JAGS Version 3.3.0 installation manual
Contents
1. source opt intel composerxe 2011 bin compilervars sh intel64 Then call the configure script with the Intel compilers CC icc CXX icpce F77 ifort configure 1 3 7 Using Clang JAGS has been built with the clang compiler for C and C version 3 1 The configuration was LD llvm 1d CC clang CXX clang configure In this configuration the gfortran compiler was used for Fortran and the C code was linked to the GNU standard C library libstdc rather than the version supplied by the LLVM project libc 1 4 Solaris JAGS has been successfully built and tested on the Intel x86 platform under Solaris 11 using the Sun Studio 12 3 compilers configure CC cc CXX CC F77 f95 CFLAGS x03 xarch sse2 FFLAGS x03 xarch sse2 CXXFLAGS x03 xarch sse2 The Sun Studio compiler is not optimized by default Use the option x03 for optimization NB This is the letter O not the number 0 In order to use the optimization flag x03 you must specify the architecture with the xarch flag The options above are for an Intel processor with SSE2 instructions This must be adapted to your own platform To compile a 64 bit version of JAGS add the option m64 to all the compiler flags Solaris provides two versions of the C standard library libCstd which is the default and libstlport4 which conforms more closely to the C standard JAGS may be linked to the stlport4 library by adding the opti2. out implib liblapack dll a liblapack def liblapack a L lblas lgfortran 10 3 2 Compiling JAGS Unpack the JAGS source tar xfvz JAGS 3 3 0 tar gz cd JAGS 3 3 0 and configure JAGS for a 32 bit build CC gcc m32 CXX g m32 F77 gfortran m32 configure LDFLAGS L path to import libs W1 enable auto import where path to import libs is a directory that contains the 32 bit import libraries libblas dll a and liblapack dll a This must be an absolute path name and not relative to the JAGS build directory After the configure step type make win32 install This will install JAGS into the subdirectory win inst32 Note that you must go straight from the configure step to make win32 install without the usual step of typing make on its own The win32 install target resets the installation prefix and this will cause an error if the source is already compiled To install the 64 bit version clean the build directory make clean reconfigure JAGS for a 64 bit build CC gcc m64 CXX g m64 F77 gfortran m64 configure LDFLAGS L path to import libs W1 enable auto import Then type make win64 install This will install JAGS into the subdirectory win inst64 With both 32 bit and 64 bit installations in place you can create the installer Normally you will want to distribute the blas and lapack libraries with JAGS In this case put the 32 bit DLLs and import libraries in
3. and the must not be followed by any spaces export CC usr bin clang export CXX usr bin clang export CFLAGS g 0s mmacosx version min 10 6 isysroot Applications Xcode app Contents Developer Platforms MacO0SX platform Developer SDKs Mac0SX10 8 sdk arch i386 arch x86_64 export CXXFLAGS g 0s mmacosx version min 10 6 isysroot Applications Xcode app Contents Developer Platforms Mac0SX platform Developer SDKs Mac0SX10 8 sdk arch i386 arch x86_64 export FFLAGS g 0s mmacosx version min 10 6 isysroot Applications Xcode app Contents Developer Platforms Mac0SX platform Developer SDKs MacOSX10 8 sdk arch i386 arch x86_64 export LDFLAGS mmacosx version min 10 6 arch i386 arch x86_64 2 4 Configuration To configure the package type configure disable dependency tracking with included 1tdl This instruction should complete without reporting an error 2 5 Compile To compile the code type make j 8 The number 8 indicates the number of build threads that should be run In general this is best as twice the number of CPU cores in the computer Most current Macs have four core CPUs If your machine is different you may want to change the number in the instruction Again this instruction should complete without errors 2 6 Install Finally to install JAGS you need to be using an account with administration privileges Type sudo make install This will ask for your account pass
