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titleCommon terminal commands

COMMON TERMINAL COMMANDS

TO OPEN GDA CLIENT

Code Block
 $ gda client

TO OPEN THE BEAMLINE SYNOPTIC 

Code Block
$ tlauncher -f diad 

TO OPEN YOUR DATA FOLDER 

Code Block
$ cd dls/k11/data/2023/<VISIT NUMBER>/ 
$ gio open .

FIJI/IMAGE J

Code Block
$ Module load imageJ/2019 
$ imagej

SAVU 

Code Block
$ module load savu

To configure a process list

Code Block
$ savu_config -i <path to savu list>

To submit a job (requires ssh to Wilson)

Code Block
savu_mpi <raw data> <process list> <output dir>

DAWN

Code Block
$ module load dawn 
$ dawn32G
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titleDawn on DIAD

DAWN on DIAD

  • How to install dawn

  • DIAD example diffraction + imaging data

  • Cheat sheets

  • Videos?

  • Work out the main features that we use on DIAD:

    • Visualise the patterns

    • Visualise the 3d Volumes?

    • Slice/Re-slice direction

    • View sinograms

    • Apply filters

    • If anything takes more than 5 clicks - Jake to fix.

The following will load dawn in linux with access to 32GB of memory. 

Code Block
module load dawn 
dawn32G

image-20240628-125330.pngImage Modified

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titleSavu on DIAD

Load Savu:

  1. Open terminal

  2. Config the process list to make sure you are happy. BL scientist may do this for you.

  3. To submit savu jobs to the cluster use:

Code Block
ssh wilson
module load

...

 savu/4.2-slurm
savu_mpi <IN_FILE> <PROCESS_LIST> <OUT_FOLDER> -d <TMP_FOLDER> 

Edit process lists:

Code Block
module load savu
// Will load savu in cwd and allow you to create processlists. You cannot submit to cluster using this module. 
// This should be done in a normal terminal, do not ssh into wilson

savu_config - i xxxxx.nxs 
// Where "xxxx.nxs" is the path of your process list (ie. 3x_fd_vo_AST_tiff.nxs). 
// This command will open up the savu config with this process list. 
// You can omit -i xxxx.nxs to open config with an empty list. You will then need to populate savu with each process


disp -a
// This will display each process module and the parameters that you can change. 
// Use -avv for more detailed information.

fg /ctrl + z
// Will bring savu config to foreground / Send config to background to allow you to run savu_mpi in the same terminal window

add RemoveAllRings 2
// will add the module RemoveAllRings to position 2 in the process list. If no number is included it will add to the end.

rem 2
// will remove module at position 2 in the list

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