Starlink Software Collection - Download and Install 2018A

2018A release notes

Two main distributions of the 2018A release of the Starlink Software Collection are available, built on CentOS 6 and on OSX:

• Linux (64-bit, CentOS 6) (955 MB .tar.gz, MD5 sum: 681e5311a1fb7b32329a6c183612d640)

• OS X (64-bit, Intel) (743 MB .tar.gz, MD5 sum: 48364514da90db4853173738362ff119)

To check the MD5 checksum of your downloaded file, run either the md5sum, md5, or md5deep command, depending on which you have installed.

If you downloaded the OSX release before July 20th 2018 there was a bug in the cfitsio library that prevented FITS files from being read -- you won't be able to run convert's 'ndf2fits' or 'fits2ndf' commands. You can either redownload the repo, or if you have 'otool' and 'install-name-tool' on your machine you can download the bash script from patch1, set the $STARLINK_DIR variable at the top of the script correctly and then fix your installation.

The above CentOS 6 Linux distribution is built on glibc 2.12. Older versions of glibc might not work and are currently not supported. To check your glibc version, type "rpm -qi glibc" on RedHat-related distributions.

This Mac OS X software was built on Yosemite, but is believed to run on all versions from Snow Leopard onwards. Please note that the East Asian Observatory does not, however, have access to versions of OS X prior to Yosemite for testing or bug fixing.

We also have two new experimental builds, built on CentOS 7 and on Ubuntu 17.10. We do not run these systems routinely at EAO so these builds have had less testing than our CentOS 6 and OSX builds:

• CentOS 7 (64-bit, CentOS 7 Linux) (984 MB .tar.gz, MD5 sum: 11a2446bb238a52aa17cf0427dfb1efe)

• Ubuntu 17.10 (64-bit, Ubuntu 17.10 Linux) (1.1 GB .tar.gz, MD5 sum: 241dd79e28c5d5fb2f670a611cd96ee5)

Information on some of the most important libraries and their versions on each Linux build system:

Parties interested in releases for other platforms can email <scicom AT SPAMFREE eao DOT hawaii DOT edu>. Please note that the East Asian Observatory primarily runs CentOS 6 Linux operationally, so all other builds are on a best-efforts basis and may not be as thoroughly tested.

Installation instructions

Linux (all builds)

The tar file will unzip into a star-2018A/ directory in the directory where you downloaded the tar file. This release can be placed anywhere. When using the software, set the STARLINK_DIR environment variable to the location of the star-2018A/ directory, i.e. if you had unzipped it into a /home/person/software directory, then the STARLINK_DIR environment variable would be set to /home/person/software/star-2018A.

The CentOS6 release requires glibc 2.12 and fairly recent versions of the X11 libraries. Up-to-date CentOS and older Fedora Core 6 are distributions that are known to work. We welcome reports of successful installation on other distributions. On Arch Linux you may require old libraries from the AUR such as libgfortran6, ncurses5-compat-libs, libjpeg6 and libpng12.

Ubuntu 16.04 requires various packages to run the CentOS6 build: We believe the full list you will need is:

sudo apt-get install gcc gfortran x11-common libjpeg62-dev libxft-dev libsm-dev libxt-dev

The CentOS6 build may require older versions of various libraries if you wish to run it on very modern linux -- if these are not available in the standard repos they may be available from custom repos. Otherwise you can try our newer builds, or build Starlink yourself from source.

OS X

This OS X software was built on Yosemite and we believe it works correctly on all versions from Snow Leopard onwards. However, EAO does not have the resources to test on all older versions of OS X and we now only have Yosemite OS X machines available in house.

The tar ball will unzip into a star-2018A/ directory in the directory where you downloaded and un-tarred the tar file. This release can be placed and run from anywhere.

OS X REQUIREMENTS

1. An up-to-date XQuartz X11 distribution must be installed. If you already have XQuartz installed but need to update it, you can run the application and go to the top menu and select: X11->Check for X11 updates. If you need to install the software, it can be found here: http://xquartz.macosforge.org/landing.

