/event/590227/contributions/2612892/attachments/1486530/2308743/ForumOntrackerDetector_mechanics.pdf

Demonstrator

Modules

Pad size: 1.3 x 1.3 mm2

Module size: 40 x 20 mm2

450 pads/ module

ELMB++

• Pros:
  • optical fibres, no CANbus, no electrical ground
  • (possibly) more radiation hard
• Cons:
  • not available at the moment

TDR

Comments (DCS-related)

• Markus Elsing: L 358 FLEX cables: number of connected modules limited by FLEX bandwidth?
• Maurice Garcia-Sciveres: calibrations
• Philippe Farthouat:
  • sec. 6.4.2 time needed to upload the 1024 configuration registers of an ASIC
  • MUX: who is developing; time scale
  • ELMB++: availability
• Michel Raymond: L 4832 one PT100 per heater or per cover/vessel?
• Richard Teuscher:
  • chap 8, humidity sensors: type, location, read-out software
  • sec. 8.3 ELMB2 as backup if ELMB++ not available
• Kevin Einsweiler:
  • sec. 6.6: voltage monitoring: automated action in case of high currents or voltage drops or relying only on Interlock triggered by large temperature variations?
  • MUX: who is developing; time scale

My remarks:

• HV ramp up/down according to SB condition
• L 2882 total monitoring range is of 90°C
• L 2889 proposed->provided
• L 2915 mux->MUX's or multiplexers

-- DavideCaforio - 2019-04-10