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INSTALL.md

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BAT - Bayesian Analysis Toolkit

This document provides a short description of how to compile and use BAT on your computer.

Platforms

BAT has been developed on Linux. The installation, unit tests, and examples are run and known to work on Linux and Mac OS X. On Linux, we test with gcc and on Mac OS X we use clang but both compilers should work on either platform.

Windows is not supported.

Dependencies

It is understood that all commands shown below are to be entered into a terminal.

Required: Basic tools

BAT itself uses only C++03 features. Compilation and tests work fine with gcc >= 4.3 and clang >= 3.3. But recent versions of ROOT (see below) may require a C++11 compliant compiler.

Under Debian or Ubuntu, you can install the essential requirements with

sudo apt-get install build-essential curl

In order to use the development version of BAT instead of an official release, some more packages are needed

sudo apt-get install autoconf automake git-core libtool

Building and installing works with automake >= 1.10. To run the tests, a more recent version is needed, v1.15 is known to be sufficient.

Required: ROOT

ROOT is an object-oriented data-analysis framework. At http://root.cern.ch/, you can obtain the source code as well as binary distributions for a number of Linux distributions and Mac OS X versions. We advise to download the latest production release of ROOT. BAT is compatible with ROOT >=5.34.19 and ROOT 6. We regularly run unit tests with ROOT 5 and ROOT 6 to ensure backward compatibility.

On Linux, an alternative is to check your package manager for the availability of ROOT packages. Usually these packages are rather old but often they are good enough to build BAT. For example on Ubuntu systems, you can conveniently install the requirements with

sudo apt-get install libroot-graf2d-postscript-dev libroot-graf3d-g3d-dev libroot-math-foam-dev libroot-math-minuit-dev libroot-math-physics-dev libroot-math-mathmore-dev libroot-roofit-dev root-system-bin

Note

For the interface to RooFit/RooStats, ROOT must be compiled with support for RooFit and MathMore, the latter relies on the GNU scientific library (GSL).

Optional: Cuba

Cuba is a library containing general-purpose multidimensional integration algorithms. It can be obtained from http://www.feynarts.de/cuba/. BAT is compatible with Cuba versions 3.3 through at least 4.2.

Cuba is not necessary to run BAT. We recommend it for model comparison where expensive integrals are needed. Cuba provides integration routines tuned for performance, which are useful for integration in problems with not too many dimensions (~10). By default, Cuba will evaluate in parallel and take all idle cores; the number of cores can be set through an environment variable. For a single core, set

CUBACORES=1

The recommended way to get Cuba is to configure BAT with the option

--with-cuba=download

This will download a compatible version of Cuba to the local subdirectory external/cuba-VERSION, compile it, and configure BAT to use it.

If you want to compile Cuba manually, make sure it is built with position-independent code:

./configure CFLAGS='-fPIC -O3 -fomit-frame-pointer -ffast-math -Wall'
make
make install

Building

Obtaining BAT

You can download the latest release of BAT from http://mpp.mpg.de/bat/. Open a terminal, unpack the tarball usually named like BAT-x.x.tar.gz (here x.x is the version number) and switch to the directory

tar -xzf BAT-x.x.tar.gz
cd BAT-x.x

Alternatively, you can clone the git repository https://github.com/bat/bat (we recommend using the master branch):

git clone https://github.com/bat/bat
cd bat
./autogen.sh

Now start the configuration with

./configure

This will check your system for all components needed to compile BAT and set up the paths for installation. You can add the option --prefix=/path/to/install/bat to ./configure. The BAT library files will then be installed to $prefix/lib and the include files to $prefix/include. The default installation prefix is /usr/local, which requires super-user privileges.

You can list all available options using

./configure --help

In the following, we describe the most useful options in detail.

ROOT

The configure script checks for ROOT availability in the system and fails if ROOT is not installed. You can specify the ROOTSYS directory using --with-rootsys=/path/to/rootsys

BAT support for RooFit/RooStats is turned off by default. The feature can be turned on explicitly with --enable-roostats. The configure script will check whether the version of ROOT is sufficient and whether ROOT was compiled with RooFit/RooStats support.

openMP

Support for openMP threading to run multiple Markov chains in parallel is available through the configure option --enable-parallel; it is disabled by default. This requires a version of gcc accepting the -fopenmp flag, anything >= 4.2 should suffice. Note that if threads are enabled, the default number of threads actually used is implementation dependent and may also depend on the current load of the CPU. Manual control over the number of threads is achieved entirely by openMP means such as setting the environment variable OMP_NUM_THREADS before running an executable.

