Important Notes and Bug Reports

Release of Reflex based workflows for VLT pipelines

A number of VLT pipelines deliver workflows compatible with Reflex 2.6. You can browse the available pipelines here.

Software prerequisites installation

The VLT workflows and Reflex depend on a number of packages that must be installed, namely gcc, gzip, make, Java 7, python, pyfits, wxPython, matplotlib and numpy. There are at least three ways to install all the dependencies:

  • Distribution package managers. This usually requires software installation rights.
    • Fedora official repositories (version 18 or later). It is very easy to install all the dependencies using the official yum repositories. Using root access execute the following commands in a terminal:     yum upgrade     yum install python-matplotlib python-matplotlib-wx wxPython pyfits numpy java-openjdk python gcc-c++ zlib-devel make gzip tar If you also want to install Gasgano (not the default), then install the following additional package:     yum install java-1.7.0-openjdk-devel NOTE: Please note that pyfits version must be less than 3.2. If you have pyfits 3.2, you will need to downgrade it.
    • Fedora 17 and CentOS 6.4 official repositories. It is very easy to install all the dependencies using the official yum repositories. Using root access execute the following commands in a terminal:     yum upgrade     yum install python-matplotlib python-matplotlib-wx wxPython pyfits numpy java-1.7.0-openjdk python gcc-c++ zlib-devel make gzip tar If the operating system is 64 bits: update-alternatives --set java /usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java If it is 32 bits: update-alternatives --set java /usr/lib/jvm/jre-1.7.0-openjdk/bin/java
    • Ubuntu official repositories (version 12.10 or later). It is very easy to install all the dependencies using the official apt repositories. Just execute in a terminal the following commands (you might be prompted for your password):     sudo apt-get update     sudo apt-get upgrade     sudo apt-get install python-matplotlib python-wxgtk2.8 python-pyfits python-numpy default-jre g++ zlib1g-dev make gzip tar If you also want to install Gasgano (not the default), then install the following additional package:     apt-get install default-jdk
    • Ubuntu 12.04 or Debian 7 official repositories. It is very easy to install all the dependencies using the official apt repositories. Just execute in a terminal the following commands (you might be prompted for your password):     sudo apt-get update     sudo apt-get upgrade     sudo apt-get install python-matplotlib python-wxgtk2.8 python-pyfits python-numpy openjdk-7-jre g++ zlib1g-dev make gzip tar update-java-alternatives --jre --set java-1.7.0-openjdk-amd64
    • Mac OS X MacPorts. If you have MacPorts installed, issue the following commands to install the python modules and software needed to compile the pipelines:     sudo port selfupdate     sudo port upgrade outdated     sudo port install py27-matplotlib py27-wxpython-2.8 py27-numpy py27-pyfits pkgconfig autoconf automake libtool     sudo port select --set python python27 Please make sure that the version of python used is the one from MacPorts by adding /opt/local/bin first in your path. This depends on your shell. For bash:     export PATH=/opt/local/bin:$PATH In some shells you might have to do a rehash:     rehash

      You would have to install a compiler (Xcode) with gcc preferibile (currently clang compiler support is experimental) and a Java 7 virtual machine separately as well.

      If you are building with Gasgano support (not the default), you have to install the Java development kit and make it known to the installation procedure with this extra command:     export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/ This procedure is known to work correctly in OS X 10.6 Snow Leopard, OS X 10.7 Lion and OS X 10.8 Mountain Lion.
  • Scisoft 7.7 or greater. Scisoft is a collection of software that includes all the prerequisites. It is officially supported only for Fedora 11. Consult the webpage for installation instructions.

    For Mac users there is an unofficial port that can be downloaded from scisoftosx. Note also that python and wxpython have to be installed additionally, since Scisoft for Mac does not include them.

  • Individual package installation. If you still need to install the dependencies manually because your operating system distribution does not contains them, this is the list of packages to install:

Installation procedure

The recommended installation procedure is to use the install_reflex script. Follow this instructions:

  1. Check that you have all the software prerequisites
  2. Download install_reflex
  3. Make it executable:     chmod u+x install_reflex
  4. Execute the installation script. This will install Reflex, the supported pipelines and demo data. The script will ask for an installation directory (install_dir) as well as download and data directories.     ./install_reflex If the software prerequisites are not met the script will fail, or in the case of optional packages (python modules) it will prompt whether you want to continue. If this happens, go to Software prerequisites:
  5. Execute Reflex:     install_dir/bin/reflex
This script will allow install the pipelines with available workflows as well as Reflex itself. It requires an Internet connection, since it retrieves all the packages directly from the net. Please read section Software prerequisites to make sure that you have the needed software before running the script. The script will detect if there is any missing software, but it won't attempt to install it.

The script also has limited support for reinstallation of software if new versions of the pipelines or Reflex are available.

The current installation procedure is known to work in the following operating systems:

  • Fedora 15 and above (i386 and x86_64)
  • Ubuntu 10.04 and above (i386 and x86_64)
  • Scientific Linux 5.3 (i386 only)
  • Mac OS X 10.6 and above (x86_64 only)

Manual Installation of all the software

This installation procedure installs the pipeline and the workflow first, and then Reflex is used on top of an existing pipeline installation. It is a more advanced setup and therefore it is recommended only for advanced users.
  1. Download and make a regular installation of the pipeline. Note that if you already have an installed version which includes the workflow, it is also possible to use it.
  2. Make sure that esorex can access the uves recipes using the following command:     esorex --recipes
  3. Download and install Reflex
  4. Start Reflex and open the workflow located in the installation directory of the pipeline:     installation_dir/share/reflex/workflows/pipeline-x.x.x
  5. Demo data can be found in this table under column "Demo Data Sets".
  6. If you have run Reflex in the same machine and account previously, you might have to remove directories ~/KeplerData and ~/.kepler to clean the cache.

Running Reflex

We recommend to read the tutorials prepared to sucessfully execute the workflows in a matter of minutes. It can be downloaded from this table under column "Documentation". For more detailed information, you can read the pipeline user manual which can also be downloaded from the same table.

Bug Reports

If you experience an unexpected behavior of any component of Reflex or the pipeline recipes package, please, first refer to the list of known problems and limitations in the workflow tutorial, the pipeline manual, or the Reflex user manual, in this order.

For any other issues or requests, please, send a report to the ESO User Support Department, describing:        

  • the Reflex and pipeline version, and the version of other components (e.g., Gasgano, EsoRex, ...) you are using
  • the version of your OS and C compiler
  • the version of python and required python modules
  • 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