ApCoCoALib:CompilationInstructions

This page describes how to compile the most recent version of ApCoCoALib which you can check out from our subversion repository. To compile the versions which you can find under Downloads please follow also these instructions but with respect to the respective build specifications.

Requirements

You need at least the following libraries:

Library	Recommended	Minimum	Dependencies	Notes
CoCoALib	0.99.28	-	GMP	-
GMP	4.3.1	4.2.4	4.1.4	M4, libtool	-
Boost	1.39	1.36	none	System, Filesystem & Thread needed for ApCoCoA-Server

Optional:

Library	Recommended	Minimum	Dependencies	Notes
BLAS	?	?	none	for ABM & numerical functions
Lapack	3.2.1	-	BLAS	for ABM & numerical functions
LinBox	1.1.6	1.1.6	BLAS, Givaro, Lapack, GMP, libtool	-
Boost	1.39	1.36	none	Thread & Program Options needed for Border Basis Framework
IML	1.0.2	1.0.2	GMP, ATLAS, libtool	-
Givaro	3.2.16	3.2	none	-
ATLAS	3.8.3 (stable)	3.8.3	none	-

The Config File

ApCoCoALib lets you choose which of the optional features you want to compile in a very flexible way. Usually you store all build related configuration parameters in a file called lib.config and pass its location to the configure script via the --with-libconfig= parameter. The lib.config file looks as follows.

 ######################
 # Mandatory settings #
 ######################
 
 # Path to your Boost library include directory, e.g.
 #BOOSTFLAGS=-I"/home/skaspar/lib/boost_1_38_0/include/boost-1_38"
 BOOSTFLAGS=   # Mandatory, cannot be left empty
 
 # Linker flags of your Boost thread libraries plus linker flags of
 # additional libraries needed by Boost, e.g.
 #BOOSTLIBS="/home/skaspar/lib/boost_1_38_0/lib/libboost_thread-gcc43-mt.a" \
 #          -lpthread
 BOOSTLIBS=   # Mandatory, cannot be left empty
 
 #####################
 # Optional features #
 #####################
 
 # Uncomment the following flag if you want to use the
 # Border Basis Framework
 #BBFFLAGS=-DUSEBBFramework
 BBFFLAGS=   # Can be left empty if you do not want to use
             # the Border Basis Framework
 
 # Linker flags of your Boost program_options and thread
 # libraries plus linker flags of additional libraries needed
 # by Boost, e.g.
 #BBFLIBS="/home/skaspar/lib/boost_1_38_0/lib/libboost_program_options-gcc43-mt.a" \
 #        "/home/skaspar/lib/boost_1_38_0/lib/libboost_thread-gcc43-mt.a" \
 #        -lpthread
 BBFLIBS=   # Can be left empty if you do not want to use
            # the Border Basis Framework
 
 # Uncomment the following flag if you want to use
 # IML-driven computations    
 #IMLFLAGS=-DUSEIML
 
 # Path to your IML include directory, e.g.
 #IMLFLAGS:=$(IMLFLAGS) -I"/home/skaspar/lib/iml-1.0.2/include"
 
 IMLFLAGS:=$(IMLFLAGS)   # Can be left empty if you do not
                         # want to use IML-driven
                         # computations
 
 # Linker flags of your IML library plus linker flags of
 # additional libraries needed by IML, e.g.
 #IMLLIBS="/home/skaspar/lib/iml-1.0.2/lib/libiml.a" \
 #        -lcblas \
 #        -latlas \
 #        "/usr/lib/libgmp.a"
 IMLLIBS=  # Can be left empty if you do not want to use
           # IML driven computations
 
 # Uncomment the following flag if you want to use LinBox-
 # driven computations
 #LINBOXFLAGS=-DUSELinBox
 
 # Path to your LinBox include directory plus path to
 # additional include directories needed by LinBox, e.g.
 #LINBOXFLAGS:=$(LINBOXFLAGS) \
 #            -I"/home/skaspar/lib/linbox-1.1.6/include" \
 #            -I"/home/skaspar/lib/givaro-3.2.13rc1/include"
 LINBOXFLAGS:=$(LINBOXFLAGS)   # Can be left empty if you
                               # do not want to use LinBox-
                               # driven computations
 