The default version of clang does not implement openMP.

Cuba

If you configured BAT with the option --with-cuba=download, BAT will download, compile, and use Cuba automatically. For manual configuration, use the configure option --with-cuba[=DIR] to enable Cuba. If you installed Cuba including the partview executable, the Cuba installation path will be derived from its location. Otherwise, the configure script will search for libcuba.a and cuba.h in the system paths. If you manually specify the Cuba install path as DIR, configure will look in DIR/lib/ and DIR/include/ instead. For more fine-grained control, use --with-cuba-include-dir=/path/to/cuba/header and --with-cuba-lib-dir=/path/to/cuba/lib.

Advanced options

If you want to be able to step through BAT line by line with a debugger, use --enable-debug. This slows down execution as it turns off code optimization but it improves the compilation time. Another way to speed up the build is to create only shared libraries if you don't need static libraries: --disable-static. Finally, you can reduce the output to the terminal with --enable-silent-rules.

Compile

After a successful configuration, run

make
make install

to compile and install BAT. Note that depending on the setting of the installation prefix you might need super-user privileges to be able to install BAT and run sudo make install instead of plain make install. In the former case, you might need to run sudo ldconfig just once to help the loader pick up the new libraries immediately.

System setup

After installation, BAT offers two mechanisms to make BAT available:

  1. The script bat-config returns details of the BAT installation directories and compilation settings; see bat-config.

  2. The file bat.pc contains the same information as above and can be used by the more powerful pkg-config; e.g.,

     pkg-config --modversion bat
 pkg-config --libs bat

If you do not install BAT to the system directories, you need to manually add the path to bat-config, bat.pc, the libraries, and the include files to the search paths. Depending on your shell, the set of commands on linux for bash-compatible shells is

BATPREFIX="/bat/install/prefix"
export PATH="$BATPREFIX/bin:$PATH"
export CPATH="$BATPREFIX/include:$CPATH"
export LD_LIBRARY_PATH="$BATPREFIX/lib:$LD_LIBRARY_PATH"
export PKG_CONFIG_PATH="$BATPREFIX/lib/pkgconfig:$PKG_CONFIG_PATH"

and for csh-compatible shells is

set BATPREFIX = /bat/install/prefix
setenv PATH              "${BATPREFIX}/bin:${PATH}"
setenv CPATH             "${BATPREFIX}/include:${CPATH}"
setenv LD_LIBRARY_PATH   "${BATPREFIX}/lib:${LD_LIBRARY_PATH}"
setenv PKG_CONFIG_PATH   "${BATPREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}"

If you want to make BAT permanently available, add the above commands to your login script, for example to .profile or to .bashrc.

On Mac OS X you do not have to set up LD_LIBRARY_PATH because we use the rpath option to make BAT compatible with the SIP feature enabled by default on Mac OS X starting with El Capitan.

Updating $CPATH is required if you work with interactive ROOT macros that use BAT (both for ROOT 5 and 6).

The minimal setup does not require setting PKG_CONFIG_PATH to run BAT unless you want to integrate BAT into another probject using pkg-config. BAT itself does not use pkg-config.

Including BAT in your project

The most basic way to compile and link a file example.cxx with BAT is

gcc `bat-config --cflags` `bat-config --libs` example.cxx -o

In a makefile, simply query bat-config to set appropriate variables. However, there will be an error at runtime, for example in interactive ROOT macros, if

libBAT.so, libBATmodels.so, libBATmtf.so,
libBAT.rootmap, libBATmodels.rootmap, libBATmtf.rootmap

are not in the directories searched by the library loader; see above how to setup the LD_LIBRARY_PATH and the CPATH.

Interactive ROOT macros

Due to problems in ROOT 6.02.00, it is important to create an instance of a BAT class before calling any free function defined in the BAT libraries. Else cling will emit confusing error messages. For example, the right order would be

int main() {
    BCLog::OpenLog("log.txt");
    BCAux::SetStyle();
    ...
}

instead of the other way around around because OpenLog creates a singleton object.

Contact

Please consult the BAT web page http://mpp.mpg.de/bat/ for further information. In case of questions or problems, please don't hesitate to create an issue at https://github.com/bat/bat/issues/ or contact the authors directly via email through [email protected].