AMBER pipeline recipes

A release of the AMBER pipeline recipes is now available !

A release of the AMBER pipeline recipes is now available and can be downloaded.

Together with the data processing modules, we also provide two standalone applications for running them:

Gasgano, a GUI for data browsing and organisation, providing an intuitive and comprehensive interface to pipeline recipes that are based on the ESO Common Pipeline Library (CPL).
EsoRex, a command-line driven utility to launch pipeline recipes, which can be used either as an interactive tool, or can be embedded into scripts for automating some of the data reduction tasks.

AMBER pipeline recipes public version:

The public version of the AMBER pipeline recipes is 2.3.7, and it is included in the pipeline distribution kit amber-kit-2.3.7.tar.gz together with the following packages:

the qfits library, version 6.2.0
the Common Pipeline Library (CPL), version 3.1
Gasgano distributions for Linux, version 2.2.7
EsoRex, version 3.6.1

AMBER pipeline recipes System Requirements

At present, the AMBER pipeline recipes package is certified only for:

Linux RedHat 9.0
Scientific Linux 4.0

You may anyway try to install and run the pipeline recipes package on other distributions assuming that you have the gcc compiler version 3.2 or newer available.

Installing and running the AMBER pipeline recipes 2.3.7

To install the AMBER pipeline recipes 2.3.7 you will need to retrieve the pipeline distribution kit, unpack and install it.

Prerequisites:

To install this software package, the GNU C compiler (gcc) version 3.2 or newer must be available on your system.
To install the latest graphical front-end Gasgano version 2.2.7 and configure it properly the Java Developer Kit (JDK) version 1.5.0 must be available on your system and the variable JAVA_HOME should be set accordingly. If the JDK is not installed you may download it from the official Sun Java page distribution. Furthermore, the related java executable must be in your PATH.

Gasgano is known to be resource-intensive: see details of memory and CPU usage in Appendix A of the Gasgano User's Manual.

Note:: In order to retrieve the distribution kit, you may need to configure your Web browser so that it knows how to deal with the files we distribute, i.e., compressed tar files (.tar.gz filename extension). If you click on one of the links below, your browser should display a file selection panel; if you end up instead with a page full of strange characters, you may try clicking on the link while holding the Shift key down, or configure your browser.

Installation procedure:

Change directory to where you want to retrieve the AMBER pipeline recipes package. It can be any directory of your choice but not:
- $HOME/gasgano
- $HOME/.esorex
Download the software necessary for running the pipeline recipes:
- AMBER pipeline recipes distribution kit 2.3.7 (amber-kit-2.3.7.tar.gz, ~13 Mb)
Verify the checksum value of the tar file with the cksum command. It should be:

1644595549 12885777 amber-kit-2.3.7.tar.gz
Unpack using the following command:

tar -xzvf amber-kit-2.3.7.tar.gz
Install: after moving to the top installation directory,

cd amber-kit-2.3.7

it is possible to perform a simple installation using the available installer script (recommended):

./install_pipeline

(BEWARE: the execution may take a few minutes).

By default the script will install the AMBER recipes, Gasgano, EsoRex, all the necessary libraries, and the static calibration tables, into a directory tree rooted at $HOME. A different path may be specified as soon as the script is run. For instance (user input is boldfaced):
$ ./install_pipeline I am about to install the following software packages: qfits-6.2.0.tar.gz cpl-3.1.tar.gz esorex-3.6.1.tar.gz gasgano-2.2.7.tar.gz amber-2.3.7.tar.gz - with the following pipeline calibration file(s): amber-calib-2.3.7.tar.gz The software installation will be organised in bin/, lib/ and include/ directories, while the calibration files will be installed in a calib/ directory. Where should I install the software packages ? [/home/dummy] /home/dummy/pipelines Where should I install the pipeline calibration files ? [/home/dummy/pipelines] /home/dummy/calibrations
In this case the software is installed under the directory /home/dummy/pipelines, and the static calibration tables under /home/dummy/calibrations/amber-2.3.7

The only exception to all this is the Gasgano tool, that will always be installed under the directory $HOME/gasgano. Note that the installer will move an existing $HOME/gasgano directory to $HOME/gasgano.old before the new Gasgano version is installed.

Important: the installation script would ensure that any existing Gasgano and EsoRex setup would be inherited into the newly installed configuration files (avoiding in this way any conflict with other installed instrument pipelines).

Please follow the instructions shown at the end of a successful installation script: they will indicate how to set your PATH and CPLDIR variables in your machine in order to run the pipeline. Alternatively, it is possible to perform a manual installation (experienced users only): the README file located in the top installation directory contains more detailed information about a step-by-step installation.

Executing the AMBER pipeline recipes 2.3.7

Using Gasgano

To run the Gasgano GUI, just add $HOME/gasgano/bin to your PATH environment variable:

    export PATH="$HOME/gasgano/bin:"$PATH

You should also define an environment variable CPLDIR to point to the same path specified for the installation. The instructions displayed at the end of a successful installation script will indicate how to set your PATH and CPLDIR variables in your machine in order to run the pipeline. Possible files to update are:

    $HOME/.bashrc
    $HOME/.profile

Finally, enter the command

    gasgano
If the Gasgano main panel appears, then you have successfully installed Gasgano. Make sure, however, that the expected Gasgano 2.2.7 release is running: the version number is listed at the top of the main Gasgano panel.
Refer to the Gasgano User's Manual to learn how to browse data and run pipeline recipes. Refer to the AMBER Pipeline User Manual for detailed information about the recipes usage.

Using EsoRex

The EsoRex executable should be available in the bin directory under your installation path (see above). The $PATH environment variable should be upgraded accordingly (similarly as done for Gasgano).
Refer to the EsoRex web page for details about the related features and options.

Documentation

The AMBER Pipeline User Manual (1.0) (~4 Mb, 60 pages), is available here for download. Note that the manual is also included in the AMBER pipeline kit, in the file AMBER_PipelineUserManual.pdf.

The GASGANO Users' Manual (~1.2 Mb, 66 pages) is available for download in the Gasgano web page.

On the EsoRex web page some online documentation about EsoRex can be found.

The CPL manuals are available on the CPL web pages.

In case of problems when opening the documents directly from your web browser, the files may be first saved on disk, and then opened with Acrobat Reader.

Bug Reports

If you experience an unexpected behavior of any component of the AMBER pipeline, please send a report to the ESO User Support Department, describing:

the AMBER pipeline recipes package release, and the release of other components (e.g., Gasgano, EsoRex, ...) you are using
the version of your OS
the exact sequence of actions that were performed before the problem occurred
what were precisely the symptoms and the possible error message(s)
whether the problem is repeatable