Set up PSDM software - Revision history

Aaron at 21:31, 6 November 2018

2018-11-06T21:31:37Z

← Older revision		Revision as of 21:31, 6 November 2018
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			THIS IS DEPRECATED. psana is now provided using conda. [https://exafel.github.io/docs/psana-cctbx-instal Directions].

	Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>></code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.		Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>></code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.

Aaron at 17:22, 28 May 2015

2015-05-28T17:22:45Z

← Older revision		Revision as of 17:22, 28 May 2015
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	== Prerequisites ==		== Prerequisites ==

	The [https://confluence.slac.stanford.edu/display/~~PCDS~~/~~Data~~+~~Management~~ Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''psana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.		The [https://confluence.slac.stanford.edu/display/PSDM/Software+Distribution Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''psana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.
	{\| class="wikitable sortable"		{\| class="wikitable sortable"
	\|-		\|-

Aaron at 09:30, 26 February 2015

2015-02-26T09:30:25Z

← Older revision		Revision as of 09:30, 26 February 2015
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	~~{{ mbox~~		Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>></code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.
	~~\| type = notice~~
	~~\| text =~~ Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>></code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.
	}}


	== Prerequisites ==		== Prerequisites ==

	The [https://confluence.slac.stanford.edu/display/PCDS/Data+Management Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''~~pyana~~'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.		The [https://confluence.slac.stanford.edu/display/PCDS/Data+Management Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''psana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.
	{\| class="wikitable sortable"		{\| class="wikitable sortable"
	\|-		\|-
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	== External links ==		== External links ==

	* [https://confluence.slac.stanford.edu/display/~~PCDS~~/~~Pyana~~+User+Manual ~~Pyana~~ User Manual]		* [https://confluence.slac.stanford.edu/display/PSDM/psana+-+User+Manual Psana User Manual]
	* [https://confluence.slac.stanford.edu/display/~~PCDS~~/~~Analysis+Workbook.+~~Packages+and+Releases ~~Analysis Workbook.~~ Packages and Releases]		* [https://confluence.slac.stanford.edu/display/PSDM/Packages+and+Releases Packages and Releases]

Hattne: Add NERSC to the table.

2014-03-03T21:09:03Z

Add NERSC to the table.

← Older revision		Revision as of 21:09, 3 March 2014
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	\| <code>/net/viper/raid1/psdm</code>		\| <code>/net/viper/raid1/psdm</code>
	\| Only available on viper.lbl.gov		\| Only available on viper.lbl.gov
			\|-
			\| NERSC
			\| <code>/global/project/projectdirs/lcls/psdm-carver</code>
			\| Only to be used on the carver system
	\|-		\|-
	\| SLAC		\| SLAC

Hattne: Updated link to PSDM installation instructions.

2014-02-28T23:44:01Z

Updated link to PSDM installation instructions.

← Older revision		Revision as of 23:44, 28 February 2014
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	\|		\|
	\|}		\|}
	The PSDM software distribution is supported on the most popular flavors of Linux and is installed at several sites worldwide. Separate installation and maintenance instructions are provided by the PSDM project at [https://confluence.slac.stanford.edu/display/~~PCDS~~/~~PSDM~~+~~software+distribution~~ PSDM software distribution]. The package can be installed anywhere on the filesystem, and it is generally possible to install it without superuser privileges.		The PSDM software distribution is supported on the most popular flavors of Linux and is installed at several sites worldwide. Separate installation and maintenance instructions are provided by the PSDM project at [https://confluence.slac.stanford.edu/display/PSDM/Software+Distribution PSDM software distribution]. The package can be installed anywhere on the filesystem, and it is generally possible to install it without superuser privileges.


	== Create a test release and an analysis package ==		== Create a test release and an analysis package ==

Hattne: Migrated note about prompt.

2014-02-07T09:43:41Z

Migrated note about prompt.

← Older revision		Revision as of 09:43, 7 February 2014
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			{{ mbox
			\| type = notice
			\| text = Note that throughout the instructions <code>$</code> denotes the prompt of any unprivileged user on the system. Certain shells may be configured to use <code>%</code> or <code>></code> for that purpose. The prompt should <em>not</em> be included in the commands typed to the shell.
			}}


	== Prerequisites ==		== Prerequisites ==

Hattne: Simplification.

2014-02-07T08:21:40Z

Simplification.

← Older revision		Revision as of 08:21, 7 February 2014
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	$ sit_setup		$ sit_setup
	$ newpkg <i>my_ana_pkg</i>		$ newpkg <i>my_ana_pkg</i>
	Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i> above, ~~as well as the location of the <i>myrelease</i> directory~~ are common, but nevertheless arbitrary, choices.		Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i> above, are common, but nevertheless arbitrary, choices.

	These steps only need to be performed once.		These steps only need to be performed once.


