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If you are on a psana machine, set up your environment by adding these lines to .bashrc (or your start up script):
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# PSANAPsocake (Run 18 or newer) source /reg/g/psdm/etc/psconda.sh -py3 # Psocake (Run 17 or older) source /reg/g/psdm/etc/psconda.sh # CrystFEL source /reg/g/cfel/crystfel/crystfel-dev/setup-sh # CCP4 (version may change) source /reg/common/package/ccp4-7.1/bin/ccp4.setup-sh # XDS export PATH=/reg/common/package/XDS-INTEL64_Linux_x86_64:$PATH |
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$ psocake -e cxitut13 -r 10 -d DscCsPad -n 11 -m sfx |
Note: GUI widgets may not respond properly when the GUI is first displayed. Clicking on the terminal window or resizing the GUI will fix this.
During the experiment, you have access to psfehhiprioq Fast Feedback System which allows you to run psocake from Fast Feedback (FFB) nodes. To do this, append -a ffb. Note that only psfehhiprioq psffb has access to the data on FFB:
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$ psocake -e cxitut13 -r 10 -d DscCsPad -n 11 -m sfx -a ffb |
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$ ls /reg/d/psdm/cxi/cxitut13 calib ftc hdf5 resresults scratch usr xtc |
calib: This is where all psana calibration is stored. Detector geometry, pedestals, gain, common mode constants, and bad pixelmap.
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scratch: This is where psocake saves all the files like .cxi and .stream. This directory is not backed up, so important files need to be move to /res.
results (or res): This is the results directory which is backed up on tape. After completing your analysis, your results/data should be moved here.
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$ bqueues | grep ps psnehhiprioq 117 Open:Active - - - - 0 0 0 0 psfehhiprioq 117 Open:Active - - - - 0 0 0 0 psnehprioq 116 Open:Active - - - - 0 0 0 0 psfehprioq 116 Open:Active - - - - 0 0 0 0 psnehq 115 Open:Active - - - - 0 0 0 0 psfehq 115 Open:Active - - - - 520 276 244 0 psdebugq 114 Open:Active - - - - 0 0 0 0 psanaq 112 Open:Active - - - - 7466 6612 854 0 psnehidleq 70 Open:Active - - - - 96 0 96 0 psfehidleq 70 Open:Active - - - - 104 0 0 104 psanaidleq 70 Open:Active - - - - 552 432 0 120 |
At the time of writing this documentation, psanaq is quite busy processing 7466 jobs. 6612 jobs are pending. 854 jobs are currently running. For more information on which queue you are allowed to use, see Batch System Analysis JobsNodes And Queues#BatchNodes
Click "Launch peak finder”. You can check the status of launched jobs by typing "bjobs" in your Terminal. This will display the job ID and the status amongst other information.
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