4. lib If you are building a 64 bit version of JAGS this may not be appropriate for your system On Fedora and other RPM based distributions for example 64 bit libraries should be installed in lib64 and on Solaris 64 bit libraries are in a subdirectory of lib e g lib amd64 if you are using a x86 64 processor whereas on Debian and other Linux distributions that conform to the FHS the correct installation directory is lib To ensure that JAGS libraries are installed in the correct directory you should supply the libdir argument to the configure script e g configure libdir usr local 1ib64 It is important to get the installation directory right when using the rjags interface between R and JAGS otherwise the rjags package will not be able to find the JAGS library 1 1 2 Configuration for a private installation If you do not have administrative privileges you may wish to install JAGS in your home directory This can be done with the following configuration options export JAGS_HOME HOME jags or wherever you want it configure prefix JAGS_HOME For more detailed control over the installation directories type configure help and read the section Fine tuning of the installation directories With a private installation you need to modify your PATH environment variable to include JAGS_ HOME bin You may also need to set LD_LIBRARY_PATH to include JAGS_ HOME lib On
5. the sub directory win runtime32 and the 64 bit DLLs and import libraries in the sub directory win runtime64 They will be detected and included with the distribution Make sure that the file makensis exe provided by NSIS is in your PATH For a typical installation of NSIS on 64 bit windows PATH PATH c Program files x86 NSIS Then type make installer After the build process finishes the self extracting archive will be in the subdirectory win 11
6. DFLAGS L path to my libs R path to my libs 1 2 1 Multithreaded BLAS and LAPACK Some high performance computing libraries offer multi threaded versions of the BLAS and LAPACK libraries Although instructions for linking against some of these libraries are given below this should not be taken as encouragement to use multithreaded BLAS Testing shows that using multiple threads in BLAS can lead to significantly worse performance while using up substantially more computing resources 1 3 GNU Linux GNU Linux is the development platform for JAGS and a variety of different build options have been explored including the use of third party compilers and linear algebra libraries 1 3 1 Fortran compiler The GNU FORTRAN compiler changed between gcc 3 x and gcc 4 x from g77 to gfortran Code produced by the two compilers is binary incompatible If your BLAS and LAPACK libraries are linked against libgfortran then they were built with gfortran and you must also use this to compile JAGS Most recent GNU Linux distributions have moved completely to gcc 4 x However some older systems may have both compilers installed Unfortunately if g77 is on your path then the configure script will find it first and will attempt to use it to build JAGS This results in a failure to recognize the installed BLAS and LAPACK libraries In this event set the F77 variable at configure time F77 gfortran configure 1 3 2 BLAS and LAPACK The BLAS and LAPACK lib
7. JAGS Version 3 3 0 installation manual Martyn Plummer Bill Northcott 1 October 2012 JAGS is distributed in binary format for Microsoft Windows Mac OS X and most Linux distributions The following instructions are for those who wish to build JAGS from source The manual is divided into three sections with instructions for Linux Unix Mac OS X and Windows 1 Linux and UNIX JAGS follows the usual GNU convention of configure make make install which is described in more detail in the file INSTALL in the top level source directory On some UNIX platforms you may be required to use GNU make gmake instead of the native make command On systems with multiple processors you may use the option j to speed up compilation e g for a quad core PC you may use make j4 1 1 Configure options At configure time you also have the option of defining options such as e The names of the C C and Fortran compilers e Optimization flags for the compilers JAGS is optimized by default if the GNU compiler gcc is used If you are using another compiler then you may need to explicitly supply optimization flags e Installation directories JAGS conforms to the GNU standards for where files are in stalled You can control the installation directories in more detail using the flags that are listed when you type configure help 1 1 1 Configuration for a 64 bit build By default JAGS will install all libraries into usr local
