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Welcome to the XFELMay2019 wiki!
These notes are here to enable quick reproduction of analysis at XFEL. Please document import aspects of the analysis tools here. Be brief, but clear.
More detailed documentation is here:
https://docs.google.com/document/d/1-t6IVIgW5v4c1h8NEXOttyI2ro-rJ3YPysrXIUM2zxo/edit
Commissioning log book:
in.xfel.eu/elog/SQS+Proposal+2430/
Community experiment log book: https://in.xfel.eu/elog/SQS+Proposal+2176/
in.xfel.eu/elog/SQS+Proposal+2430/
Moving runs to maxwell server:
https://in.xfel.eu/metadata/proposals
The offline analysis is done on the DESY Maxwell servers. The Maxwell servers cannot be accessed from the terminals in the control room. They may be accessed from your laptop.
ssh -Y [email protected]
ssh -Y max-exfl
module load anaconda3/5.2For comissioning:
git clone /gpfs/exfel/exp/SQS/201921/p002430/usr/Software/kuschelware.gitFor community experiment:
git clone /gpfs/exfel/exp/SQS/201802/p002176/usr/Software/kuschelware.gitThis is a local repo that we’ll push to the online git repo at the end of the experiment.
navigate to the git directory, and run
chmod +x INSTALL.sh
./INSTALL.shAs you add materials / analysis code, update the README.md with documentation for your script. Also add inline documentation for what your code is doing.
Once you are done with updates, execute the following commands:
git add NEWFILE
git commit -a -m “Message documenting changes”
git pushOnce these changes are done. Your code will be available to everyone using the git repo.
To grab newest analysis, type git pull
We are having issues with permission.
In case of permissions issues, execute chmod g+rws -R /.../GITDIRECTORY
The online analysis is done from the terminals in the hutch.
Open terminal
ssh USERNAME@exflonc##
Replace ## with: 36 for hutch, 30-35 when hutch has beam.
Upon logging in
Follow directions identical to the offline installation.
module load anaconda3/5.2
karabo-bridge-serve-files PATH PORTPATH points to H5 file or run directory of H5s PORT some computer port greater than 1000
Located in kuschelware/scripts.
Calculates the background on the TOF.
Run as ./xfelmay2019-bgcalc.py STREAM tof
where STREAM='live' or 'tcp://127.0.0.1:PORT' and PORT is the PORT from the karabo-bridge.
Display brightest image of the last 50, the background subtracted image, and the intensity integrated image over real time.
Run as ./xfelmay2019-imagepreview.py STREAM
where STREAM='live' or 'tcp://127.0.0.1:PORT' and PORT is the PORT from the karabo-bridge.
Display live and averaged tof trace, as well as the ROI integrated TOF trace over real time.
Run as ./xfelmay2019-toflive.py STREAM
where STREAM='live' or 'tcp://127.0.0.1:PORT' and PORT is the PORT from the karabo-bridge.
Displays a green (okay) or red (bad) image if a run contains the correct datastreams.
Run like ./xfelmay2019-offlineDAQalive.sh PATH_TO_EXPERIMENT START_RUN
In the event the above scripts crash with a missing keyword argument exception, then it is likely that the name of a detector changed in the DAQ.
Output of xfelmay2019-offlineDAQalive will turn red in this event.
To diagnose, run
karabo-bridge-glimpse tcp://10.253.0.142:6666 to look for the new detector name. Then the libraries in kuschelware/xfelmay2019 need to be updated with the new path / key combinations to specify detectors.
Copy his stuff
Module load exfel exfel_anaconda3
./setup.py
./start.pyIn theory, this can run online analysis for us, but we were unable to start the software using our unix accounts. Hopefully, a happy marriage between our code and his can happen when he returns next week.
Useful thing for controls??? Shows pressures, experiment, change voltages, yada, yada
Commissioning experiment:
/gpfs/exfel/exp/SQS/201921/p002430
Methane cluster experiment:
/gpfs/exfel/exp/SQS/201802/p002176
/raw : contains H5 files
/proc : ?????
/scratch : scratch directory for intermittent files during processing
/usr : longer term storage for analysis files
Look in
/gpfs/exfel/exp/SQS/201802/p002176/scratch
Run 217 argon TOF calibration data
Runs 266-268 scan the chamber height.
Run 393 is a long scan with TOF and MCP at static conditions.
Run 445 has TOF and MCP.
Karabo (python) https://karabo-data.readthedocs.io/en/latest/index.html https://in.xfel.eu/readthedocs/docs/karabofai/en/latest/index.html# https://in.xfel.eu/readthedocs/docs/karabo/en/latest/index.html https://in.xfel.eu/readthedocs/docs/data-analysis-user-documentation/en/latest/karabo_bridge/py-client.html https://karabo-data.readthedocs.io/en/latest/Demo.html
Cheetah http://www.desy.de/~barty/cheetah/Cheetah/EuXFEL_data_analysis.html