The software can be found in stash and can be cloned like this:
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git clone https://stash.desy.de/scm/agipd/calibration.git |
Establish environment of the offline cluster on Maxwell:
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module load anaconda/3 |
If you want to use HDFView to look at HDF5 files, you need to load the xray module:
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module load xray |
XFEL mode
Run:
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cd <repo_location> ./job_scripts/sbatch_analyse.py --input_dir <input_dir> --output_dir <output_dir> --type <measurement_type> --run_list <run numbers> --run_type all |
e.g.
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./job_scripts/sbatch_analyse.py --input_dir /gpfs/exfel/exp/SPB/201730/p900009 --output_dir /gpfs/exfel/exp/SPB/201730/p900009/scratch/user/kuhnm/tmp --type dark --run_list 819 820 821 --run_type all |
when running without sbatch (local, sequencially) is required: add option --no_slurm
NOTE: In XFEL mode it is required to set the parameters input_dir, output_dir, type, and run_list on the command line. The software will NOT take these parameters from the .yaml file!!
CFEL mode
With config file
Adjust config file
- create a new configuration file (e.g. by copying an already existing one) into <repo-path>/conf/<my_conf_name>.ini
e.g. /gpfs/cfel/fsds/labs/agipd/calibration/shared/shared/calibration/conf/M314.ini - open the configuration file
- minimum parameters to adjust:
- module
- temperature
- current: multple currents can be gathered at once (comma separated list)
- input_dir in the all section
e.g.
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module = M314 temperature = temperature_m15C [drscs] current = itestc80, itestc150, itestc20 [all] input_dir = /gpfs/cfel/fsds/labs/agipd/calibration/raw/302-303-314-305 output_dir = /gpfs/cfel/fsds/labs/agipd/calibration/processed/ |
Run
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cd <repo_location> ./job_scripts/sbatch_analyse.py --config <config_file> --cfel --type <measurement_type> |
e.g.
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cd <repo_location> ./job_scripts/sbatch_analyse.py --config M314 --cfel --type dark |
The measurement type can also be defined statically in the config file.
From command line
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cd <repo_location> ./job_scripts/sbatch_analyse.py --input_dir <input_dir> --output_dir <output_dir> --cfel --module <module> --temperature <temperature> --type <measurement_type> --run_type all |
e.g.
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./job_scripts/sbatch_analyse.py --input_dir /gpfs/cfel/fsds/labs/agipd/calibration/raw/315-304-309-314-316-306-307 --output_dir /gpfs/exfel/exp/SPB/201730/p900009/scratch/user/kuhnm/tmp/cfel --cfel --module M304 --temperature temperature_m25C --type dark --run_type all |
when running without sbatch (local, sequencially) is required: add option --no_slurm
Annotation: from command line is not completely consistent because only the default (static) currents and safety factors can be used.