2. A recent Java JDK must be installed to use the Starjava programs such as topcat, splat stilts and frog. This can be found at http://www.oracle.com/technetwork/java/javase/downloads/index.html. To check if you have Java installed already, open a terminal, type java -version and see if the command is found, and if you have 1.8 installed.

There should not be any other dependencies for installing the OS X build; this is a change from previous releases which required manual installation of various libraries.

OS X Catalina

We have had reports of issues with non-trusted developer warnings on OSX Catalina. We do not have access to any OSX Catalina machines to test this, but it has been reported to us that running the following command on the Starlink top level directory solves the problem:

find . -type f -exec xattr -d com.apple.quarantine {} \; 

Post-installation Run-up

Before you can run the Starlink Software Collection, you need to run our setup scripts. This will have to be done every time you open a new terminal, before you can run any Starlink commands.

If your terminal is running bash or other sh-like shell (this is the usual default on modern Linux distributions and Mac OS X) please type the following commands into your terminal:

export STARLINK_DIR=/star-2018A

source $STARLINK_DIR/etc/profile

If you have installed your star-2018A somewhere other than into the root directory (/) you would instead set the first command to point to the location of the installed star-2018A/ directory.

e.g., if you had put it in your home directory, you would type:

export STARLINK_DIR=/home/MyUserName/star-2018A

source $STARLINK_DIR/etc/profile

Some astronomy departments still set up their computers to use tcsh as the default shell instead of bash. The setup process is similar, but the commands are slightly different. If you have installed star-2018A into the root directory, you will need to type the following commands into your terminal:

setenv STARLINK_DIR /star-2018A

source $STARLINK_DIR/etc/cshrc

source $STARLINK_DIR/etc/login

And again, similar to the bash shell instructions above, if you have installed star-2018A into a different directory you will have to give the path to that directory in your first command (and still run the following two commands) e.g.:

setenv STARLINK_DIR /home/MyUserName/star-2018A

You can now run Starlink commands within your current terminal.

Any time you wish to start using Starlink Software in a new terminal, you will need to run the appropriate 2 or 3 commands above again. For convenience, you could save these commands into an alias.

Running Software Packages

For most command line packages, typing the name of a package will make its commands available to use, tell you that it has been loaded, and tell you what command to run to find out more about the package. For example, try typing:

kappa

into your terminal.

Some Starlink software also launches a graphical interface. If you type:

gaia &

into your terminal, the GAIA data visualization software will launch and you can load in astronomy maps and cubes to view (both SDF and FITS formats are supported).

IMPORTANT NOTE (for Linux only in this release)

The setup scripts put the 'Starlink' version of various libraries into your LD_LIBRARY_PATH variable. Unfortunately, this means that after sourcing the Starlink setup scripts, other command line programs (such as e.g. CASA) may not work inside the terminal in which you sourced StarLink. To get around this, simply:

1. Don't source the Starlink scripts by default (e.g. don't put the commands into your .bashrc, .profile, .login or .cshrc files), but instead source them manually every time you're running Starlink software.

2. Run other software (such as CASA) in a different terminal from the one in which you are running Starlink.

The OS X build of Starlink does not need to set the equivalent path ($DYLD_LIBRARY_PATH), so Mac OS X users do not need to worry about this.

ORAC-DR for WFCAM

Because of the large size of WFCAM calibration files, they have been split off from the main download tarballs, as not everybody will be reducing WFCAM data using ORAC-DR. These calibrations can be downloaded here (1.06GB .tar.gz). The tar file will unzip into a wfcam/ directory in the directory you downloaded the tar file to. To install these calibration files, copy the directory into the $STARLINK_DIR/bin/oracdr/cal/ directory, thus creating the $STARLINK_DIR/bin/oracdr/cal/wfcam/ directory containing the calibration files.

This file has changed for the 2015B release to include flatfield images for the 1.644FeII filter. These were created in 2012 (Kapuahi release) but not previously made publicly available. If you downloaded the tar ball for intervening releases after Lehuakona, you only need to download it again should you require the additional FeII flats.