8. Linux this is not necessary as the location of libjags and libjrmath is hard coded into the JAGS binary 1 2 BLAS and LAPACK BLAS Basic Linear Algebra System and LAPACK Linear Algebra Pack are two libraries of routines for linear algebra They are used by the multivariate functions and distributions in the bugs module Most unix like operating system vendors supply shared libraries that provide the BLAS and LAPACK functions although the libraries may not literally be called blas and lapack During configuration a default list of these libraries will be checked If configure cannot find a suitable library it will stop with an error message You may use alternative BLAS and LAPACK libraries using the configure options with blas and with lapack configure with blas lmyblas with lapack lmylapack If the BLAS and LAPACK libraries are in a directory that is not on the default linker path you must set the LDFLAGS environment variable to point to this directory at configure time LDFLAGS L path to my libs configure At runtime if you have linked JAGS against BLAS or LAPACK in a non standard location you must supply this location with the environment variable LD_LIBRARY_PATH e g LD_LIBRARY_PATH path to my libs LD_LIBRARY_PATH Alternatively you may hard code the paths to the blas and lapack libraries at compile time This is compiler and platform specific but is typically achieved with L
9. l the command line tools into usr This is done within Xcode from Preferences gt Downloads Components This setup should be able to build the JAGS sources and also source packages in R All the necessary libraries such as BLAS and LAPACK are included in the standard MacOS install 2 2 Prepare the source code Move the downloaded JAGS X X X tar gz package to some suitable working space on your disk and double click the file This will decompress the package to give a folder called JAGS X X X where X X X is the version number Open the Terminal app from Applications Utilities This gives you a UNIX shell know as bash In the Terminal window after the prompt type ed followed by a space In the Finder drag JAGS X X X folder into the Terminal window and hit return If this worked for you typing ls followed by a return will list the contents of the JAGS folder 2 3 Set up the environment Executable files on MacOS can contain code for more than one CPU architecture 1386 x86_64 or ppc Executables with more than one architecture are described as fat The instructions below will build a fat binary of JAGS containing 32 bit i386 and 64 bit x86 64 code which will run on 10 6 10 7 and 10 8 This is compatible with current CRAN distributions of R and the rjags module In your Terminal window type the following instructions which set up the environment for the build Note that there is no space after platform
10. mples of linking to MKL using this layered model are given below These examples are for GCC compilers on x86_64 The choice of interface layer is important on x86_64 since the Intel Fortran compiler returns complex values differently from the GNU Fortran compiler You must therefore use the interface layer that matches your compiler mkl_intel or mkl_gf For further guidance consult the MKL Link Line advisor at http software intel com en us articles intel mkl link line advisor Recent versions of MKL include a shell script that sets up the environment variables necessary to build an application with MKL source opt intel composerxe 2011 mk1 bin mklvars sh intel64 After calling this script you can link JAGS with a sequential version of MKL as follows configure disable shared with blas lmkl_gf_1p64 lmkl_sequential lmkl_core lpthread Note that libpthread is still required even when linking to sequential MKL Threaded MKL may be used with configure disable shared with blas lmkl_gf_1p64 lmkl gnu thread lmkl_core liomp5 lpthread The default number of threads will be chosen by the OpenMP software but can be controlled by setting OMP_NUM_THREADS or MKL_NUM_THREADS See the warning in section 1 2 1 however 1 3 6 Using Intel Compilers JAGS has been successfully built with the Intel Composer XE compilers To set up the environment for using these compilers call the compilervars sh shell script e g
11. ndows You need some familiarity with Unix in order to follow the build instructions but once built JAGS can be installed on any PC running windows where it can be run from the Windows command prompt 3 1 Preparing the build environment You need to install the following packages e The TDM GCC compiler suite for Windows e MSYS e NSIS including the AccessControl plug in We used the TDM GCC compilers based on the MinGW w64 project http tdm gcc tdragon net This distribution was chosen because it allows us to build a version of JAGS that is statically linked against the gcc runtime library This in turn is neces sary to have a functional rjags package on Windows We also tried Rtools http www murdoch sutherland