Using the pre-built cctbx at LCLS

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cctbx.xfel is installed for general use at LCLS on the S3DF cluster. To log into S3DF, either use the command line: 

 ssh -YAC <username>@s3dflogin.slac.stanford.edu
 ssh -YAC psana

Or use NoMachine, using the host s3dfnx.slac.stanford.edu.

Once logged in, source the setup.sh file provided: 

 source /sdf/group/lcls/ds/tools/cctbx/setup.sh

All DIALS and cctbx.xfel commands will be available.

This setup files does the following:

  • Set up psana by exporting environment variables needed to find the XTC streams with the X-ray crystallographic data
  • Sets `umask 002`, which propagates file permissions nicely when using group accounts
  • Sources the cctbx.xfel sources
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