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Here is an overview of the steps needed to work out the internal alignment of the full vertex detector. Each step is described in more detail below.

  1. Production a Millepede input binary
  2. Run millepede using mille.bin creating a resulting file with correction to the constants, e.g. millepede.res
  3. Create a new compact detector description with the new corrections, e.g. compact_new.xml
    1. java -cp hps-distribution-3.0.4-SNAPSHOT-bin.jar org/hps/svt/alignment/BuildMillepedeCompact -c compact.xml millepede.res -o compact_new.xml 
    2. Use option "-r" to replace instead of adding to existing constants in the compact.xml
  4. Create a new detector with this new compact_new.xml file.
Production of a Millepede binary input

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file

The Millepede input binary file is obtained through the following steps:

  1. Reconstruct real data with GBL (to this purpose, you need to include the GblOutputDriver in your steering file).

    1. For Montecarlo data:

      1. run the readoout with the steering file (for instance, for test run data: HPS2014ReadoutNoPileup.lcsim)
      2. run the recon with the steering file (for instance, for test run data: HPS2014OfflineNoPileUp.lcsim)
    2. For real data you can use whatever steering file (usually the most update version will work)  but remember to include the mentioned GblOutputDriver drivers as mentioned above, if they are not present (usually they are not, for production purposes):
      <driver name="GBLOutputDriver"/>
      ...
       <driver name="GBLOutputDriver" type="org.hps.recon.tracking.gbl.GBLOutputDriver">
               <debug>0</debug>
               <isMC>false</isMC>        
                <gblFileName>${outputFile}.gbl</gblFileName>
      </driver>
    3. For the purpose of alignment you are reccommended to drop ghost hits, including in the HelicalHitDriver driver the following line:
      <rejectGhostHits>true</rejectGhostHits>

  2. Check that at the end of reconstruction a out.gbl ascii file (or, named as you decided in the GblOutputDriver) is produced.
  3. Remember that by default the geometry is taken from the database. If you want to force the use of your own geometry, you must provide it in the compact.xml file in a given detector. For MonteCarlo data, set the run number to zero during readout and reconstruction. This is done adding the flag -Drun=0 when running the readout. For real data, use the -DdisableSvtAlignmentConstants flag.. IMPORTANT: remember to re-compile hps-java before running each time you change the compact.xml file! (this is the most common error).
  4. The out.gbl file is read by a python procedure, called gbltst-hps.py. You must download with git the current version of the software from the github repository as described in the following. This will create a hps-gbl directory. After having configured your account and username for git usage, issue the following commands:
    (the second and third command need to be issued just upon installation, and they are needed since some directories with utility files are shared with other software packages which will be described later).
    Once you have downloaded the code

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  1. , remember to install the GBL software, if you already haven't it. In a directory parallel to hps-gbl download the GBL software using svn:

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    • (or check the newest release, and get it). To compile it:
    • cd GeneralBrokenLines/cpp
    • mkdir build; cd build
    • cmake ../
    • make install
    • make doc (if you want it)
      Note: if you have installed the latest cmake version, probably it

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    • won't compile. You must prevent the compilation to search for C++11 support (the default for newest cmake). To do this, you have to set as compilation flag -std=c++0x adding it to the c++ compilation line. Either you do it in the cmake configuration files, or (quickest) you add by hand this flag at the end of the CXX_FLAGS line, in

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    • these two files:

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      • GeneralBrokenLines/cpp/build/CMakeFiles/GBL.dir/flags.make
      • GeneralBrokenLines/cpp/build/examples/CMakeFiles/GBLpp.dir/flags.make
    2. the
  2. The gbl python procedure reads the out.gbl file and prepares the binary read by Millepede. You must run python from the hps-gbl directory. This is the shortest syntax (-h shows all possible options):
  3. cd hps-gbl
    • python gbltst-hps.py $GBLFILE --name $OUTNAME --ntracks $MAXTRKS --nopause --save
      You can provide the input gbl filename, the output file name and the
    5. nmber
    • number of tracks to be processed as logical names in a shell script.way
      A heap of pdf files are produced containing plots of several quantities for top/bottom halves, with long names that should be self-explaining (but at the moment they are not and they are too long, this
    6. must
    • needs to be improved). You will also file a .root file containing the single root histograms, and a .ps file containing a summary of the plots ready to be printed.
      The file gbltst-hps.py contains the instructions to extract the useful information on tracks and hits from the ascii file and write the input file for Millepede; it reruns GBL on the tracks. If you want to add/
    7. modify
    • change some of the output plots/histograms, you have to modify both the gbl_plots.py file (in which they have to be booked) and the gbltst-hps.py file, in which they have to be filled.
      See the help (or, better, the code) for indication to further functionalities:
      •  python gbltst-hps.py --help
      Note: root must be compiled including the python support, otherwise python stops with an error complaining about root libraries missing. A good idea is to put in your profile and instruction to run automatically $ROOTSYS/bin/thisroot.(c)sh, which provides the correct root-python environment and libraries for your system.
      At the end of python processing, you should also find a MilleBinaryISN.dat file (the name could slightly change), which is the input file to be read by Millepede.
Running Millepede
  1. Once you run GBL on the out.gbl file, you can check the quality of the alignment/geometry studying residuals, kinks, pulls and several other useful distributions. All histograms are contained in a file named gbl_$OUTNAME_somethingElseDependingOnTheFlags.root. A set of useful root macros can be found here:The master branch contains macros which are compliant to root v5.34, the branch root6 contains macros working with root6 as well (this is the development branch). In the git bundle you can find a README file with some indications about how to run the macros, and what they do. Note: due to a reversed sign in the magnetic field coordinates in the GBL procedure, the charge of tracks in the produced rootfile is reversed as well (keep this in mind when analysing the data in this rootfile). In many cases, also the u-v axes have to be flipped to provide the correct orientation of the sensors in the space (this is already done almost everywhere in the macros). By inspecting the trend of residuals and distributions one can judge which are the most critical degrees of freedom to float in the following Millepede iteration.

Running Millepede
  1. Once you have the binary file, millepede is ready run from the hps-mille directory. This directory is setup downloading the Millepede software by github using the following commandRemember to compile the fortran sources of the MillepedeII software. It comes with the git bundle (or you can download it from https://www.wiki.terascale.de/index.php/Millepede_II) but you have to compile it in your system (note: with gfortran you might have to slightly modify the Makefile by hand, because have the binary file, millepede is ready run from the hps-mille directory. This directory is setup downloading the Millepede software by github using the following commandRemember to compile the fortran sources of the MillepedeII software. It comes with the git bundle (or you can download it from https://www.wiki.terascale.de/index.php/Millepede_II) but you have to compile it in your system (note: with gfortran you might have to slightly modify the Makefile by hand, because its version is frozen and not aligned anymore to more modern gfortran versions/libraries).
  2. To run millepede use the following commands:
    • cd hps-mille
    • ./runMP.py -i../hps-gbl/milleBinaryISN.dat -M NAMES
    where NAMES is a list of parameters coded via the following regexp: L(1-6)[AS]?[hs]?[tb]_([tr])([uvw]) having the following meaning:
    1. 1-6: layer number
    2. A: axial, S: stereo
    3. h: hole, s: slot
    4. t: top, b:bottom
    5. _t: translation, _r: rotation
    6. u, v, w: coordinates on the sensor reference system
    if some of the parameters preceded by "?" are omitted, both the choices are selected
    Millepede produces as output, among several files, the millepede.res file which contains the corrections found by Millepede for the floated parameters.
     
    1. , v, w: coordinates on the sensor reference system
    if some of the parameters preceded by "?" are omitted, both the choices are selected
    Millepede produces as output, among several files, the millepede.res file which contains the corrections found by Millepede for the floated parameters.
    To keep track of the subsequent iterations, it is wiser to store them file that can be read automatically by the runMP.py procedure. The file is called floatoptions.py and it contains a series of "options", each of them containing a list of sensors to be floated in the same or multiple iterations, coded following the regexp pattern described above. The user can add as many options as needed, ordering them by consecutive numbers which are then used to label a "switch number" used to select the needed option upon running the procedure. The corresponding command to be issued is:
    • ./runMP_batch.py --run --files milleBinaryISN.dat -s switchNumber -b
    The output file will be labeled with the title string provided in the option definition and the sequence of desired floating operations (keep it simple because when its gets too long -usually for several iterations in one go or multiple sensor floatings- the procedure breaks).

Create a new compact based on Millepede corrections

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