PulsarAstronomy.net
The Pulsar Astronomy Network

people/

projects/

tex/

login/

The login/ directory contains the login scripts, and the various environment variables that are used for pulsar work at ATNF. The login scripts are owned by the psrmgr user account and should not be modified without extreme care.

There are also “user defined” login scripts located in login/extra/. These have the form [name].cshrc where [name] is the name that is used to add this script to the PSR_EXTRA variable used by the pulsar login script. This can be used to create optional login variables for non-standard software or pipelines.

people

This is a location that users may use to store their own files. Create a subdirectory of people/ with your username, so that your files can be easily identified. Please do not fill this area with large files!

projects

This area is similar to people/ however it is for projects (e.g. ppta, fermi timing etc) to store shared files. Folders can only be created here by psrmgr.

tex

This is the “standard” tex/ directory, containing papers, drafts, bibtex files (including psrrefs), etc.

dev/$LOGIN_ARCH contains “dev” binaries, libraries, headers, etc. This is the $PREFIX for “dev” software, and so there should exist, at a minimum, a dev/$LOGIN_ARCH/bin path.

If you have loaded the pulsar login script, then you will also find this disk located at $PSRHOME. All paths in this guide should be considered to be relative to $PSRHOME unless otherwise stated.

The pulsar login script also defines a new value for $LOGIN_ARCH which is a combination of the debian “codename” of the OS and the machine architecture (as returned by `uname -m`). Currently (as of May 2011) there are three supported architectures: etch_i686, lenny_i686 and lenny_x64_86. Thus, paths such as $PSRHOME/linux/bin are replaced by paths such as $PSRHOME/dist/etch_i686/bin. The full details of this are discussed below.

For a guide on how to load the ATNF pulsar group shared software into your environment, see ATNFPulsarLogin.

Layout of /psr

The disk normally called “/psr” is mounted at /pulsar/psr, though on some machines there is a symlink from /psr to /pulsar/psr. It is best to always assume that the disk will be at /pusar/psr however, as this will work on any computer, rather than just those specifically with the /psr symlink.

If you have loaded the ATNFPulsarLogin, then you will also find this disk located at $PSRHOME. All paths in this guide should be considered to be relative to $PSRHOME unless otherwise stated.

The ATNFPulsarLogin also defines a new value for $LOGIN_ARCH which is a combination of the debian “codename” of the OS and the machine architecture (as returned by `uname -m`). Currently (as of May 2011) there are three supported architectures: etch_i686, lenny_i686 and lenny_x64_86. Thus, paths such as $PSRHOME/linux/bin are replaced by paths such as $PSRHOME/dist/etch_i686/bin. The full details of this are discussed below.

$PSRHOME has the following subdirectories:

dev
dist
login
people
projects
tex

These will be discussed below

dev/

The dev/ path contains developmental software. This includes: source code currently under development, “untested” or “unsupported” software, “customised” versions of standard software or simply software that is not commonly used enough to be in the main distribution.

dev/ contains the following primary subdirectories

dev/cvshome
dev/cvsroot
dev/$LOGIN_ARCH

the dev/cvshome and dev/cvsroot are the pulsar group local CVS repositories. This mainly contains archival software, however there are a number of important files stored in here, such as the catalogue files for psrcat.

@dev/$LOGIN_ARCH contains “dev” binaries, libraries, headers, etc. This is the $PREFIX for “dev” software, and so there should exist, at a minimum, a dev/$LOGIN_ARCH/bin@@ path.

dist/

The dist/ path contains the “distribution” install of software. This code can only be updated by the “psrmgr” unix account to prevent accidental overwriting of files with “make install”. All users of the “psrmgr” account are expected to take care to avoid installing “broken” code in this location. Trials of these packages can be installed in dev/ to first check that they are working.

The dist/ path has the following subdirectories:

dist/src
dist/share
dist/$LOGIN_ARCH

As with dev/, the software is installed with the $PREFIX set to dist/$LOGIN_ARCH, and so there will exist dist/$LOGIN_ARCH/bin, dist/$LOGIN_ARCH/lib, dist/$LOGIN_ARCH/include, etc.