	== External links ==		== External links ==

Hattne: Cleanup

2014-02-07T08:18:55Z

Cleanup

← Older revision		Revision as of 08:18, 7 February 2014
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	== Prerequisites ==		== Prerequisites ==

	~~<!-- XXX What's PSDM? -->~~		The [https://confluence.slac.stanford.edu/display/PCDS/Data+Management Photon Science Data Management (PSDM)] software distribution must be installed. The PSDM software distribution provides ''pyana'', which is a critical dependency of ''cctbx.xfel''. Its installation root directory affects the absolute paths used in the following instructions and differs from site to site. Some common installation root directories are listed below.

	The ~~PSDM software distribution must be installed. PSDM provides installation and maintenance instructions at~~ [https://confluence.slac.stanford.edu/display/PCDS/~~PSDM+software~~+~~distribution~~ PSDM software distribution]. The ~~distribution can be installed anywhere on the filesystem; it is generally possible to install the~~ PSDM software distribution ~~without superuser privileges~~.

	~~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 root directory
	!class="unsortable"\| Notes		! class="unsortable"\| Notes
	\|-		\|-
	\| BNL		\| BNL
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	\|		\|
	\|}		\|}
			The PSDM software distribution is supported on the most popular flavors of Linux and is installed at several sites worldwide. Separate installation and maintenance instructions are provided by the PSDM project at [https://confluence.slac.stanford.edu/display/PCDS/PSDM+software+distribution PSDM software distribution]. The package can be installed anywhere on the filesystem, and it is generally possible to install it without superuser privileges.


	== Create a test release and an analysis package ==		== Create a test release and an analysis package ==

	~~In what follows it is assumed that the PSDM software distribution is installed at~~ <~~code~~>~~/reg/g/psdm</code>. Substitute <code>/reg/g/psdm~~</~~code~~> ~~with the appropriate path in the instructions below. These steps only need to be performed once.~~		A <i>test release</i>, which refers to a particular release of the PSDM distribution, 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 test releases and analysis packages are covered in [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Quick+Tour Analysis Workbook. Quick Tour]. To prepare the environment for using the PSDM software distribution, bash-users should source <code>ana_env.sh</code>,
			$ . <b><i>/path/to/psdm</i></b>/etc/ana_env.sh
	~~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]. ~~In a bash shell,~~ the environment ~~is prepared~~ for PSDM ~~using~~		where <code><b><i>/path/to/psdm</i></b></code> should be replaced with the path to the installation root directory. csh-users should source <code>ana_env.csh</code> instead,
	$ . /~~reg~~/g/psdm/etc/ana_env.sh		% source <b><i>/path/to/psdm</i></b>/etc/ana_env.csh
	~~For~~ csh, ~~the corresponding command is~~		Sourcing <code>ana_env.sh</code> or <code>ana_env.csh</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/psdm/etc/ana_env.csh		test -r <b><i>/path/to/psdm</i></b>/etc/ana_env.sh && . <b><i>/path/to/psdm</i></b>/etc/ana_env.sh
	Sourcing <code>ana_env.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/psdm/etc/ana_env.sh && . /~~reg~~/g/psdm/etc/ana_env.sh
	to <code>~/.bashrc</code>, or		to <code>~/.bashrc</code>, or
	test -r /~~reg~~/g/psdm/etc/ana_env.csh && source /~~reg~~/g/psdm/etc/ana_env.csh		test -r <b><i>/path/to/psdm</i></b>/etc/ana_env.csh && source <b><i>/path/to/psdm</i></b>/etc/ana_env.csh
	to <code>~/.cshrc</code> as appropriate.		to <code>~/.cshrc</code> as appropriate. This ensures the environment is properly prepared for non-interactive shells, <i>e.g.</i> the shells that are used to run jobs submitted to the cluster. To also be able to use the PSDM software from interactive shells, it is recommended that bash-users put
			test -r ~/.bashrc && . ~/.bashrc
	This ensures the environment is properly prepared for non-interactive shells, <i>e.g.</i> the shells that are used to run jobs submitted to the cluster. To also be able to use the PSDM software from interactive shells, it is recommended that bash-users put
	test -r ~~"${HOME}~~/.bashrc" && . ~~"${HOME}~~/.bashrc"
	near the top of <code>~/.bash_profile</code>. There is no need to edit any additional files for csh-users, because csh always reads <code>~/.cshrc</code>.		near the top of <code>~/.bash_profile</code>. There is no need to edit any additional files for csh-users, because csh always reads <code>~/.cshrc</code>.

	A test released based on the most current ~~LCLS software~~ is then set up in the current working directory using		A test released based on the most current PSDM distribution is then set up in the current working directory using
	$ newrel ana-current <i>myrelease</i>		$ newrel ana-current <i>myrelease</i>
	$ cd <i>myrelease</i>		$ cd <i>myrelease</i>
	$ sit_setup		$ sit_setup
	$ newpkg <i>my_ana_pkg</i>		$ newpkg <i>my_ana_pkg</i>
	Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i>, as well as the location of the <i>myrelease</i> directory are common, but nevertheless arbitrary, choices.		Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i> above, as well as the location of the <i>myrelease</i> directory are common, but nevertheless arbitrary, choices.

