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GammaLib modules

Getting GammaLib

Before you start

The procedure for building and installing GammaLib is modeled on GNU software distributions. You do not need to have system administrator privileges to compile and to install GammaLib.

You will need the following to build the software:

  • About 200 MB of free disk space.
  • An ANSI C++ compiler. We recommend building GammaLib with the GNU g++ compiler.
  • GNU make
  • The cfitsio library for FITS file support together with the developer package that includes the cfitsio.h header.

Note that GammaLib compiles also in the absence of the cfitsio library, yet without cfitsio, FITS file reading or writing is not supported.

Furthermore, the following optional packages are supported but are not required to compile :

  • Python, including the Python developer package that includes the Python.h header file. If Python is present, the GammaLib Python module will be built and installed, allowing to script all GammaLib functionalities from within Python.
  • readline, including the readline developer package that provides the readline.h header file. If readline is present, the packages are used to enhance the user interface when entering parameters for ftools applications (see this section).

If you plan to modify or to extend the GammaLib source code, the following software is also required on your system:

  • GNU autoconf and automake is needed to rebuild the configure script and Makefile.am resource files following configuration modifications.
  • swig is needed to rebuild the Python wrappers following Python interface modifications. Make sure to install the latest swig version to guarantee the largest possible compatibility of the Python wrappers.
  • Doxygen is needed to rebuild the software reference manual following code modifications.

The following sections provide some information about the installation of cfitsio and readline.

Installing cfitsio

HEASARC’s cfitsio library comes on many Linux distributions as pre-compiled binary, and there are good chances that the package is already installed on your system. For Mac OS X, cfitsio can be installed from MacPorts or Homebrew. If you use a pre-compiled binary, make sure that also the developer package is installed on your system. The developer package provides the cfitsio.h header file which is needed to compile in FITS file support in GammaLib. Please refer to the documentation of your Linux distribution to learn how to install pre-compiled binary packages (note that the installation of pre-compiled binary packages usually requires system administrator privileges).

If you need (or prefer) to install cfitsio from source, you can download the latest source code from http://heasarc.gsfc.nasa.gov/fitsio. Detailed installation instructions can also be found on this site. We recommend that you install cfitsio as a shared library in the same directory in which you will install GammaLib, so that cfitsio is automatically found by the GammaLib configure script. By default, GammaLib gets installed into the directory /usr/local/gamma.

You can install version 3.290 of cfitsio (the version that was available when writing this manual) by executing the following command sequence ($ denotes the UNIX shell prompt):

$ wget ftp://heasarc.gsfc.nasa.gov/software/fitsio/c/cfitsio3290.tar.gz
$ tar xfz cfitsio3290.tar.gz
$ cd cfitsio
$ ./configure --prefix=/usr/local/gamma
$ make shared
$ sudo make install

The --prefix=/usr/local/gamma option specifies the directory into which cfitsio gets installed. We choose here the default GammaLib installation directory /usr/local/gamma. As this directory is a system directory, we need to use sudo for installation. If you decide to install cfitsio into a local directory which is owned by yourself, it is sufficient to type make install to install the library.

Installing readline

The readline package comes on all Linux distributions that are known to us as pre-compiled binary, and it is almost certain that readline is already installed on your system. Very often, however, the readline developer package that provides the readline.h header file is not installed, and you need to install this package yourself to enable readline support for GammaLib. Please refer to the documentation of your Linux distribution to learn how to install pre-compiled binary packages (note that the installation of pre-compiled binary packages usually requires system administrator privileges).

If you need (or prefer) to install readline from source, you need also to install the ncurses library that is required by readline. Here is the command line sequence that will install ncurses (version 5.9) and readline (version 6.2) in the GammaLib default install directory /usr/local/gamma from source:

$ wget http://ftp.gnu.org/gnu/ncurses/ncurses-5.9.tar.gz
$ tar xfz ncurses-5.9.tar.gz
$ cd ncurses-5.9
$ ./configure --prefix=/usr/local/gamma
$ make
$ sudo make install
$ cd ..
$ wget http://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz
$ tar xfz readline-6.2.tar.gz
$ cd readline-6.2
$ ./configure --prefix=/usr/local/gamma
$ make
$ sudo make install

Note that sudo is only needed if you are not the owner of the install directory.

Installing

Downloading

You get the latest version of GammaLib here.

Configuring

Once you’ve downloaded and uncompressed GammaLib, step into the GammaLib source code directory and type

$ ./configure

to configure the library for compilation. Make sure that you type ./configure and not simply configure to ensure that the configuration script in the current directory is invoked and not some other system-wide configuration script.

