Setup - Revision history

Aaron: /* Prerequisities */

2015-03-05T19:09:51Z

Prerequisities

← Older revision		Revision as of 19:09, 5 March 2015
Line 4:		Line 4:
	== Prerequisities ==		== Prerequisities ==

	''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.		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"
	\|-		\|-

Hattne: Add NERSC to the table.

2014-03-03T21:10:03Z

Add NERSC to the table.

← Older revision		Revision as of 21:10, 3 March 2014
Line 18:		Line 18:
	\|-		\|-
	\| CCI, LBNL		\| CCI, LBNL
			\|
			\|
			\| No central, shared installation available
			\|-
			\| NERSC
	\|		\|
	\|		\|
Line 28:		Line 33:
	\|}		\|}
	''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'' 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 ==

Hattne: Removed creating of ./lsf.sh symbolic link.

2014-02-11T00:37:01Z

Removed creating of ./lsf.sh symbolic link.

← Older revision		Revision as of 00:37, 11 February 2014
Line 51:		Line 51:
	$ ln -fns <b><i>/path/to/cctbx/sources</i></b>/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 <b><i>/path/to/cctbx/sources</i></b>/cctbx_project/xfel/cxi/lsf.sh .~~
	$ scons		$ scons
	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.		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.

Hattne: Cleanup.

2014-02-07T09:40:06Z

Cleanup.

← Older revision		Revision as of 09:40, 7 February 2014
Line 4:		Line 4:
	== 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~~.		''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.

	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
	\|-		\|-
	\| 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.


	~~== Linking~~ ''cctbx.xfel'' to '~~'pyana'' ==~~		To make the ''cctbx.xfel'' analysis modules available to PSDM's ''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 .		$ ln -s <b><i>/path/to/cctbx/sources</i></b>/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. -->~~		<!--


	~~== 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.

Hattne: Moved scratch-area setup to tutorial.

2014-02-05T18:52:05Z

Moved scratch-area setup to tutorial.

← Older revision		Revision as of 18:52, 5 February 2014
Line 59:		Line 59:

	<!-- 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. -->		<!-- 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~~

Hattne: Reorganized for consistency with PSDM setup

2014-02-05T18:42:55Z

Reorganized for consistency with PSDM setup

← Older revision		Revision as of 18:42, 5 February 2014
Line 1:		Line 1:
	''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.~~		<!-- XXX Should probably rename this page to "Set up ''cctbx.xfel''" or some such -->

	~~== One-time setup ==~~

	~~These steps need only be performed once before using ''cctbx.xfel''.~~		== Prerequisities ==

	~~=== LCLS quick start ===~~		''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.

	~~See [[Set up PSDM software]]~~. ~~Linking the~~ ''cctbx.xfel'' ~~analysis modules to the analysis package is described~~ in ~~[[#Linking cctbx.xfel to pyana\|Linking cctbx.xfel to pyana]]~~.		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"
			\|-
			! Site
			!class="unsortable"\| Installation root directory
			!class="unsortable"\| Notes
			\|-
			\| BNL
			\| <code>/usr/local/crys_test/cctbx</code>
			\|
			\|-
			\| CCI, LBNL
			\|
			\| No central installation available
			\|-
			\| SLAC
			\| <code>/reg/g/cctbx/sources</code>
			\|
			\|}
			Developers will generally have ''cctbx.xfel'' installed in their home directory.

	~~=== ''cctbx.xfel'' setup ===~~
	~~To start using an installation of ''cctbx.xfel'', the environment has to be configured. The details depend on the user's shell.~~

	~~<ul>~~		== ''cctbx.xfel'' setup ==
	~~<li>~~
	~~For a bash(1) shell, <code>setpaths.sh</code> should be sourced from the shell configuration files. To do that, add~~
	~~<pre>test -r "/reg/g/cctbx/build/setpaths.sh" && \~~
	~~. "/reg/g/cctbx/build/setpaths.sh"</pre>~~
	~~to <code>~/.bashrc</code>. This ensures the environment is properly prepared for non-interactive shells, ''e.g.'' the shells that are used to run jobs on the cluster. To also be able to use~~ ''cctbx.xfel'' ~~from interactive shells, ''e.g.'' the shell started after logging in to a host, it is recommended to put~~
	~~<pre>test -r "${HOME}/.bashrc" && . "${HOME}/.bashrc"</pre>~~
	near the top of <code>~/.bash_profile</code>. These changes will not take effect until a new shell is started. To start using the ''cctbx.xfel'' environment from the running shell, source <code>setpaths.sh</code> on the command line,
	~~<pre>. /reg/g/cctbx/build/setpaths.sh</pre>~~
	~~</li>~~

	~~<li>~~		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.
	~~csh(1)-users should instead source <code>setpaths~~.~~csh</code>~~. ~~Add~~		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.
	<~~pre~~>~~test -r "/reg/g/cctbx/build/setpaths.csh" && \~~
	~~source "~~/reg/g/cctbx/build~~/setpaths.csh"~~</~~pre>~~
	~~to <~~code>~/.~~cshrc~~</code>~~. There is no need to edit any additional files for interactive shells. To set up the environment for the running shell, execute~~
	~~<pre>source~~ /reg/g/cctbx/build~~/setpaths.csh~~</~~pre~~>
	on the ~~command line~~.
	~~</li>~~
	~~</ul>~~

