swissFEL202507

Convergent Beam Diffraction cystallography experiment at the Bernina beamline with the Junfrau detector

Beamtime directory: /sf/bernina/exp/25g_chapman

analysis scripts

SSH to ra (see SSH below)

calculate whitefield

$ cd /sf/bernina/exp/25g_chapman/work/git/swissFEL202507/slurm
$ sbatch submit_whitefield.sh <run_number>

This outputs:

$ h5ls -r /sf/bernina/exp/25g_chapman/work/whitefield/whitefield_run<run_number>.h5 
/                        Group
/std                     Dataset {16448, 1030}
/whitefield              Dataset {16448, 1030}

which is required by the streak finder.

calculate streaks

$ cd /sf/bernina/exp/25g_chapman/work/git/swissFEL202507/slurm
$ sbatch submit_streakfinder.sh <run_number>

if you wish to change the peak finding parameters edit the file: /sf/bernina/exp/25g_chapman/work/git/swissFEL202507/slurm/streak_finder_params.json

this outputs a list of streaks to:

$ h5ls -r /sf/bernina/exp/25g_chapman/work/streaks/streaks_run<run_number>.h5
/                        Group
/counts                  Dataset {737404}
/file_index              Dataset {26573}
/file_name               Dataset {737404}
/fs0_ss0_fs1_ss1_im      Dataset {737404, 4}
/pulse_id                Dataset {26573, 1}
/ss0_fs0_ss1_fs1_slab    Dataset {737404, 4}

plot powder

load jupyter notebook from /sf/bernina/exp/25g_chapman/work/git/swissFEL202507/analysis/plot_powder.ipynb

Links

• SwissFEL Google doc
• XWiki page
• Mattermost link
• SciLog

External SSH access

SSH works for me! Here is my process.

You can just do terminal 1 and terminal 2 steps if you don't care about having non-password ssh connections after establishing the first ssh connection.

SSH

$ cat .ssh/config
Host *.psi.ch
        ControlMaster auto
        ControlPath ~/.ssh/controlmasters/%r@%h:%p
        ControlPersist yes
$ mkdir ~/.ssh/controlmasters

terminal 1:

• $ ssh ext-morgan_a@hopx.psi.ch
• enter password
• enter mfa
• leave terminal running

terminal 2:

• $ ssh -J ext-morgan_a@hopx.psi.ch ext-morgan_a@ra.psi.ch
• enter password
• leave terminal running

you now have access to ra cluster

terminal 3:

• $ ssh ext-morgan_a@ra.psi.ch

You now have access to ra without entering a password or MFA.

There is probably a way to configure ssh to make this easier.