LCLS-CXI-1008449

• Experiment Directory: /sdf/data/lcls/ds/cxi/cxi100844924
• SLACK chat: https://app.slack.com/client/E7SAV7LAD/C092393PP2B
• elog: https://pswww.slac.stanford.edu/lgbk/lgbk/cxi100844924/eLog

SSH access

# optional
ssh-keygen 
ssh-copy-id amorgan@s3dflogin.slac.stanford.edu

ssh -Y amorgan@s3dflogin.slac.stanford.edu

# optional
ssh-keygen 
ssh-copy-id psana

ssh psana
cd /sdf/data/lcls/ds/cxi/cxi100844924

To transfer files over ssh:

rsync -vrtlpzh --progress -e 'ssh -A -J amorgan@s3dflogin.slac.stanford.edu:22' amorgan@psana:/sdf/data/lcls/ds/cxi/cxi100844924/results/h5out/r0105_powder.h5 .p

Github push permissions

Point ssh to deployed key for automatic push permissions:

echo "Host LCLS-CXI-1008449 github.com
Hostname github.com
IdentityFile /sdf/scratch/lcls/ds/cxi/cxi100844924/scratch/LCLS-CXI-1008449/ssh/github_rsa" >> ~/.ssh/config

this is not needed if you want to edit then push using your own github account + keys.

Sourcing environment

Sources two envs, om must be installed for the second environment.

cd scratch/LCLS-CXI-1008449
source ./source_this

Look at frames

after ssh'ing (as above with -Y argument)

python analysis/look_at_frames.py <run_number>

Installing om

Make a directory to save the om, and copy the current working version.

    mkdir ~/software
    cp -r /sdf/home/p/padams/software/om ~/software

Move to the directory you created and run the install script.

    cd ~/software/om
    ./tools/scripts/installation/instal.sh -p ~/software/install

Running om (backend)

Make sure that variables are correctly set in the script.

cd om_scripts
./run_om [run]

Running om (gui)

Ensure that the backend is running, and that tcp ip address is correctly set.

cd om_scripts
./run_gui

Geometry conversion

Requires sourced environment.

geometry_convert -f 0-end.data -o [out file name]

Generating masks

cd mask
python psana_mask.py -s exp=cxi100844924:run=16 -d jungfrau4M -o [out file name]

Editing masks

Requires source environment.

cheetah_view.py [hdf5 file]