 # Linker flags of your LinBox library plus linker flags
 # of additional libraries needed by LinBox, e.g. 
 #LINBOXLIBS=/home/skaspar/lib/linbox-1.1.6/lib/liblinbox.a \
 #           -lgmpxx \
 #           /home/skaspar/lib/givaro-3.2.13rc1/lib/libgivaro.a
 LINBOXLIBS=   # Can be left empty if you do not
               # want to use LinBox-driven
               # computations
 
 # Uncomment the following flag if you do not want
 # to use the BLAS and Lapack libraries
 NUMFLAGS=-DUSENoLapack
 
 # Uncomment the following flag if you want to use
 # the BLAS and Lapack libraries and you are using
 # Linux or Cygwin
 #NUMFLAGS=-DUSEF77Lapack
 
 # Uncomment the following flag if you want to use
 # the BLAS and Lapack libraries provided by the
 # Accelerate Framework on MacOSX
 #NUMFLAGS=-DUSEAccFW
 
 # Linker flags of your BLAS and Lapack libraries
 # plus linker flags of additional libraries needed
 # by BLAS and/or Lapack.
 #
 # Example flags on a Linux or cygwin system
 #NUMLIBS=-llapack -lblas -latlas
 #  
 # Example flags on a MacOSX system using the
 # the Accelerate Framework
 #NUMLIBS=-bind_at_load -framework accelerate
 NUMLIBS=   # Can be left empty if you do
            # not want to use the BLAS and
            # Lapack libraries

Step by Step build instructions

New: Building ApCoCoA with CMake

Get a copy of the sources for CoCoALib from http://cocoa.dima.unige.it/cocoalib/changelog-0.99.html and ApCoCoALib from the subversion repository.

 $> svn co svn://apcocoa.org/ ApCoCoA

Build the CoCoALib. You should consult the CoCoALib documentation in case of problems.

Go to the ApCoCoA directory and do the following (note again that CMake 2.6 is required). Making the directory build may seem strange at first, however, it has the advantage that all generated code resides only within this directory and the original src-directory is not polluted.

 $> cd ApCoCoA
 $> mkdir build
 $> cd build
 $> ccmake ..

ccmake starts an curses dialog that allows you to configure the necessary project settings. See also the cmake documentation

1. Type c. Starting ccmake the first time, this will probably raise some errors which is ok when your libraries are not in standard locations.
2. Edit the respective lines (type Enter to edit). In particular, you should provide the paths to Boost and the CoCoA directory (see below). In case you must also supply compiler flags such as -m64, type t to toggle between the initial "sparse" item selection and the full variable selection.
3. Type c. If errors occur, go to step 2. If no errors occur, type e.
4. Type g.

Finally,

 $> make

The tests will have to be started explicitly:

 $> make check

or

 $> ctest -V

where -V also prints the output of the test scripts.

We conclude with the description of the most common flags to be set with ccmake

• APCOCOA_USE_* Setting one or more of these to ON will (after c) turn on more flags to be set.
• COCOA_ROOT Must be set to the CoCoA directory which contains the folders lib and include.
• BOOST_ROOT must be set to the directory containing the boost lib and include directories.
• Boost_USE_STATIC_LIBS must be set to ON.
• GMP_LIBRARY, GMP_LIBRARY_DIR must be set to the static GMP libraries.
• CMAKE_CXX_FLAGS Add here -m64 and the like.
• CMAKE_EXE_LINKER_FLAGS Add here additional linker flags like -pthread or (on Mac) -bind_at_load -framework accelerate.
• ENABLE_TESTING If set to OFF the tests in src/Tests will not be compiled.

Advanced usage of CMake is collected on the page Working with CMake

Old: Building ApCoCoA

Get a copy of the sources for CoCoALib from http://cocoa.dima.unige.it/cocoalib/changelog-0.99.html and ApCoCoALib from the subversion repository.