com Rtools Although the resulting JAGS library is functional it is not compatible with R loading the rjags package causes R to crash on exit TDM GCC has a nice installer available from Sourceforge follow the links on the main TDM GCC web site Ensure that you download the MinGW w64 sjlj version as this is capable of producing both 32 bit and 64 bit binaries Select a Recommended C C installation and customize it by selecting the Fortran compiler which is not installed by default After installation to force the compiler to use static linking delete any import libraries files ending in dll a in the TDM GCC tree MSYS the Minimal SYStem is part of the MinGW project It provides a bash shell for you t
12. o build Unix software Download the MinGW installer from http www mingw org We used mingw get inst 20120426 exe Run the installer and select MSYS Basic System There is no need to install the MinGW Developer Toolkit if you are working with a release tarball of JAGS It is not necessary to install any of the compilers that come with MinGW as we shall be using the TDM versions To make MSYS use the TDM compilers edit the file c mingw msys 1 0 etc fstab to read c MinGW64 mingw MSYS creates a home directory for you in c mingw msys 1 0 home username where username is your user name under Windows You will need to copy and paste the source files for LAPACK and JAGS into this directory The Nullsoft Scriptable Install System http nsis sourceforge net allows you to create a self extracting executable that installs JAGS on the target PC These instructions were tested with NSIS 2 46 You must also install the AccessControl plug in for NSIS which is available from http nsis sourceforge net AccessControl_plug in The plug in is distributed as a zip file which is unpacked into the installation directory of NSIS 3 1 1 Building LAPACK Download the LAPACK source file from http www netlib org lapack to your MSYS home directory We used version 3 4 1 You need to build LAPACK twice once for 32 bit JAGS and once for 64 bit JAGS The instructions below are for 32 bit JAGS To build 64 bit versions repeat the in
13. on library stlport4 to CXXFLAGS The configure script automatically detects the Sun Performance library which implements the BLAS LAPACK functions 2 Mac OS X There have been big changes in Apple s developer tools in the last couple of years Currently this may change at any time the core suite of tools are contained in Xcode This is now a single app which contains the command line tools in Xcode app Contents Developer usr instead of installing them in usr as was the previous arrangement The most recent version of Xcode 4 5 can be downloaded free from the App Store This version will only run on Lion 10 7 x and Mountain Lion 10 8 x If you are trying to build on an earlier version of MacOS you will need to download an older version of Xcode from the Mac Dev Center at http developer apple com This is no longer free You will need to sign up on the Mac Developer Program which costs 99 per year The program gives you access to many more resources including an Apple signed developer certificate which can be used to sign your code The instructions that follow assume you are using MacOS 10 7 or 10 8 and have the free Xcode from the App Store 2 1 Required tools If you wish to build from a released source package i e JAGS 3 3 0 tar gz you will need Xcode and the gfortran package which you can find by following the tools directory link on the R for Mac OS X page on CRAN You will also need to instal
14. raries from Netlib http www netlib org should be pro vided as part of your Linux distribution If your Linux distribution splits packages into user and developer versions then you must install the developer package e g blas devel and lapack devel Suse Linux Enterprise Server SLES does not include BLAS and LAPACK in the main distribution They are included in the SLES SDK on a set of CD DVD images which can be downloaded from the Novell web site See http developer novell com wiki index php SLES_SDK for more information 1 3 3 ATLAS On Fedora Linux pre compiled atlas libraries are available via the atlas and atlas devel RPMs These RPMs install the atlas libraries in the non standard directory usr lib atlas or usr 1ib64 at1las for 64 bit builds to avoid conflicts with the standard blas and lapack RPMs To use the atlas libraries you must supply their location using the LDFLAGS variable see section 1 2 configure LDFLAGS L usr lib atlas Runtime linking to the correct libraries is ensured by the automatic addition of usr lib atlas to the linker path see the directory etc 1d so conf d so you do not need to set the en vironment variable LD_LIBRARY_PATH at run time 1 3 4 AMD Core Math Library The AMD Core Math Library acml provides optimized BLAS and LAPACK routines for AMD processors To link JAGS with acm1 you must supply the acm1 library as the argument to with blas It is not necessary to se
