matlab

MATLAB scripts and functions

Installation of reconstruction routine for micro-tomography data acquired at the P05 imaging beamline (IBL) or P07 high energy material science beamline (HEMS) at PETRA III at DESY, both operated by Helmholtz-Zentrum Hereon.

1. Log in to a GPU node on the HPC cluster MAXWELL at DESY. Nodes in the partitons 'max-fs-display' and 'max-display' can be accessed from anywhere. For more information on how to connect to the cluster, see https://docs.desy.de/maxwell/documentation/fastx4/. However these display nodes come with a load manager which kills your processes if they consume too much memory of CPU power.

   If this happens, you have to allocate and connect to a node on a different partition which is more powerful. First connect to the MAXWELL cluster (via a display node or similar). In a terminal execute the following command to allocate a node on our Hereon partition 'hzg' non-exclusively (oversubscribe):

   salloc --partition=hzg --oversubscribe --time=7-00:00:00

   In case you don't get an allocation on our 'hzg' partition you can include other paritions with more nodes but which can be less powerful. Modify the parameter if necessary.

   salloc --partition=hzg,allgpu --mem=500G -c 40 --oversubscribe --time=7-00:00:00

   Then connect to the allocated node using ssh:

   ssh -Y $SLURM_NODELIST

2. Download the latest MATLAB files from GitHub:

   Open a terminal and run:

   git clone https://github.com/moosmann/matlab.git

   OR

   Update to latest version: Fetch latest version of the 'master' branch from the remote repository 'origin' and reset/overwrite all local changes. New files that were created locally and which do not exist in the latest branch are not deleted.

   git fetch origin master & git reset --hard origin/master

   Before updating you can back-up local files by branching if necessary:

   git add --all git commit -m "COMMIT MESSAGE" git branch NAME_OF_BRANCH

   To check which files were modified and which new (untracked files):

   git status

3. How to start the tomographic reconstruction routine:

   (3.1) Change directory to the 'matlab' folder:

   cd matlab

   (3.2) Start MATLAB using the following script:

   ./startmatlab.sh

   The script automatically sets environment variables in order to use a local installation of the ASTRA toolbox, starts MATLAB, and sets the MATLAB search paths. (Note that this will overwrite local MATLAB user settings, for details see 'startup.m'.)

   (If 'startmatlab.sh' is not executable: chmod +x startmatlab.sh)

   (3.3) If not already open, open 'p05_reco' (also for P07 scans) in MATLAB located at './matlab/experiments/p05/' e.g. enter 'edit p05_reco' in MATLAB's command line.

   (3.4) Edit/check the reconstruction parameters, at least you have to modify 'par.scan_path'.

   (3.5) Start the reconstruction by one of the following:

   • Type 'p05_reco' in MATLAB's command line
   • Click 'RUN' button in editor tab
   • Type 'F5' key when cursor focus is in the 'p05_reco.m' file

   (3.6) Optinal: The reconstruction can be automatically looped over all data sets acquired during a beamtime and/or over different reconstruction parameters. How to set up a loop script to reconstruct several data sets: help p05_create_reco_loop