Difference between revisions of "Setup"
| Line 3: | Line 3: | ||
== Run once == | == Run once == | ||
| − | <u>Configure pyana</u> | + | <u>Configure ''pyana''</u> |
| − | Configuration files for pyana and cctbx.xfel are generally placed in a | + | Configuration files for ''pyana'' and ''cctbx.xfel'' are generally placed in a directory in your home account named ~/myrelease or ~/analisys-rel. Follow [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Quick+Tour these instructions from SLAC] to configure ''pyana''. |
| − | <u>Configure cctbx.xfel</u> | + | <u>Configure ''cctbx.xfel''</u> |
| − | The simplest way to configure your environment to run cctbx.xfel is to run this command (bash(1) users): | + | 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 | . /reg/d/ffb/cxi/temp/cctbx/cctbx_build/setpaths.sh | ||
| Line 25: | Line 25: | ||
source "/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: | + | 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" | test -r "${HOME}/.bashrc" && . "${HOME}/.bashrc" | ||
| − | A job submitted to the cluster will typically run cctbx.xfel from a non-interactive shell. | + | A job submitted to the cluster will typically run ''cctbx.xfel'' from a non-interactive shell. |
| − | <u>Linking pyana to cctbx.xfel</u> | + | <u>Linking ''pyana'' to ''cctbx.xfel''</u> |
| − | Run these commands to associate pyana and cctbx.xfel together: | + | Run these commands to associate ''pyana'' and ''cctbx.xfel'' together: |
$ cd ~/myrelease/my_ana_pkg | $ cd ~/myrelease/my_ana_pkg | ||
$ ln -s /reg/d/ffb/cxi/temp/cctbx/cctbx_project/xfel/cxi/cspad_ana src | $ ln -s /reg/d/ffb/cxi/temp/cctbx/cctbx_project/xfel/cxi/cspad_ana src | ||
| Line 39: | Line 39: | ||
== Run each time on logging on to SLAC == | == 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: | + | 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 | $ cd ~/myrelease | ||
$ sit_setup | $ sit_setup | ||
Revision as of 22:50, 25 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
Configure pyana
Configuration files for pyana and cctbx.xfel are generally placed in a directory in your home account named ~/myrelease or ~/analisys-rel. Follow these instructions from SLAC to configure pyana.
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/setpaths.sh" && \ . "/reg/d/ffb/cxi/temp/cctbx/setpaths.sh"
csh(1) users should instead add these lines to ~/.cshrc
test -r "/reg/d/ffb/cxi/temp/cctbx/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
