1. Generation of the small data hdf5 files

The small data generation takes advantage of the local development of the PSANA framework. It can be customized and run both again the xtc files while they are being written on the ffb system (ongoing experiment only) as well as against the .xtc files on the offline system,. Parallel computing has been built-in. For a typical experiment Silke will set up the code in the directory /reg/d/psdm/<hutch>/<expname>/results/smalldata_tools for the offline running or /cds/data/drpsrcf/<hutch>/<experiment>/scratch/smalldata_tools when running in the new ffb.

A "driver" python file (typically called smd_producer.py in the producers subdirectory) can then be edited to, e.g., choose and optimize a different ROI on area detectors, define beam center for radial integration, define delay time range and bin sizes, etc. How to set up this "userData" or reduced data / feature extracted data is described in more detail in A. Configuring smalldata production.

The output will be saved to a directory that can be specified, by default this will be:

/reg/d/psdm/<hutch>/<expname>/hdf5/smalldata or /cds/data/drpsrcf/<hutch>/<experiment>/scratch/hdf5/smalldata

The filenames will be of the form: <expname>_Run<runnr>.h5

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Setup and automatic production

During the experiment we will produce the smallData files automatically. Since Run 18, we are using the Automatic Run Processing for that. During experimental setup, we usually take test runs of the appropriate length to set up production to finish close to the end of run. Jobs can be rerun and stopped. The job will print out where is it. We can set up a second job, started when the hdf5 production is done that can either make data quality plots or produce the binned data.

While the processing is generally done from the elog (ARP), if you would like to run an interactive test job with only a few events, you can use:
./arp_scripts/submit_smd.sh -r <#> -e <experiment_name> --nevents <#> --interactive

The full list of options is here:

(ana-4.0.30-py3) -bash-4.2$ ./arp_scripts/submit_smd.sh -h
submit_smd.sh:
        Script to launch a smalldata_tools run analysis

        OPTIONS:
                -h|--help
                        Definition of options
                -e|--experiment
                        Experiment name (i.e. cxilr6716)
                -r|--run
                        Run Number
                -d|--directory
                        Full path to directory for output file
                -n|--nevents
                        Number of events to analyze
                -q|--queue
                        Queue to use on SLURM
                -c|--cores
                        Number of cores to be utilized
                -f|--full
                        If specified, translate everything
                -D|--default
                        If specified, translate only smalldata
                -i|--image
                        If specified, translate everything & save area detectors as images
                --norecorder
                        If specified, don't use recorder data
                --nparallel
                        Number of processes per node
                --postTrigger
                        Post that primary processing done to elog to seconndary jobs can start
                --interactive
                        Run the process live w/o batch system