Setup

cctbx.xfel is installed at SLAC for general use. Before it can be used, the following setup commands need to be run to configure the environment.

Run once

These steps need only be performed once before using cctbx.xfel.

LCLS release setup

cctbx.xfel extends a release of the LCLS analysis packages with a set of analysis modules. A test release, which refers to a particular release of the LCLS packages, is represented by a directory in the file system, often called analysis-rel or myrelease. An analysis package within the test release in turn refers to the files implementing the analysis modules of cctbx.xfel.

Installation of a "test release" and analysis packages is covered in Analysis Workbook. Quick Tour. Linking the cctbx.xfel analysis modules to the analysis package is described in Linking pyana to cctbx.xfel.

Configure cctbx.xfel

The simplest way to configure your environment to run cctbx.xfel is to run this command (bash(1) users):

. /reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.sh

csh(1) users should use this command:

source /reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.csh

To make these changes persistent, bash(1) users are encouraged to add these lines to ~/.bashrc

test -r "/reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.sh" && \
 . "/reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.sh"

csh(1) users should instead add these lines to ~/.cshrc

test -r "/reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.csh" && \
 source "/reg/d/ffb/cxi/temp/cctbx/cctbx-build/setpaths.csh"

Note: to avoid surprises when running cctbx.xfel from a non-interactive shell, it is recommended that bash(1) users edit ~/.bash_profile, and put this line near the top:

test -r "${HOME}/.bashrc" && . "${HOME}/.bashrc"

A job submitted to the cluster will typically run cctbx.xfel from a non-interactive shell.

Linking cctbx.xfel to pyana

Run these commands to associate pyana and cctbx.xfel:

$ cd ~/myrelease/my_ana_pkg
$ ln -s /reg/d/ffb/cxi/temp/cctbx/cctbx_project/xfel/cxi/cspad_ana src
$ cd ..
$ scons

The last step compiles the analysis modules just linked in.

Run each time on logging on to SLAC

Whenever you log on to a fresh shell at SLAC, before you can use any portion of cctbx.xfel that uses pyana, you must run these commands:

$ cd ~/myrelease
$ sit_setup

Test the installation

At SLAC, test that it is working by e.g.

$ cd ~/myrelease
$ cxi.pyana -c /reg/d/ffb/cxi/temp/cctbx/tutorials/setup/test.cfg /reg/d/ffb/cxi/temp/Feb2013calib/e290-r0069-s00-c00.xtc

This should start a viewer, displaying dark-subtracted averages from an XTC stream.