	=== Linking ''cctbx.xfel'' to ''pyana'' ===		In a bash shell, the environment is prepared for ''cctbx.xfel'' using
			$ . /reg/g/cctbx/build/setpaths.sh
			For csh, the corresponding command is
			% source /reg/g/cctbx/build/setpaths.csh
			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
			test -r "/reg/g/cctbx/build/setpaths.sh" && \
			. "/reg/g/cctbx/build/setpaths.sh"
			to <code>~/.bashrc</code>, or
			test -r "/reg/g/cctbx/build/setpaths.csh" && \
			source "/reg/g/cctbx/build/setpaths.csh"
			to <code>~/.cshrc as appropriate</code>.


			== Linking ''cctbx.xfel'' to ''pyana'' ==

	Run these commands to associate ''pyana'' and ''cctbx.xfel'':		Run these commands to associate ''pyana'' and ''cctbx.xfel'':
Line 39:		Line 52:
	$ sit_setup		$ sit_setup
	$ cd ~/myrelease/my_ana_pkg		$ cd ~/myrelease/my_ana_pkg
	$ ln -s /reg/g/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src		$ ln -fns /reg/g/cctbx/sources/cctbx_project/xfel/cxi/cspad_ana src
	$ cd ..		$ cd ..
	$ ln -s /reg/g/cctbx/sources/cctbx_project/xfel/cxi/lsf.sh .		$ ln -s /reg/g/cctbx/sources/cctbx_project/xfel/cxi/lsf.sh .
Line 45:		Line 58:
	The last step compiles the analysis modules just linked in.		The last step compiles the analysis modules just linked in.

	~~=== Setup your scratch area ===~~		<!-- 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:		Create a scratch folder and populate it with some directories that will be used during this tutorial, changing <username> to your SLAC account name:

Line 55:		Line 72:
	$ mkdir averages		$ mkdir averages
	$ mkdir results		$ mkdir results


	== 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

	== Test the installation ==		== Test the installation ==
	At SLAC, test that it is working by e.g.		At SLAC, test that it is working by <i>e.g.</i>
	$ cd ~/myrelease		$ 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 (-c) 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.

Hattne: Link to separate page for PSDM setup.

2014-02-03T23:11:24Z

Link to separate page for PSDM setup.

@@ Line 7: / Line 7: @@
 === LCLS quick start ===
-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 the package. Details about installing of a test release and analysis packages are covered in [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Quick+Tour Analysis Workbook.  Quick Tour].  Assuming the LCLS software is installed at <code>/reg/d/psdm</code>, the LCLS environment is prepared in a bash(1) shell using
+See [[Set up PSDM software]].  Linking the ''cctbx.xfel'' analysis modules to the analysis package is described in [[#Linking cctbx.xfel to pyana|Linking cctbx.xfel to pyana]].
 === ''cctbx.xfel'' setup ===

Hattne: Bug fix for csh

2014-02-03T23:05:42Z

Bug fix for csh

← Older revision		Revision as of 23:05, 3 February 2014
Line 21:		Line 21:
	to <code>~/.bashrc</code>, or		to <code>~/.bashrc</code>, or
	<pre>		<pre>
	test -r /reg/g/psdm/etc/ana_env.csh && . /reg/g/psdm/etc/ana_env.csh		test -r /reg/g/psdm/etc/ana_env.csh && source /reg/g/psdm/etc/ana_env.csh
	</pre>		</pre>
	to <code>~/.cshrc</code> as appropriate. A test released based on the most current LCLS software is then set up using		to <code>~/.cshrc</code> as appropriate. A test released based on the most current LCLS software is then set up using

Aaron: /* Linking cctbx.xfel to pyana */

2014-01-26T09:57:19Z

Linking cctbx.xfel to pyana

@@ Line 66: / Line 66: @@
   $ scons
 The last step compiles the analysis modules just linked in.
 == Run each time on logging on to SLAC ==

Aaron: /* Test the installation */

2014-01-26T08:57:36Z

Test the installation

← Older revision		Revision as of 08:57, 26 January 2014
Line 76:		Line 76:
	At SLAC, test that it is working by e.g.		At SLAC, test that it is working by e.g.
	$ cd ~/myrelease		$ cd ~/myrelease
	$ cxi.pyana -c /reg/~~d/ffb/cxi/temp~~/cctbx/tutorials/setup/test.cfg /reg/d/~~ffb~~/cxi/~~temp~~/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. ~~There will be~~ a ~~delay as~~ misses ~~in the stream are displayed first before~~ hits.		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 (-c) and an XTC file. For more information, see the [[Overview]] and other tutorial pages.		More specifically, this command starts pyana with a configuration file (-c) and an XTC file. For more information, see the [[Overview]] and other tutorial pages.