The dist/src path contains the source code that is installed in dist/$LOGIN_ARCH. This code is all checked out via anonymous CVS (or similar) so that they can be updated by any psrmgr user. Code that is built here is expected to be build for all supported architectures. This means that currently any update here requires building on each of the three “buildhosts”.

Software, or files, which are not architecture specific (e.g. locations pointed to by $TEMPO2, $PSRCAT_RUNDIR or python/java/etc codes) are stored in dist/share.

ATNF Pulsar Group Software

Many external users may need to use the ATNF pulsar software, so this is a guide as to the software installed and the way that it is laid out.

For a guide on how to load the ATNF pulsar group shared software into your environment, see ATNFPulsarLogin.

tcsh/csh users

bash users

If you are one of the very few users who use bash as their default shell, you can load (in your .bashrc) the bash login script:

e.g.

export PSR_EXTRA=“ppta java-1.6”
. /pulsar/psr/login/psr.bashrc

Note that bash is not yet supported by the ATNF computer group, so you are somewhat on your own here for now!

If you have not customised your .cshrc or .login files, you may find it useful to simply copy over the example files.

cp -i ~/.cshrc ~/.cshrc.bak
cp -i ~/.login ~/.login.bak
cp -i /u/psrmgr/psr.cshrc ~/.cshrc
cp -i /u/psrmgr/psr.login ~/.login

Otherwise, you can continue through these steps to modify your login file by hand.

Step 0: Backup your existing .login/.cshrc files.

Make a backup! If you break your login, you will want to be able to go back to an old verison.

setenv PSR_EXTRA ″

You may wish to change the value of PSR_EXTRA to load any additional login scripts. Note that these “extra” scripts are not as carefully checked as the main login script, and so may have errors that cause issues when you login, or load software that is not supported on all architectures.

PSR_EXTRA options are delimited by spaces. For example,

PSR_EXTRA=“ppta java-1.6”

would load the login script to define the ppta pipeline variables, and also the login script that uses enables java 1.6, and some of the pulsar java software that requires this.

Step 4: Test your new environment

Log out, and log in

ATNF Pulsar Software

This page describes how to set up your ATNF user account to take advantage of the pulsar group software.

The login scripts themselves are stored in /pulsar/psr/login/psr.cshrc (or /pulsar/psr/login/psr.bashrc if you are using bash).

tcsh/csh

Most users will use tcsh as their login shell, so should follow this guide.

You will want to load the pulsar group login script in your ~/.login and ~/.cshrc file. Because of the way the ATNF login system works, you will need to modify both the .login and .cshrc file.

Step 1: Remove any reference to the old login script

The old login script ($PSRHOME/csh_script/PSR.cshrc) is deprecated, and will be disabled after 24th May 2011. Edit your ~/.login and ~/.cshrc files and remove any references to this old login script.

Step 2: Add the login script to your .login file.

You will want to source the pulsar login script towards the end of your ~/.login file. This must be done after the ATNF scripts are loaded. Typically this would be in the section labelled:

#-----------------------------------------------------------------------------
# Personalized login processing. 
#-----------------------------------------------------------------------------

Then add the following to the login script:

# load the pulsar login scripts!
if ( -e /pulsar/psr/login/psr.cshrc ) then
   source /pulsar/psr/login/psr.cshrc
endif

Step 3: Add the login script to your .cshrc file.

The ~/.login file is only called when you log in to a machine, however when you e.g. start a new terminal, this is not loaded. We must therefore also load this in the .cshrc file. We cannot load it only in the .cshrc file, since the .login file is loaded after the .cshrc file (if it is going to be called) and the ATNF login scripts overwrite many of the variables set by the pulsar login script. We can check if the .login file will be called, and load the pulsar login script in .cshrc if we know that the .login file will not be called. In the section labeled

#-----------------------------------------------------------------------------
# Personalized cshrc processing.
#-----------------------------------------------------------------------------

Add the following to your .cshrc file:

setenv PSR_EXTRA “java-1.6”
# Load the pulsar login scripts
if ( ! $?loginsh ) then
# Only load it here if we are not going to call .login later
# If we call .login then we load it from there
       if ( -e /pulsar/psr/login/psr.cshrc ) then
               source /pulsar/psr/login/psr.cshrc
       endif
endif