Set up PSDM software

Prerequisites

The 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.

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

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 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

A test release, which refers to a particular release of the PSDM distribution, 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 test releases and analysis packages are covered in Analysis Workbook. Quick Tour. To prepare the environment for using the PSDM software distribution, bash-users should source ana_env.sh,

$ . /path/to/psdm/etc/ana_env.sh

where /path/to/psdm should be replaced with the path to the installation root directory. csh-users should source ana_env.csh instead,

% source /path/to/psdm/etc/ana_env.csh

Sourcing ana_env.sh or ana_env.csh 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 /path/to/psdm/etc/ana_env.sh && . /path/to/psdm/etc/ana_env.sh

to ~/.bashrc, or

test -r /path/to/psdm/etc/ana_env.csh && source /path/to/psdm/etc/ana_env.csh

to ~/.cshrc as appropriate. This ensures the environment is properly prepared for non-interactive shells, e.g. 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

near the top of ~/.bash_profile. There is no need to edit any additional files for csh-users, because csh always reads ~/.cshrc.

A test released based on the most current PSDM distribution 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 above, as well as the location of the myrelease directory are common, but nevertheless arbitrary, choices.

These steps only need to be performed once.

External links

• Pyana User Manual
• Analysis Workbook. Packages and Releases