Setup: Difference between revisions
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These steps need only be performed once before using ''cctbx.xfel''. | 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 <code>analysis-rel</code> or <code>myrelease</code>. 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 [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Quick+Tour Analysis Workbook. Quick Tour]. Linking the ''cctbx.xfel'' analysis modules to the analysis package is described in [[#Linking ''pyana'' to ''cctbx.xfel''|''Linking pyana to cctbx.xfel'']]. | |||
=== Configure ''cctbx.xfel'' === | === Configure ''cctbx.xfel'' === | ||
Revision as of 02:10, 27 September 2013
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 pyana to cctbx.xfel
Run these commands to associate pyana and cctbx.xfel together:
$ cd ~/myrelease/my_ana_pkg $ ln -s /reg/d/ffb/cxi/temp/cctbx/cctbx_project/xfel/cxi/cspad_ana src $ cd .. $ scons
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.