fperakis / swissfel-bernina

Data analysis repository for experiments at SwissFEL Inlcudes code to: - read data from .json files - do angular integration - calculate pump-probe signal

SwissFEL-BERNINA

Data analysis repository for Time-Resolved X-Ray Diffraction (TR-XRD) experiments at the Bernina instrument of SwissFEL, PSI.

Inlcudes code to:

• read data from .json files
• do angular integrations
• calculate pump-probe signal

---

Installation on a SwissFEL machine

1. First connect to psi server:

$ ssh -X [email protected]

2. Then connect to the ra-cluster:

$ ssh ra

3. Make sure to activate bernina conda environment

$ source /sf/bernina/bin/anaconda_env

IMPORTANT NOTE: your ~/.bashrc should contain:

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

#Setup the environment for the PSI pmodules
#idocumentation : https://amas.psi.ch/Pmodules
if [ -f /etc/scripts/pmodules.sh ]; then
        . /etc/scripts/pmodules.sh
fi

4. Then download the repo:

$ git clone https://github.com/fperakis/SwissFEL-Bernina.git

---

To run in parallel:

salloc -n 12 mpirun ./process.py -r 1 -s 18000

with the desired run number (-r integer).

Right now there are some issues:

• you have to specify the number of shots with -s or it processes zero shots (bug, will be fixed)
• we cannot submit batch jobs (not sure how to get MPI to play nice with SLURM)

---

To submit batch jobs using Slurm do:

$ cd scripts
$ ./submit_jobs.sh 0001_test # submits run0001_test.json with default parameters

For help how to run submit_jobs.sh, do: $ ./submit_jobs.sh

Useful Slurm commands:

$ sinfo # check idle nodes
$ squeue -u ext-user # check jobs submitted by user 'ext-user'
$ scancel 1438285 # kill job with id 1438285
$ sbatch job.sh # to submit job to the default partition, with allocation time of 1 hour
$ sbatch -p week job.sh # to submit to the partition with longer allocation time (2 days if not specified)
$ sbatch -p week -t 4-5:30:00 job.sh # to submit job with time limit of 4 days, 5 hours and 30 minutes (max. allowed time limit is 8 days)

See here for more info about computer cluster analysis at SwissFEL: https://www.psi.ch/photon-science-data-services/offline-computing-facility-for-sls-and-swissfel-data-analysis

and here for information related to SSH: https://www.psi.ch/computing/ssh