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| − | <!-- XXX Should probably rename this page to "Set up ''cctbx.xfel''" or some such -->
| + | Cctbx.xfel is installed at SLAC for general use. Before it can be used, the following setup commands need be run to configure the environment. |
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| − | == Prerequisities ==
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| − | ''cctbx.xfel'' must be [[Installation | installed]] before it can be used. The installation root directories affect the absolute paths used in the following instructions and differ from site to site. Some common installation root directories are listed below.
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| − | {| class="wikitable sortable"
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| − | |-
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| − | ! Site
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| − | !class="unsortable"| Installation build directory
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| − | !class="unsortable"| Installation source directory
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| − | !class="unsortable"| Notes
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| − | | BNL
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| − | | <code>/usr/local/crys_test/cctbx/cctbx_build</code>
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| − | | <code>/usr/local/crys_test/cctbx</code>
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| − | |-
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| − | | CCI, LBNL
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| − | | No central, shared installation available
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| − | |-
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| − | | NERSC
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| − | | No central, shared installation available
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| − | |-
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| − | | SLAC
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| − | | <code>/reg/g/cctbx/build</code>
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| − | | <code>/reg/g/cctbx/sources</code>
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| − | |}
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| − | ''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 [[Set up PSDM software | prepared for the PSDM software distribution]].
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| − | == ''cctbx.xfel'' setup ==
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| − | 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.
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| − | In what follows <code><b><i>/path/to/cctbx/build</i></b></code> and <code><b><i>/path/to/cctbx/sources</i></b></code> 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
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| − | $ . <b><i>/path/to/cctbx/build</i></b>/setpaths.sh
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| − | From a csh, the corresponding command is
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| − | % source <b><i>/path/to/cctbx/build</i></b>/setpaths.csh
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| − | Sourcing <code>setpaths</code> only modifies the environment of the <em>current shell</em>, and would have to be repeated every time a new shell is started. To make the changes persistent, add
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| − | test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh && \
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| − | . <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh
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| − | to <code>~/.bashrc</code>, or
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| − | test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh && \
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| − | source <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh
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| − | to <code>~/.cshrc</code> as appropriate.
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| − | To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'',
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| − | $ cd <b><i>/path/to/test/release</i></b>
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| − | $ sit_setup
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| − | $ cd <b><i>my_ana_pkg</i></b>
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| − | $ ln -fns <b><i>/path/to/cctbx/sources</i></b>/cctbx_project/xfel/cxi/cspad_ana src
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| − | $ cd ..
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| − | $ scons
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| − | where <code><b><i>/path/to/test/release</i></b></code> and <code><b><i>my_ana_pkg</i></b></code> are the path to the test release and the name of the analysis package chosen while [[Set up PSDM software | setting up the PSDM software distribution]]. The last step compiles the ''cctbx.xfel'' analysis modules. These steps need only be performed once.
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| − | <!--
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| − | At SLAC, test that it is working by <i>e.g.</i>
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| − | $ cxi.pyana -c /reg/g/cctbx/tutorials/setup/test.cfg /reg/d/ana11/cxi/data/Mar2013calib/xtc/e236-r0004-s00-c00.xtc
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| − | This should start a viewer, displaying dark-subtracted averages from an XTC stream. Press the green run button to see the images. This particular stream has a series of misses at its beginning; hits will appear presently. More specifically, this command starts ''pyana'' with a configuration file (<code>-c</code>) and an XTC file. For more information, see the [[Overview]] and other tutorial pages.
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Cctbx.xfel is installed at SLAC for general use. Before it can be used, the following setup commands need be run to configure the environment.
