Using the pre-built cctbx at LCLS: Difference between revisions

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

@@ Line 1: / Line 1: @@
-''cctbx.xfel'' is installed for general use at LCLS.  To use it, source the setup.sh file provided:
+''cctbx.xfel'' is installed for general use at LCLS on the S3DF cluster.  To log into S3DF, either use the command line:
-<code>
+  ssh -YAC <username>@s3dflogin.slac.stanford.edu
-   source /reg/g/cctbx/conda_build/setup.sh
+   ssh -YAC psana
-</code>
-Alternatively, add these lines to your .bashrc file (bash users):
+Or use NoMachine, using the host <code>s3dfnx.slac.stanford.edu</code>.
-<code>
+Once logged in, source the setup.sh file provided:
-  source /reg/g/cctbx/conda_build/miniconda2/etc/profile.d/conda.sh
-  conda activate myEnv
-  source /reg/g/cctbx/conda_build/build/setpaths.sh
-</code>
-Likewise for csh users:
+  source /sdf/group/lcls/ds/tools/cctbx/setup.sh
-<code>
+All ''DIALS'' and ''cctbx.xfel'' commands will be available.
-  source /reg/g/cctbx/conda_build/miniconda2/etc/profile.d/conda.csh
-  conda activate myEnv
-  source /reg/g/cctbx/conda_build/build/setpaths.csh
-</code>
-Then log in as normal.  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
-/reg/g/cctbx was last updated Aug 9, 2019