Build the CoCoALib. You should consult the CoCoALib documentation in case of problems.

Build the ApCoCoALib: Unpack the tarball in the same directory as CoCoALib-0.99. This is the default location that ApCoCoALib will look for. You can change it but at the moment this requires editing of the COCOA_DIR_NAME in the file configuration/autoconf.mk. We will offer the location of CoCoALib as a config option in the libconfig file in a later release.

Again, please note that

• the CoCoALib directory must be named as CoCoALib-0.99
• the CoCoALib and ApCoCoALib directory must reside in the same directory.

Now run configure:

[mabshoff@dhcp75 ApCoCoALib-0.99]$ ./configure
ERROR: Specified config file is not a readable file: ""
Please specify a config file for the external numerical libraries via --with-libconfig

You get an error because ApCoCoALib needs to be told where to find several external libraries and options. One option is to set CONFIG_LIB="lib.config" in the configure script and create the file called lib.config with the following text:

# we don't want to compile in any numerical libraries
NUMFLAGS=-DUSENoLapack 

With this config file you deactivate all numerical methods provided by ApCoCoALib. Chances are you do not want to do this. But since building the numerical libraries can be a little complicated we provide precompiled libraries and config examples at http://apcocoa.org/hg/NumLibs/file/ FIXME: Add more details and tarballs.

In case you have Mac Os X as your operating system, it is very easy to include the numerical Libraries. Per default, you have an installed Accelerate Framework, which includes BLAS and Lapack, which are the numerical libraries we currently use. To activate the accelerate framework, your lib.config should include the lines:

NUMFLAGS=-DUSEAccFW

# linker options:
NUMLIBS=-bind_at_load -framework accelerate

With a working set of libraries we rerun configure and get:

[mabshoff@dhcp75 ApCoCoALib-0.99]$ ./configure  --with-libconfig=../NumLibs/lib.config.USEF77Lapack
The C++ compiler is g++ 4.1.1 20070105 (Red Hat 4.1.1-51)
The C++ optimized compilation flags are "-Wall -pedantic -fPIC -O2"
Using GMP library version 4.2.1 found in "/usr/local/gmp-4.2.1-static/lib/libgmp.a".
and GMP header file found in "/usr/local/gmp-4.2.1-static/include/gmp.h" 
Configuration process complete: info saved in configuration/autoconf.mk
-----------------------------------------------------------------------

Everything is fine now. Just enter

 make

and the ApCoCoAServer as well as the ApCoCoALib should be build.

In case of problems please complain in the forum.

Building External Dependencies

Visualization of the build dependencies

The arrows of the following pictures indicate the order of the libraries to be built, e.g. you have to build the GMP before CoCoALib.

Linux example build (Fedora 18 with gcc-4.7.2)

Go to the directory all source files should be downloaded in. Let <ApCoCoA-PATH> be the path to this directory.

This guide installs all libraries in the default directories, i.e. using the prefix /usr/local/. If you want to install the files somewhere else, use the appropriate flags during the build process of the packages.

Note: You must have 'admin rights to perform all steps of this guide and all lines starting with #. are comments.

Use your package manager to install the necessary packages; e.g.

yum install bzip2 cmake gcc-c++ gdb gfortran glibc-static gnome-applets libtool libgfortran-static libstdc++-static make patch subversion zlib

GMP (5.0.5)

wget ftp://ftp.gmplib.org/pub/gmp-5.0.5/gmp-5.0.5.tar.bz2
tar -xjvf gmp-5.0.5.tar.bz2
cd gmp-5.0.5
./configure --enable-cxx
make
make check
make install
cd ..

CoCoALib (0.9945)

wget http://cocoa.dima.unige.it/cocoalib/tgz/CoCoALib-0.9945.tgz
tar -xzvf CoCoALib-0.9945.tgz
cd CoCoALib-0.9945
./configure --with-libgmp=/usr/local/lib/libgmp.a
make
cd ..