	~~== Keeping up to date with PSDM releases==~~

	~~<!-- XXX THIS IS NOT TO BE RUN UNTIL LATER -->~~

	Since the ''cctbx.xfel'' modules do not critically depend on any particular version of the PSDM software, it is generally possible to closely track the latest version of the PSDM distribution. To upgrade to the current PSDM release, do		These steps only need to be performed once.
	~~$ cd myrelease~~
	~~$ relupgrade ana-current~~
	~~If <code>relinfo</code> does not output <code>ana-current</code> after that, one can edit <code>~/myrelease/.sit_release</code> manually~~ to ~~that effect~~. ~~Then rebuild~~
	~~$ scons -c~~
	~~$ scons~~


	== External links ==		== External links ==

	* ~~More detailed manual:~~ [https://confluence.slac.stanford.edu/display/PCDS/Pyana+User+Manual Pyana User Manual]		* [https://confluence.slac.stanford.edu/display/PCDS/Pyana+User+Manual Pyana User Manual]
	* [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Packages+and+Releases Analysis Workbook. Packages and Releases]		* [https://confluence.slac.stanford.edu/display/PCDS/Analysis+Workbook.+Packages+and+Releases Analysis Workbook. Packages and Releases]

Hattne: Comments, thanks to mamin@.

2014-02-05T21:20:59Z

Comments, thanks to mamin@.

← Older revision		Revision as of 21:20, 5 February 2014
Line 51:		Line 51:

	== Keeping up to date with PSDM releases==		== Keeping up to date with PSDM releases==

			<!-- XXX THIS IS NOT TO BE RUN UNTIL LATER -->

	Since the ''cctbx.xfel'' modules do not critically depend on any particular version of the PSDM software, it is generally possible to closely track the latest version of the PSDM distribution. To upgrade to the current PSDM release, do		Since the ''cctbx.xfel'' modules do not critically depend on any particular version of the PSDM software, it is generally possible to closely track the latest version of the PSDM distribution. To upgrade to the current PSDM release, do

Hattne: Moved bash_profile code from cctbx.xfel setup page.

2014-02-05T18:43:43Z

Moved bash_profile code from cctbx.xfel setup page.

← Older revision		Revision as of 18:43, 5 February 2014
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	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]. In a bash shell, the environment is prepared for PSDM using		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]. In a bash shell, the environment is prepared for PSDM using
	$ . /reg/g/psdm/etc/ana_env.sh		$ . /reg/g/psdm/etc/ana_env.sh
	or		For csh, the corresponding command is
	% source /reg/g/psdm/etc/ana_env.csh		% source /reg/g/psdm/etc/ana_env.csh
	~~for a csh.~~ Sourcing <code>ana_env.sh</code> or <code>ana_env.csh</code> 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		Sourcing <code>ana_env.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/psdm/etc/ana_env.sh && . /reg/g/psdm/etc/ana_env.sh		test -r /reg/g/psdm/etc/ana_env.sh && . /reg/g/psdm/etc/ana_env.sh
	to <code>~/.bashrc</code>, or		to <code>~/.bashrc</code>, or
	test -r /reg/g/psdm/etc/ana_env.csh && source /reg/g/psdm/etc/ana_env.csh		test -r /reg/g/psdm/etc/ana_env.csh && source /reg/g/psdm/etc/ana_env.csh
	to <code>~/.cshrc</code> as appropriate. A test released based on the most current LCLS software is then set up in the current working directory using		to <code>~/.cshrc</code> as appropriate.
	~~<!-- $ cd -->~~
			This ensures the environment is properly prepared for non-interactive shells, <i>e.g.</i> the shells that are used to run jobs submitted to the cluster. To also be able to use the PSDM software from interactive shells, it is recommended that bash-users put
			test -r "${HOME}/.bashrc" && . "${HOME}/.bashrc"
			near the top of <code>~/.bash_profile</code>. There is no need to edit any additional files for csh-users, because csh always reads <code>~/.cshrc</code>.

			A test released based on the most current LCLS software is then set up in the current working directory using
	$ newrel ana-current <i>myrelease</i>		$ newrel ana-current <i>myrelease</i>
	$ cd <i>myrelease</i>		$ cd <i>myrelease</i>
	$ sit_setup		$ sit_setup
	$ newpkg <i>my_ana_pkg</i>		$ newpkg <i>my_ana_pkg</i>
	Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i>, are common, but nevertheless arbitrary, choices.		Note that the names for the test release and the analysis package, <i>myrelease</i> and <i>my_ana_pkg</i>, as well as the location of the <i>myrelease</i> directory are common, but nevertheless arbitrary, choices.

	== Keeping up to date with PSDM releases==		== Keeping up to date with PSDM releases==