Setup: Difference between revisions

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== Prerequisities ==
== Prerequisities ==


''cctbx.xfel'' must be installed, which in turn requires the PSDM software distribution to be set up.  See [[Set up PSDM software]] for the latter and [[Installation]] for the former.  ''cctbx.xfel'' can be installed anywhere on the filesystem where write access is granted.
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.
 
The installation root directory affects the absolute paths used in these instructions and differs from site to site.  Some common installation root directories are listed below.
{| class="wikitable sortable"
{| class="wikitable sortable"
|-
|-
! Site
! Site
!class="unsortable"| Installation root directory
!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 directory and the user's shell.
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 it is assumed that ''cctbx.xfel'' is installed at <code>/reg/g/cctbx/build</code>.  Substitute <code>/reg/g/cctbx/build</code> with the appropriate path in the instructions below.  These steps need only be performed once.
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
In a bash shell, the environment is prepared for ''cctbx.xfel'' using
From a csh, the corresponding command is
  $ . /reg/g/cctbx/build/setpaths.sh
  % source <b><i>/path/to/cctbx/build</i></b>/setpaths.csh
For csh, the corresponding command is
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 /reg/g/cctbx/build/setpaths.csh
  test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh && \
Sourcing <code>setpaths.sh</code> or <code>ana_env.csh</code> 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
   . <b><i>/reg/g/cctbx/build</i></b>/setpaths.sh
  test -r "/reg/g/cctbx/build/setpaths.sh" && \
   . "/reg/g/cctbx/build/setpaths.sh"
to <code>~/.bashrc</code>, or
to <code>~/.bashrc</code>, or
  test -r "/reg/g/cctbx/build/setpaths.csh" && \
  test -r <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh && \
   source "/reg/g/cctbx/build/setpaths.csh"
   source <b><i>/reg/g/cctbx/build</i></b>/setpaths.csh
to <code>~/.cshrc as appropriate</code>.
to <code>~/.cshrc</code> as appropriate.


 
To make the ''cctbx.xfel'' analysis modules available to PSDM's ''pyana'',
== Linking ''cctbx.xfel'' to ''pyana'' ==
  $ cd <b><i>/path/to/test/release</i></b>
 
Run these commands to associate ''pyana'' and ''cctbx.xfel'':
  $ cd ~/myrelease
  $ sit_setup
  $ sit_setup
  $ cd ~/myrelease/my_ana_pkg
  $ cd <b><i>my_ana_pkg</i></b>
  $ ln -fns /reg/g/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src
  $ ln -fns <b><i>/path/to/cctbx/sources</i></b>/cctbx_project/xfel/cxi/cspad_ana src
  $ cd ..
  $ cd ..
$ ln -s /reg/g/cctbx/sources/cctbx_project/xfel/cxi/lsf.sh .
  $ scons
  $ scons
The last step compiles the analysis modules just linked in.
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.


<!-- XXX Should check this with Andy or so; this can probably be done better.  Perhaps note that using -fns will zap any old src link in place. -->
<!--
 
 
== Setup your scratch area ==
 
<!-- XXX This should probably be moved out of the general installation instructions -->
Create a scratch folder and populate it with some directories that will be used during this tutorial, changing <username> to your SLAC account name:
 
$ cd /reg/g/cctbx/tutorials/scratch/
$ mkdir <username>
$ cd <username>
$ mkdir darks
$ mkdir averages
$ mkdir results
 
 
== 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 <i>e.g.</i>
At SLAC, test that it is working by <i>e.g.</i>
$ cd ~/myrelease
  $ 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.


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