Setup

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Prerequisities

The installation root directories of cctbx.xfel affect the absolute paths used in the following instructions and differ from site to site. Some common installation root directories are listed below.

Site Installation build directory Installation source directory Notes
BNL /usr/local/crys_test/cctbx/cctbx_build /usr/local/crys_test/cctbx
CCI, LBNL No central, shared installation available
NERSC No central, shared installation available
SLAC /reg/g/cctbx/build /reg/g/cctbx/sources

cctbx.xfel can be installed anywhere on the filesystem where write access is granted. Developers will generally have cctbx.xfel installed in their home directory. Even if cctbx.xfel is already installed, the environment must first be prepared for the PSDM software distribution.

cctbx.xfel setup

To start using cctbx.xfel, the environment has to be configured. The details depend on the cctbx.xfel installation root directories and the user's shell. In what follows /path/to/cctbx/build and /path/to/cctbx/sources should be replaced with the actual build and source directories of the cctbx.xfel installation. bash-users can prepare the environment for cctbx.xfel using

$ . /path/to/cctbx/build/setpaths.sh

From a csh, the corresponding command is

% source /path/to/cctbx/build/setpaths.csh

Sourcing setpaths only modifies the environment of the current shell, and would have to be repeated every time a new shell is started. To make the changes persistent, add

test -r /reg/g/cctbx/build/setpaths.sh && \
  . /reg/g/cctbx/build/setpaths.sh

to ~/.bashrc, or

test -r /reg/g/cctbx/build/setpaths.csh && \
  source /reg/g/cctbx/build/setpaths.csh

to ~/.cshrc as appropriate.

To make the cctbx.xfel analysis modules available to PSDM's pyana,

$ cd /path/to/test/release
$ sit_setup
$ cd my_ana_pkg
$ ln -fns /path/to/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src
$ cd ..
$ scons

where /path/to/test/release and my_ana_pkg are the path to the test release and the name of the analysis package chosen while setting up the PSDM software distribution. The last step compiles the cctbx.xfel analysis modules. These steps need only be performed once.