Boost (1.53.0)

wget --trust-server-name http://sourceforge.net/projects/boost/files/boost/1.53.0/boost_1_53_0.tar.bz2/download
tar -xjvf boost_1_53_0.tar.bz2
cd boost_1_53_0
./bootstrap.sh
./bjam install
cd ..

Lapack (3.4.1)

wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
tar -xzvf lapack-3.4.1.tgz
cd lapack-3.4.1
cmake .
make
make install
cd ..

Givaro (3.2.16)

tar -xzvf givaro-3.2.16.tar.gz
cd givaro-3.2.16
# the -fpermissive flag is necessary for gcc-4.7.x
./configure CXX_FLAGS=-fpermissive
make
# Note: After make check, some errors might occur. This is no problem for the build.
make check
make install
cd ..

ATLAS (3.10.0)

wget --trust-server-name http://sourceforge.net/projects/math-atlas/files/Stable/3.10.0/atlas3.10.0.tar.bz2/download
tar -xjvf atlas3.10.0.tar.bz2
cd ATLAS
mkdir ATLAS_build
cd ATLAS_build
# If CPU throttling is activated, you have to turn it off.
cpufreq-selector -g performance
../configure
make
make check
make install
# If CPU throttling has been deactivated, you have to turn it on again.
cpufreq-selector -g ondemand
cd ../..

LinBox (1.1.6)

wget http://www.linalg.org/linbox-1.1.6.tar.gz
tar -xzvf linbox-1.1.6.tar.gz
cd linbox-1.1.6
wget ftp://apcocoa.org/pub/patches/1.1.6-multiple-definitions-fix_301008.patch
patch -p1 -i 1.1.6-multiple-definitions-fix_301008.patch
# the -fpermissive flag is necessary for gcc-4.7.x
./configure CXX_FLAGS=-fpermissive --with-blas=/usr/local/atlas
make
make check
make install
cd ..

IML (1.0.3)

wget http://www.cs.uwaterloo.ca/~astorjoh/iml-1.0.3.tar.gz
tar -xzvf iml-1.0.3.tar.gz
cd iml-1.0.3
./configure --with-atlas-include=/usr/local/atlas/include/ --with-atlas-lib=/usr/local/atlas/lib/
make
make check
make install
cd ..

TBB (2013-03-14)

wget http://threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb41_20130314oss_src.tgz
tar -xzvf tbb41_20130314oss_src.tgz
cd tbb41_20130314oss
make
# cd build/linux_<system-specific>_release; e.g.
cd build/linux_intel64_gcc_cc4.7.2_libc2.16_kernel3.8.11_release
ar rcs libtbb.a concurrent_hash_map.o concurrent_queue.o concurrent_vector.o dynamic_link.o itt_notify.o \
       cache_aligned_allocator.o pipeline.o queuing_mutex.o queuing_rw_mutex.o reader_writer_lock.o \
       spin_rw_mutex.o spin_mutex.o critical_section.o task.o tbb_misc.o tbb_misc_ex.o mutex.o recursive_mutex.o \
       condition_variable.o tbb_thread.o concurrent_monitor.o semaphore.o private_server.o rml_tbb.o \
       task_group_context.o governor.o market.o arena.o scheduler.o observer_proxy.o tbb_statistics.o \
       tbb_main.o concurrent_vector_v2.o concurrent_queue_v2.o spin_rw_mutex_v2.o task_v2.o
cd ../../..

PGBC (v0.8)

wget http://github.com/svrnm/parallelGBC/archive/v0.8.zip
unzip v0.8.zip
cd parallelGBC-0.8
# Note: Using relative paths, you have to add ../ as prefix to the path (like in the example).
# Change the following lines in Makefile.rules as follows (using your specific TBB path); e.g.
#   TCMALLOC = 
#   CXXFLAGS = -fPIC -Wall -fopenmp -O2 -pipe -std=c++0x -I../../tbb41_20130314oss/include \
#              -L../../tbb41_20130314oss/build linux_intel64_gcc_cc4.7.2_libc2.16_kernel3.8.11_release/
make
cd ..