If you would like to install GammaLib in a different directory, use the optional --prefix argument during the configuration step. For example

$ ./configure --prefix=/home/myname/gamma

installs GammaLib in the gamma directory that will be located in the user’s myname home directory. You can obtain a full list of configuration options using

$ ./configure --help

If configuration was successful, the script will terminate with printing information about the configuration. This information is important in case that you encounter installation problems, and may help you to diagnose the problems. The typical output that you may see is as follows:

GammaLib configuration summary
==============================
* FITS I/O support             (yes)
* Readline support             (yes)
* Ncurses support              (yes)
* Developer configuration      (yes)
* Make Python binding          (yes)   use swig for updates
* Python                       (yes)
* Python.h                     (yes)
* Python wrappers              (yes)
* swig                         (yes)
* Multiwavelength interface    (yes)
* Fermi-LAT interface          (yes)
* CTA interface                (yes)
* COMPTEL interface            (yes)
* Doxygen                      (yes)   /usr/local/bin/doxygen
* Perform NaN/Inf checks       (yes)   (default)
* Perform range checking       (yes)   (default)
* Optimize memory usage        (yes)   (default)
* Support legacy XML format    (yes)   (default)
- Enable OpenMP                (no)
- Compile in debug code        (no)    (default)
- Enable code for profiling    (no)    (default)

The script informs whether cfitsio has been found (and eventually also gives the directories in which the cfitsio library and the header file resides), whether readline and ncurses have been found, and whether Python including the Python.h header file is available. Although none of these items is mandatory, we highly recommend to install cfitsio to support FITS file reading and writing (see Installing cfitsio), and to install Python to enable GammaLib scripting.

If cfitsio is installed on your system but not found by the configure script, it may be located in a directory that is not known to the configure script. By default, configure will search for cfitsio (in the given order) in the GammaLib install directory, in all standard paths (e.g. /usr/lib, /usr/local/lib, ...), and in some system specific locations, including /opt/local/lib for Mac OS X. Assuming that you installed cfitsio on your system in the directory /home/myname/cfitsio, you may explicitly specify this location to configure using the LDFLAGS and CPPFLAGS environment variables:

$ ./configure LDFLAGS=-L/home/myname/cfitsio/lib CPPFLAGS=-I/home/myname/cfitsio/include

Here, LDFLAGS specifies the path where the shared cfitsio library is located, while CPPFLAGS specifies the path where the cfitsio.h header file is located. Note that -L has to prefix the library path and that -I has to prefix the header file path. With the same method, you may specify any non-standard location for the readline and ncurses libraries.

The configuration script also checks for the presence of swig, which is used for building the Python wrapper files. Normally, swig is not needed to create the Python bindings as the necessary wrapper files are shipped with the GammaLib source code. If you plan, however, to modify or to extend the Python interface, you will need swig to rebuild the Python wrappers following changes to the interface.

The configuration summary informs also about all instrument dependent interfaces that will be compiled into the GammaLib library. By default, all available interfaces (multi-wavelength, Fermi/LAT, COMPTEL and CTA) will be compiled into GammaLib. If you wish to disable a particular interface, you may use the configure options --without-mwl, --without-lat, --without-com or --without-cta. For example,

$ ./configure --without-mwl --without-lat --without-com

will compile GammaLib without the multi-wavelength, the Fermi/LAT and the COMPTEL interfaces. In this case, only CTA data analysis will be supported.

GammaLib uses Doxygen for code documentation. In case that you want to install the reference manual also locally on your machine, Doxygen is needed to create the reference manual from the source code. Doxygen is also needed if you plan to modify or extend the GammaLib library to allow rebuilding the reference documentation after changes. Please read see Generating the reference documentation to learn how to build and to install the reference manual locally.

Finally, there exist a number of options that define how exactly GammaLib will be compiled.

By default, GammaLib makes use of OpenMP for multi-core processing. If you want to disable the multi-core processing, you may specify the --disable-openmp option during configuration.

Several methods are able to detect invalid floating point values (either NaN or Inf), and by default, these checks will be compiled in the library to track numerical problems. If you want to disable these checks, you may specify the --disable-nan-check option during configuration.

Range checking is performed by default on all indices that are provided to methods or operators (such as vector or matrix element indices, sky pixels, event indices, etc.), at the expense of a small speed penalty that arises from these verifications. You may disable these range checkings by specifying the --disable-range-check option during configuration.

In a few places there exists a trade-off between speed and memory requirements, and a choice has to be made whether faster execution or smaller memory allocation should be preferred. By default, smaller memory allocation is preferred by GammaLib, but if you are not concerned about memory allocation you may specify the --disable-small-memory option during configuration to speed up the code.

If you develop code for GammaLib you may be interested in adding some special debugging code, and this debugging code can be compiled in the library by specifying the --enable-debug option during configuration. By default, no debugging code will be added to GammaLib.

Another developer option concerns profiling, which may be of interest to optimize the execution time of your code. If you would like to add profiling information to the code (which will be at the expense of execution time), you may specify the --enable-profiling option during configuration, which adds the -pg flags to the compiler. By default, profiling is disabled for GammaLib.

Mac OS X options

The Mac OS X environment is special in that it supports different CPU architectures (intel, ppc) and different addressing schemes (32-bit and 64-bit). To cope with different system versions and architectures, you can build a universal binary by using the option

$ ./configure --enable-universalsdk[=PATH]

The optional argument PATH specifies which OSX SDK should be used to perform the build. By default, the SDK /Developer/SDKs/MacOSX.10.4u.sdk is used. If you want to build a universal binary on Mac OS X 10.5 or higher, and in particular if you build 64-bit code, you have to specify --enable-universalsdk=/.

