Setup: Difference between revisions
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== Prerequisities == | == Prerequisities == | ||
''cctbx.xfel'' | 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. | ||
{| class="wikitable sortable" | {| class="wikitable sortable" | ||
|- | |- | ||
! Site | ! Site | ||
!class="unsortable"| Installation | !class="unsortable"| Installation build directory | ||
!class="unsortable"| Installation source directory | |||
!class="unsortable"| Notes | !class="unsortable"| Notes | ||
|- | |- | ||
| BNL | | BNL | ||
| <code>/usr/local/crys_test/cctbx/cctbx_build</code> | |||
| <code>/usr/local/crys_test/cctbx</code> | | <code>/usr/local/crys_test/cctbx</code> | ||
| | | | ||
Line 19: | Line 19: | ||
| CCI, LBNL | | CCI, LBNL | ||
| | | | ||
| No central installation available | | | ||
| No central, shared installation available | |||
|- | |||
| NERSC | |||
| | |||
| | |||
| No central, shared installation available | |||
|- | |- | ||
| SLAC | | SLAC | ||
| <code>/reg/g/cctbx/build</code> | |||
| <code>/reg/g/cctbx/sources</code> | | <code>/reg/g/cctbx/sources</code> | ||
| | | | ||
|} | |} | ||
Developers will generally have ''cctbx.xfel'' installed in their home directory. | ''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]]. | ||
== ''cctbx.xfel'' setup == | == ''cctbx.xfel'' setup == | ||
To start using ''cctbx.xfel'', the environment has to be configured. The details depend on the ''cctbx.xfel'' installation root | 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 | 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 | ||
$ . <b><i>/path/to/cctbx/build</i></b>/setpaths.sh | |||
From a csh, the corresponding command is | |||
$ . / | % source <b><i>/path/to/cctbx/build</i></b>/setpaths.csh | ||
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 | |||
% source / | test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh && \ | ||
Sourcing <code>setpaths | . <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh | ||
test -r | |||
. | |||
to <code>~/.bashrc</code>, or | to <code>~/.bashrc</code>, or | ||
test -r | test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh && \ | ||
source | source <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh | ||
to <code>~/.cshrc | to <code>~/.cshrc</code> as appropriate. | ||
To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'', | |||
$ cd <b><i>/path/to/test/release</i></b> | |||
$ cd | |||
$ sit_setup | $ sit_setup | ||
$ cd | $ cd <b><i>my_ana_pkg</i></b> | ||
$ ln -fns / | $ ln -fns <b><i>/path/to/cctbx/sources</i></b>/cctbx_project/xfel/cxi/cspad_ana src | ||
$ cd .. | $ cd .. | ||
$ scons | $ scons | ||
The last step compiles the analysis modules | 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. | ||
<!-- | |||
At SLAC, test that it is working by <i>e.g.</i> | At SLAC, test that it is working by <i>e.g.</i> | ||
$ cxi.pyana -c /reg/g/cctbx/tutorials/setup/test.cfg /reg/d/ana11/cxi/data/Mar2013calib/xtc/e236-r0004-s00-c00.xtc | $ cxi.pyana -c /reg/g/cctbx/tutorials/setup/test.cfg /reg/d/ana11/cxi/data/Mar2013calib/xtc/e236-r0004-s00-c00.xtc | ||
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. | 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. | ||
--> | |||
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. |
Latest revision as of 19:09, 5 March 2015
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.