PGBC (v0.8 in the case that the SSE instruction set is not enabled)

wget http://github.com/svrnm/parallelGBC/archive/v0.8.zip
unzip v0.8.zip
cd parallelGBC-0.8
wget ftp://apcocoa.org/pub/patches/sse.patch
patch -p1 -i sse.patch
# Note: Using relative paths, you have to add ../ as prefix to the path (like in the example).
# Change the following lines in Makefile.rules as follows (using your specific TBB path); e.g.
#   TCMALLOC = 
#   CXXFLAGS = -fPIC -Wall -fopenmp -O2 -pipe -std=c++0x -I../../tbb41_20130314oss/include \
#              -L../../tbb41_20130314oss/build linux_intel64_gcc_cc4.7.2_libc2.16_kernel3.8.11_release/
make
cd ..

ApCoCoALib (nightly)

Note: You must always use static libraries (*.a files) to build ApCoCoALib.

svn co https://www.apcocoa.org/svn/ApCoCoALib/trunk
mv trunk ApCoCoALib
cd ApCoCoALib
mkdir ApCoCoALib_build
cd ApCoCoALib_build
ccmake ..
# Use the GUI to configure your paths appropriately, where
#   [<button>] means push button <button> and
#   <option>=<value> means that you have to set <option> to <value> .
#     [c]; [e]
#       APCOCOALIB_BUILD_BBF=ON
#       APCOCOALIB_ENABLE_NUMERICAL=ON
#       APCOCOALIB_USE_IML=ON
#       APCOCOALIB_USE_LINBOX=ON
#       APCOCOALIB_USE_PGBC=ON
#       COCOALIB_ROOT=<ApCoCoA-PATH>/CoCoALib-0.9945
#     [c]; [e]
#       PGBC_INCLUDE_DIR=<ApCoCoA-PATH>/parallelGBC-0.8/include
#       PGBC_LIBRARY=<ApCoCoA-PATH>/parallelGBC-0.8/lib/libf4.a
#     [c]; [e]
#       TBB_INCLUDE_DIR=<ApCoCoA-PATH>/tbb41_20130314oss/include
#       TBB_LIBRARY=<ApCoCoA-PATH>/tbb41_20130314oss/build/linux_intel64_gcc_cc4.7.2_libc2.16_kernel3.8.11_release/libtbb.a
#     [c]; [e]; [t]
#   Set additional libraries for the linker; e.g.
#       ADD_LINK_LIBS=/lib/gcc/x86_64-redhat-linux/4.7.2/libgfortran.a;/lib64/librt.a
#   (The absolute path to lingfortran.a is necessary to fix compile errors of the form "'undefined reference to '_gfortran_*'".)
#   (The absolute path to librt.a is necessary to fix compile errors of the form "undefined reference to 'clock_gettime'".)
#   Set additional c++ compiler flags; e.g.
#       CMAKE_CXX_FLAGS=-fpermissive
#   (This flag is necessary if you want to buil ApCoCoA with Givaro/LinBox.)
#     [c]; [e]
#     [c]; [e]; [g]
make
make check
make examples

Windows

Compilers

MSVC 2003, MSVC 2005, Intel C++, Cygwin

CoCoALib

Build from source, prebuild packages for MSVC 2005, MSVC 2003, Cygwin

GMP

Brian Gladman's build for MSVC, from source for Cygwin/MinGW.

Note: Check if the programs bison, flex, m4 and libtool are installed in cygwin.

./configure --enable-cxx --host=i386-pc-cygwin --prefix=(install-dir)
make
make check (important!!!)
make install

BLAS/Lapack

Cygwin ships with BLAS and Lapack from netlib.org compiled as a dynamic library. These are regularly tested and do work well. Alterntively you can compile ATLAS, but there are occasional linker issues.

If you use the Microsoft's compilers you can use the Intel MKL, GotoBLAS or ATLAS 3.8.0. It is also possible to build netlib.org's BLAS and Lapack using a Fortran compiler from Intel.

