Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

The software can be found in stash and can be get like this:

Code Block
git clone https://kuhnm@stashstash.desy.de/scm/agipd/calibration.git


XFEL mode

Establish environment of the offline cluster :

Code Block
source /etc/profile.d/modules.sh; source /gpfs/cfel/cxi/common/cfelsoft-rh7/setup.sh; module load cfel-python3/latest

Run:

Code Block
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.

Code Block
./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


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.

Code Block
titleM314.ini
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

Code Block
cd <repo_location>
./job_scripts/sbatch_analyse.py --config <config_file> --cfel --type <measurement_type>

e.g.

Code Block
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

Code Block
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.

Code Block
./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.