15. structions with the flag m32 replaced by m64 and start in a clean build directory Note that you cannot cross build 64 bit BLAS and LAPACK on a 32 bit Windows system This is because the build process must run some 64 bit test programs Launch MSYS labelled as MinGW shell on the Windows Start Menu and unpack the tarball tar xfvz lapack 3 4 1 tgz cd lapack 3 4 1 Copy the file INSTALL make inc gfortran to make inc in the top level source directory Then edit make inc replacing the following lines FORTRAN gfortran m32 LOADER gfortran m32 Type make blaslib make lapacklib The compilation process is slow Eventually it will create two static libraries librefblas a and liblapack a These are insufficient for building JAGS you need to create dynamic link library DLL for each one First create a definition file libblas def that exports all the symbols from the BLAS library dlltool z libblas def export all symbols librefblas a Then link this with the static library to create a DLL libblas dll and an import library libblas dll a gcc m32 shared o libblas dll Wl out implib libblas dll a libblas def librefblas a lgfortran Repeat the same steps for the LAPACK library creating an import library liblapack dll a and DLL liblapack dll dlltool z liblapack def export all symbols liblapack a gcc m32 shared o liblapack d1ll W1
16. t the with lapack argument as acml provides both sets of functions See also section 1 2 for run time instructions For example to link to the 64 bit acml using gcc 4 0 LDFLAGS L opt acml14 3 0 gfortran64 lib configure with blas lacml lacml mv The acmv mv library is a vectorized math library that exists only for the 64 bit version and is omitted when linking against 32 bit acml On multi core systems you may wish to use the threaded acml library See the warning in section 1 2 1 however To do this link to acml_mp and add the compiler flag fopenmp LDFLAGS L opt acml4 3 0 gfortran64_mp lib CXXFLAGS 02 g fopenmp configure with blas lacml_mp lacml mv The number of threads used by multi threaded acml may be controlled with the environment variable OMP_NUM_THREADS 1 3 5 Intel Math Kernel Library The Intel Math Kernel library MKL provides optimized BLAS and LAPACK routines for Intel processors MKL is designed to be linked to executables not shared libraries This means that it can only be linked to a static version of JAGS in which the JAGS library and modules are linked into the main executable To build a static version of JAGS use the configure option disable shared MKL version 10 0 and above uses a pure layered model for linking The layered model gives the user fine grained control over four different library layers interface threading computation and run time Some exa
17. word and install the code ready to run as described in the User Manual You need to ensure usr local bin is in your PATH in order for jags to work from a shell prompt 2 7 Older versions of MacOS For instructions for building on Tiger or for older versions of R see previous versions of this manual 2 8 Tips for developers and advanced users 2 8 1 Compilers Older versions of Xcode used the gcc compiler suite Apple abandoned the gcc project when GPL3 was introduced Current Apple compilers are based on LLVM They are invoked as clang and clang Although there appear to be gcc and gxx these are actually gcc llvm with an out of date gcc 4 2 front end on LLVM These compilers are now deprecated While there are versions of current gcc available for MacOS they do not recognise the Apple specific arch flag This leads to a number of problems 2 8 2 Developer tools Now that Apple do not use gcc they have no use for many of the auxiliary GNU tools required to build it So the Xcode does not contain any of the autotools autoconf automaker and libtool If you want to work on code from the JAGS repository you will need to build and install these Other GNU tools like bison and make are available but may be very out of date because of the GPL3 issue Binaries of cvs subversion and git are included in Xcode Mercurial needs to installed separately if required 3 Windows These instructions use MinGW the Minimalist GNU system for Wi
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