Software

Warning

Please do not download large files during the tutorial or the WIFI network will overload. We will distribute the software and data you need via USB sticks.

To participate in the tutorial you should bring a Mac or Linux laptop.

This page describes how to install the software we need for the tutorial and how to check that it works properly.

If you have a Windows laptop, you can install VirtualBox and then install Linux in a virtual machine. It’s best to install a Linux distribution that is officially supported by the Fermi science tools (see here): unfortunately the Scientific Linux distribution is very large (over 4 GB) and Ubuntu has known problems. Therefore we recomment you try Fedora, which should be similar enough to ScientificLinux for the Scientific Linux 6 64 bit libc 2.12 binary version of the ScienceTools to work.

Check: you should be able to open a terminal and do this:

$ echo "Hello world"
Hello world
$

Overview

You should install the following software:

• Fermi Science Tools
• FTOOLS = HEASOFT (includes fv)
• ds9
• TOPCAT
• Aladin (if you want)
• Enrico

Fermi Science Tools

The main analysis software you will use for this tutorial is the Fermi data analysis software, called the Fermi science tools.

The Fermi Science Support Center web pages contain a lot of information about Fermi data access and data analysis. If you have a problem you can’t solve yourself (always try finding a solution yourself with Google first), you can contact the official NASA Fermi help desk or post in this forum.

The most important piece of advice on the Installing the Fermi Science Tools page is:

> Downloading and installing the Fermi science tools from the binary tar files below is strongly recommended. > The many minor variations in the various Unix systems makes building the tools from source challenging.

So download the binary tar file for your machine ... this will take a while because it’s about 1 GB in size. As an example, for Mac the file you get will be called ScienceTools-v9r31p1-fssc-20130410-x86_64-apple-darwin12.2.0.tar.gz or maybe if it is automatically unzipped after download it will be called ScienceTools-v9r31p1-fssc-20130410-x86_64-apple-darwin12.2.0.tar.

After download you have to set up the Fermi science tools as described here.

Check: you should be able to use the Fermi science tools from the Shell command line and via Python:

$ which gtbin
$ gtbin
# abort with CTRL + C
$ which python
$ python
>>> import UnbinnedAnalysis

libcrypto and libssl shared library problem

If gtbin complains about missing libcrypto.so.10, then you need make a link to your installed version with the name requested. To do this first use locate to find your version, then cd to that directory and create a symbolic link. Example:

$ sudo -i
# locate libcrypto
/PATH TO FILE/libcrypto.so.0.9.8
# cd /PATH TO FILE/
# ln -s libcrypto.so.0.9.8 libcrypto.so.10

You see either a file called libcrypto.so.0.9.8 or libcrypto.so.1.0.0. If locate finds a file called libcrypto.so.1.0.0, use that file instead of the libcrypto.0.9.8 version.

After creating the libcrypto link, try to run gtbin. Sometimes a similar error regarding libssl will take place, if it does repeat the steps above with thelibssl file to (hopefully) correct it.

FTOOLS = HEASOFT

Next install the FTOOLS — A General Package of Software to Manipulate FITS Files following the installation instructions on the web. To install correctly you must run the configure script found in heasoft-6.14/[platform version]/BUILD_DIR, where [platform version] corresponds to the string of your platform (e.g., x86_64-unknown-linux-gnu-libc2.5 for Linux64).

With the FTOOLS you install Fv: The Interactive FITS File Editor, a flexible tool to view and edit FITS files.

E.g. the ftlist command line tool is very handy to check what is in a given FITS file.

Use ds9 as an image viewer and fv to look at the content of Fermi event lists (called photon files).

Check: Open up a Fermi event list as described here with fv

ds9

SAOImage DS9 is one of the best viewers for astronomical 2D images and 3D cubes ... please download it from here.

Check: Download and open up the following FITS files:

• Hubble space telescope image of the Antennae Galaxies (FITS file of the 2D image)
• Fermi LAT diffuse emission model (an outdated version, used here because of the small file size) (FITS file of the 3D cube with log(energy) on the third axis).

If you want:

• Some Hubble space telescope optical images here.
• Some Chandra X-ray observatory X-ray images here

TOPCAT

TOPCAT <http://www.star.bris.ac.uk/~mbt/topcat/> is a Java program to view FITS tables. Follow the installation instructions on the web.

Aladin (optional)

Aladin — A FITS image viewer (alternative to ds9) is a nice astronomical image and catalog viewer ... an alternative to ds9.

Install it and give it a try if you want.

Enrico

Producing a spectrum (global model and flux points in energy bins) or light curve (flux points in time bins) requires calling a lot of Fermi science tools with the right parameters in the right order.

Luckily you have Enrico to help you. Enrico is a set of Python scripts that take a single config file as input where you specify what kind of analysis you want to run and the most important analysis parameters, and the run all Fermi science tools in the right order (or in parallel where possible) with the right parameters for you.

Please install Enrico as described here.

Check: To check that Enrico is installed correctly run this command:

$ enrico_setupcheck

Init file

You should create a file fermi-hero-init.sh which sets up your shell for this tutorial.

Once all software is installed all you have to do is:

$ source fermi-hero-init.sh

This is an example init file ... you’ll have to adapt the PATHs / versions to your system:

export FERMI_HERO = /Users/deil/FERMI_HERO

export HEADAS=$FERMI_HERO/heasoft-6.14/x86_64-unknown-linux-gnu-libc2.5
source $HEADAS/headas-init.sh

export FERMI_DIR=$FERMI_HERO/ScienceTools-v9r31p1-fssc-20130410-x86_64-apple-darwin12.2.0/x86_64-apple-darwin12.2.0
source $FERMI_DIR/fermi-init.sh

export ENRICO_DIR=$FERMI_HERO/enrico
source $ENRICO_DIR/enrico-init.sh

alias topcat="java -Xms512m -Xmx4024m -jar /Applications/TOPCAT.app/Contents/Resources/Java/topcat-full.jar"
alias aladin="java -Xms512m -Xmx4024m -jar /Applications/Aladin.app/Contents/Resources/Java/Aladin.jar"

# Add location of binaries to your PATH, e.g. for ds9:
export PATH=$PATH:$FERMI_HERO