Using the pre-built cctbx at LCLS: Difference between revisions
Jump to navigation
Jump to search
(Created page with "''cctbx.xfel'' is installed for general use at LCLS. To use it, add these lines to your .bashrc file (bash users): <code> source /reg/g/cctbx/conda_build/miniconda2/etc/pr...") |
No edit summary |
||
| (2 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
''cctbx.xfel'' is installed for general use at LCLS. To use | ''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 <code>s3dfnx.slac.stanford.edu</code>. | |||
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 | |||
Latest revision as of 21:42, 18 August 2026
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