Set up PSDM software: Difference between revisions

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m (Migrate comments from google document.)
(Removed most of the XXX:s.)
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<!-- XXX Prerequisites: PSDM must be installed, and it is assumed that it is properly maintained XXX On viper these paths are all wrong XXX What's PSDM?  That should either be explained here (an everybody would see it) or in the PSDM installation instructions (but then only those actually needing to install it would see it).  -->
== Prerequisites ==


<!-- XXX BELOW NEEDS SOME WORK, headings, etc -->
<!-- XXX What's PSDM? -->
If you are installing somewhere other than SLAC, follow [https://confluence.slac.stanford.edu/display/PCDS/PSDM+software+distribution these instructions] to install SLAC's PSDM suite.
<!-- XXX ABOVE NEEDS SOME WORK, headings, etc -->


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
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"
|-
! Site
!class="unsortable"| Installation root directory
!class="unsortable"| Notes
|-
| CCI, LBNL
| <code>/net/viper/raid1/psdm</code>
| Only available on viper.lbl.gov
|-
| SLAC
| <code>/reg/g/psdm</code>
|
|}
 
 
== Create a test release and 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.
 
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].  The PSDM environment is prepared in a bash(1) shell using
  $ . /reg/g/psdm/etc/ana_env.sh
  $ . /reg/g/psdm/etc/ana_env.sh
or
or
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  $ sit_setup
  $ sit_setup
  $ newpkg <i>my_ana_pkg</i>
  $ newpkg <i>my_ana_pkg</i>
<!-- XXX Should note that these names are pretty arbitrary -->
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.


<!-- XXX MAYBE HERE, MAYBE ELSEWHERE: Keeping up to date:


To upgrade to a new release, do
== Keeping up to date with PSDM releases==
psana$ relupgrade release
Where release is any valid release name under $SIT_RELDIR. Since the PHENIX modules do not critically depend on any particular version of pyana, it is possible to track ana-current, i. e.
psana$ relupgrade ana-current
If relinfo doesn’t say ana-current after that, one can edit myrelease/.sit_release manually to that effect. After an upgrade, any non-PHENIX user modules may need to upgraded, by removing their corresponding directories and re-installing them using addpkg as above (and remember to port any changes into the new module). Then rebuild
psana$ scons -c
psana$ scons


-->
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
$ 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




Revision as of 12:24, 5 February 2014

Prerequisites

The PSDM software distribution must be installed. PSDM provides installation and maintenance instructions at 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.

Site Installation root directory Notes
CCI, LBNL /net/viper/raid1/psdm Only available on viper.lbl.gov
SLAC /reg/g/psdm


Create a test release and analysis package

In what follows it is assumed that the PSDM software distribution is installed at /reg/g/psdm. Substitute /reg/g/psdm with the appropriate path in the instructions below.

A test release, which refers to a particular release of the LCLS packages, is represented by a directory in the file system, often called analysis-rel or myrelease. 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 Analysis Workbook. Quick Tour. The PSDM environment is prepared in a bash(1) shell using 

$ . /reg/g/psdm/etc/ana_env.sh

or 

% source /reg/g/psdm/etc/ana_env.csh

for a csh(1). Sourcing ana_env.sh or ana_env.csh 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 ~/.bashrc, or 

test -r /reg/g/psdm/etc/ana_env.csh && source /reg/g/psdm/etc/ana_env.csh

to ~/.cshrc as appropriate. A test released based on the most current LCLS software is then set up in the current working directory using 

$ newrel ana-current myrelease
$ cd myrelease
$ sit_setup
$ newpkg my_ana_pkg

Note that the names for the test release and the analysis package, myrelease and my_ana_pkg, are common, but nevertheless arbitrary, choices.


Keeping up to date with PSDM releases

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 

$ cd myrelease
$ relupgrade ana-current

If relinfo does not output ana-current after that, one can edit ~/myrelease/.sit_release manually to that effect. Then rebuild 

$ scons -c
$ scons


External links

Retrieved from "http://viper.lbl.gov:8080/cctbx.xfel/index.php?title=Set_up_PSDM_software&oldid=335"