A second option (which is only valid in combination with the --enable-universalsdk) allows to specify the kind of universal build that should be created:

$ ./configure --enable-universalsdk[=PATH] --with-univeral-archs=VALUE

Possible options for VALUE are: 32-bit, 3-way, intel, or all. By default, a 32-bit build will be made.

These options are in particular needed if your Python architecture differs from the default architecture of your system. To examine the Python architecture you may type:

$ file `which python`

which will return the architectures that are compiled in the Python executable:

i386     32-bit intel
ppc      32-bit powerpc
ppc64    64-bit powerpc
x86_64   64-bit intel

If Python is 32-bit (ppc, i386) but the compiler produces by default 64-bit code (ppc64, x86_64), the Python module will not work. Using

$ ./configure --enable-universalsdk=/

will force a universal 32-bit build which creates code for ppc and i386 architectures. If on the other hand Python is 64-bit (ppc64, x86_64) but the compiler produces by default 32-bit code (ppc, i386), the option

$ ./configure --enable-universalsdk=/ --with-univeral-archs=3-way

will generate a universal build which contains 32-bit and 64-bit code.

Building

Once configured you can build GammaLib by typing

$ make

This compiles all GammaLib code, including the Python wrappers, and builds the dynamic library and Python module.

GammaLib building can profit from multi-processor or multi-core machines by performing parallel compilation of source code within the modules. You can enable this feature by typing

$ make -j<n>

where <n> is a number that should be twice the number of cores or processors that are available on your machine.

In case that you rebuild GammaLib after changing the configuration, we recommend to clean the directory from any former build by typing

$ make clean

prior to make. This will remove all existing object and library files from the source code directory, allowing for a fresh clean build of the library.

Testing

GammaLib comes with an extensive unit test that allows to validate the library prior to installation. We highly recommend to run this unit test before installing the library (see Installing).

To run the unit test type:

$ make check

This will start a test of all GammaLib modules by using dedicated executables which will print some progress and success information into the console. After completion of all tests (and assuming that all instrument dependent modules are enabled), you should see the following message in your console:

===================
All 21 tests passed
===================

(Note that the exact number of tests that is conducted depends on the configuration options).

Installing

GammaLib is finally installed by typing

$ [sudo] make install

By default, GammaLib is installed in the system directory /usr/local/gamma, hence sudo needs to be prepended to enable writing in a system-level directory. If you install GammaLib, however, in a local directory of which you are the owner, or if you install GammaLib under root, you may simply specify make install to initiate the installation process.

The installation step will copy all necessary files into the installation directory. Information will be copied in the following subdirectories:

  • bin contains GammaLib environment configuration scripts (see section [sec:environment])
  • include contains GammaLib header files (subdirectory gammalib)
  • lib contains the GammaLib library and Python module
  • share contains addition GammaLib information, such as a calibration database (subdirectory caldb), documentation (subdirectory doc), and Python interface definition files (subdirectory gammalib/swig)

Setting up the GammaLib environment

Before using GammaLib you have to setup some environment variables. This will be done automatically by an initialisation script that has been installed in the bin subdirectory of the install directory. Assuming that you have installed GammaLib in the default directory /usr/local/gamma you need to add the following to your $HOME/.bashrc or $HOME/.profile script on a Linux machine:

export GAMMALIB=/usr/local/gamma
source $GAMMALIB/bin/gammalib-init.sh

If you use C shell or a variant then add the following to your $HOME/.cshrc or $HOME/.tcshrc script:

setenv GAMMALIB /usr/local/gamma
source $GAMMALIB/bin/gammalib-init.csh

You then have to source your initialisation script by typing (for example)

$ source $HOME/.bashrc

and all environment variables are set correctly to use GammaLib properly.

Generating the reference documentation

The reference documentation for GammaLib is generated directly from the source code using the Doxygen documentation system. The latest GammaLib reference manual can be found at http://cta.irap.omp.eu/gammalib/doxygen/.

The reference documentation is not shipped together with the source code as this would considerably increase the size of the tarball. In case that you want to install the reference manual also locally on your machine, you first have to create the documentation using Doxygen.

Assuming that Doxygen is available on your machine (see Configuring) you can create the reference documentation by typing

$ make doxygen

Once created, you can install the reference manual by typing

$ [sudo] make doxygen-install

By default, GammaLib is installed in the system directory /usr/local/gamma, hence sudo needs to be prepended to enable writing in a system-level directory. If you install , however, in a local directory of which you are the owner, or if you install GammaLib under root, you may simply specify make install to initiate the installation process.

The reference manual will be installed in form of web-browsable HTML files into the folder

/usr/local/gamma/share/doc/gammalib/html/doxygen

You can access all web-based GammaLib documentation locally using file:///usr/local/gamma/share/doc/gammalib/html/index.html (assuming that the GammaLib library has been installed in the default directory /usr/local/gamma).

In addition, the reference manual will also be available as man pages that will be installed into

/usr/local/gamma/share/doc/gammalib/man

To access for example the information for the GApplication class, you can type

$ man GApplication

which then returns the synopsis and detailed documentation for the requested class.