IFAE Pixel


This page is created by the pixel group of IFAE Barcelona. It is supposed to collect information about the pixel activities at IFAE, especially documentation, links, useful tips etc.

For the collection of measurement results, please refer to the IFAE Pixel Elog.

Useful Links and Documentation

General Computing

  • The general linux working areas are PIC (Barcelona) and LXPLUS (CERN).

  • Tier 3 IFAE computing dashboard: here.

  • To request a PIC account use this web interface.

Access to PIC and LXPLUS via ssh and sshfs

Login from a linux shell via ssh:
  •  ssh -Y picUserName@at3.pic.es 
  •  ssh -Y cernUserName@lxplus.cern.ch 
Attention! Make sure to be on the right pic machine! at303 has only SL 5.8, which sometimes leads to problems! E.g. at302 has SL 6.4.
  •  ssh -Y at302 
It is also possible to mount the pic or lxplus directories via sshfs to a previously created directory on the local machine. By this, you can e.g. use your advanced editor of choice that is installed locally to open the code that is saved remotely on pic/lxplus. The sshfs command has to be repeated every time the machine is started again, so it is helpful to create an alias in the profile (e.g. .bashrc).
mkdir -p pic/nfs 
sshfs picUserName@at3.pic.es:/nfs pic/nfs

mkdir -p lxplus/home
sshfs cernUserName@lxplus.cern.ch:/afs/cern.ch/user/cernUserNameInitial(oneLetter)/cernUserName lxplus/home


dCache is a file system for the storage of large data sets. It is e.g. used to backup the raw files and reconstructed files of our testbeams.

Our dCache folder on the PIC is: /pnfs-disk/pic.es/at3/projects/Pixels

The command to copy a file to dCache is:
dccp /bin/inputFile.xx /pnfs-disk/pic.es/at3/projects/Pixels/outputFolder
(answer from the help desk:) so far we haven't found a way to copy complete folder. Thus, to copy all files in a directory, you need to loop, e.g.:
for f in *.root; do dccp $f /pnfs-disk/pic.es/at3/projects/Pixels/outputFolder; done

From the pic this command works directly. If you need to copy files from lxplus the trick is that you download your file in the /tmp directory of the at3 machine with your favourite command and then you copy the file to destination with dccp command.

More information can be found here: https://giq.ifae.es/UsingdCache.pdf. If you cannot manage please call extension at IFAE 2822 and ask Alex Guinó for a joint session where he can debug what happens.


  • See the attachments below for the FEI4B manual.

USBPix Connectivity

USBPix and STControl


  • The pyBAR twiki has step-bystep installation instructions.
  • Notes on installation of pyBAR on ubuntu 14.04.



  • Notes on running the RCE system:
    • Users need accounts on pixiblsr1daq1, ask Martin Kocian for one
    • It is important to ground the HSIO board and the module power supply to a common ground
    • The HitOr lemo, if not connected to the HSIO board (pin J1), also has to be connected to the common ground
    • If the RCE gets stuck, there is a reboot pin on the front that has to be pressed with a thin tool (the RCE leds flash when rebooted)
    • To reboot the HSIO board one has to press the SW1 next to the front green LEDs (it will flash 5sec later). After the reboot of the HSIO board, one needs to reboot the RCE.
    • More information on rebooting can be found in slides from TB
    • To check the connection and status of the RCE (also reboot is possible) do:
      telnet rce16
      root (username)
      no password (just enter)
      To check the status enter: syslog
      For EXIT: exit

  • Running:
    1. If not using existing account, setup own DAQ software as described in IBL SR1 Twiki
    2. Make sure all the necessary directories and files are in place for data output, module configuration files and primlists (where 00-00-00 is your module name):
      mkdir -p data moduleconfigs/00-00-00 moduleconfigs/top primlists
      cd moduleconfigs/00-00-00
      mkdir configs fdacs masks tdacs
    3. Copy template config file 00-00-00.cfg file to moduleconfigs/00-00-00/configs. Replace module ID and make sure no masks or maps are loaded. Optionally modify chip register values.

  • Running the RCE in the AFP testbeam
    • Starting from scratch, from the pcaidarc do the following:
    • Connect to the iblecontest2 laptop (which is just outside the enclosure, on the Jura side):
      > ssh -Y -l ibl (pass: iblecon)
    • > cd work
    • > source setup_rce.sh
      This does a killall (ei, kills all the RCE related servers/processes). It does not need to be done everytime you start the calibGui or the cosmicGui.
    • > source reload_rce.sh This loads the rce library (it is also done in the start_calib.sh below).
    • > cosmicGui
      This is the data taking gui, to start taking data, you just have to press "Start Run" (it will take the previous running configuration).
    • To run the pixel module scans and also to take data in "self-trigger" mode, use:
      > source start_calib.sh
    • To reboot the HSIO board form the iblecontest2: > rebootHSIO (not always possible)

HSIO board at SR1 used during Sept 2014 tests for AFP:


see instrutions at: https://yarr.readthedocs.io/en/latest/

yarr software: https://github.com/Yarr/Yarr

yarr firmware: https://github.com/Yarr/Yarr-fw/blob/master/syn/xpressk7/README.md


see TWIKI: https://twiki.cern.ch/twiki/bin/viewauth/RD53/RD53ATesting


List of 3D/AFP testbeams.

Testbeam Reconstruction

  • Judith reconstraction framework for FEi4 based telescopes: (TO BE UPDATED)

  • EUtelescope: See the instructions to compile the Eudet software in the PIC or lxplus (UPDATED):

Official instructions: http://eutelescope.web.cern.ch/content/installation

Official ITk testbeam instructions: https://twiki.cern.ch/twiki/bin/viewauth/Atlas/ITkPixelTestBeamReconstruction

Installation script: https://cernbox.cern.ch/index.php/s/Mi6ijh2j8BYofqt


GitLab IFAE Pixel repository

The IFAE Pixel Group Repository: https://gitlab.cern.ch/ifaepix



  • Get an existing project:
  • Create a new project:
  • Upload existing project:
    • go to the ifaepix page and click on the "New Project" button
    • insert the project name (ex. my_project) and click "Create Project"
    • go in the folder of your existing project: cd my_project
    • initialise an empty repository: git init
    • link your project to the remote git repository: git remote add origin https://$CERN_USER@gitlab.cern.ch/ifaepix/my_project.git
    • add all the files in the folder to the local git repository: git add .
    • commit the changes: git commit -m"this is a comment fot the first commit of my project"
    • upload all the chages of the added files in the local repository to the remote repository: git push -u origin master
  • Typical workflow (good for small changes or simple projects with few people modifing the code at the same time):
    • check the status of the repository: git status
    • update to the last version of the code: git pull origin master
    • make changes to the files (or create new files) (ex. changed_file.cpp, changed_file.h, new_class.h )
    • add the chenged files: git add changed_file.cpp changed_file.h new_class.h
    • commit changes: git commit -m"added new functionality for bla bla bla"
    • remove crappy file: git rm crappy_file.cpp
    • commit changes: git commit -m"removed crappy file"
    • push the changes to the master repository: git push origin master
  • Advanced workflow (when making major changes to the code in a project with many people working at the same time)
    • create a new local branch: git checkout -b new_branch
    • do stuff... add changed files ... and commit changes
    • push the new branch to the remote repository: git push origin new_branch
    • when everything is working and is tested merge the new branch into the master branch: git merge new_branch master
    • solve conflicts, commit and push them to the master remote repository
    • check existing branches and current branch: git branch
    • switch to a branch: git checkout master
    • delete old/merged local branches: git branch -d new_branch
    • delete old/merged remote branches: git push origin :new_branch

ITk Modules

  • ITk Module PDR indico (22 Oct 2019)

IBL Modules

IBL Module Assembly

  • Go to EDMS and search for document 1221780.




Telescope setup

  • ifconfig on the DAQ PC
         telescope@pcaidarc:~$ ifconfig
         eth0      Link encap:Ethernet  HWaddr 00:22:4d:a9:dd:d5  
         inet addr:  Bcast:  Mask:
         eth0:1    Link encap:Ethernet  HWaddr 00:22:4d:a9:dd:d5  
         inet addr:  Bcast:  Mask:
  • sudo ifconfig eth0:1


  • Documentation: ATLAS-CDS with updated link to extra information.

Shuttle CERN to Previssin

  • Circuit 6 note: from CERN bld 33.
  • TREC, to be aothorized, do the SIT TREC training.


Moved to Internal Twiki


Submitting JINST papers to arXiv

  • arXiv has problems with the new standard JINST latex template (jinstpub.sty)
  • To make arXiv compile, comment out
    in jinstpub.sty
  • In addition, include the following files in your arXiv upload .zip or .tar file (in addition to your main.tex source file and the plots):
    • jinstpub.sty (modified as above)
    • newtxtext.sty
    • newtxtt.sty

Radiation source usage

  • There are two sources of the pixel group: an exempted Sr-90 one (37kBq), and a high activity Sr-90 one (3.7MBq) AN-7171.
  • There are also Am-241 and Cd-109 (exempted, but check)
  • The procedure to use the sources is:
    • Take source from safe box and put an entry in the log but with: name of the source, the date, if it is in or out (and destination if out) and the person.
    • If it is an exempted source: if you are using the source every day of the week, there is no need to bring it back to the bunker every day when you leave, so you lock it in the safe of the gray room and bring it to the bunker only for the week end. If you have to run tests that last more than one day, you can leave the source in the gray room with the area properly signaled as Controlled Area. But for a single use, it is best to bring the source back to the bunker after use.
Topic attachments
I Attachment History Action Size Date Who Comment
PDFpdf FE-I4B_V2.3.pdf r1 manage 9246.2 K 2015-10-13 - 15:17 SebastianGrinstein  
PNGpng Screen_shot_2014-09-30_at_10.12.53_AM.png r1 manage 500.7 K 2014-09-30 - 10:26 SebastianGrinstein  
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Topic revision: r74 - 2022-04-21 - StefanoTerzo
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