ATLAS

cd atlas-dir
mkdir ATLAS_build
cd ATLAS_build
../configure -A 6 -V 1 -b 32 --prefix=(install-dir)
make
make check
make install

IML

./configure --prefix=(install-dir) --host=i386-pc-cygwin --with-gmp-include= --with-gmp-lib= --with-atlas-include= --with-atlas-lib=
make
make check
make install

Note: Check if libtool is installed. Might lead to problems if it's not found.

LinBox

Build from source, Cygwin only at the moment. It is highly recommened that you build LinBox as a static library, there have been linking issues with a dynamic LinBox in the past. You might also need to tweak LinBox's m4 BLAS detection macros when using netlib.org's BLAS and Lapack.

Note: Check if libtool is installed. Might lead to problems if it's not found.

Linux

Compilers

g++ 3.3 up to 4.2

CoCoALib

Build from source.

./configure --with-libgmp=(path-to-libgmp.a)
make

GMP

Distribution package, build from source.

./configure --enable-cxx --prefix=(install-dir)
make
make check (important!!!)
make install

Note: --enable-cxx gives you C++ support. This is important for some of the optional libs. Check if libtool is installed on your system. The configure script makes some entries to libtool that are needed later for the configure script of linbox.

BLAS/Lapack

Distribution package, build from source: ATLAS, netlib.org, GotoBLAS, IntelMKL

ATLAS

Build from source. Install instructions:

tar -xvzf atlas3.xx.tar.gz
cd ATLAS
mkdir ATLAS_build
cd ATLAS_build
../configure --prefix=(install-dir) -b 32 (or -b 64 for 64 Bit support)
make
make check
make install

Important: For compiling ATLAS you need an extra build-directory, that must be within the directory where you extracted your files to. Call the configure-script from within the build-directory, as noted above. For further informations see atlas_install.pdf in ATLAS/doc. Please also see the .pdf if you have some kind of special architecture like 64bit.

Note for Laptop-Users: You have to set you CPU power scheme to "performance", in order to have maximum speed for the tests, that are performed during the ATLAS compiling routine. If you have a DualCore remember to do this for both cores!
To change the power scheme you can use tools like cpufrequtils, normally found within the repository of your package manager.

LinBox

Distribution package. Build from source.

./configure --prefix=(install-dir) --with-blas=(atlas-dir) --with-givaro=... --with-gmp=...
make
make check
make install

Note: Apply the Patch from the Forum, see 2nd Post. This fixes the multiple definiton errors.

Givaro

Distribution package. Build from source.

./configure --prefix=(install-dir) --with-gmp=(gmp-dir)
make
make check
make install

MacOSX

The following steps were taken on an Apple MacBook (Intel Core 2 Duo), OS X 10.4.

Compilers

Xcode 2.4.1 recommened, for current releases we are using xcode 2.5.

CoCoALib

Build from source.

Boost

This might not be the best way to supply the '-m64' argument, but it works.

 ./configure [--prefix=<path>]
 ./tools/jam/src/bin.macosxx86/bjam  -d+2 --user-config=user-config.jam architecture=x86 address-model=64 cxxflags=-m64
 ./tools/jam/src/bin.macosxx86/bjam  --user-config=user-config.jam --prefix=<> --exec-prefix=<> --libdir=<> --includedir=<>  architecture=x86 address-model=64 cxxflags=-m64 install

GMP

build from source, can be tricky, need the right patch and working xcode. Try the following:

 ./configure [--prefix=<>] --enable-cxx
 make
 make check
 make install

BLAS/Lapack

AccelerateFrameWork recommended (installed per default). Also possible: build from sources: ATLAS, netlib.org installer: IntelMKL

LinBox

build from source

Givaro

 ./configure [--prefix=<>] --with-gmp=</path/to/dir> CXXFLAGS=-m64
 make
 make install

In file givaro-config.h the flag __GIVARO_GMP_NO_CXX must not be set. Otherwise we got problems with wrong includes compiling ApCoCoA.

Linbox

Apply the patch given in http://www.apcocoa.org/forum/viewtopic.php?f=20&t=983

 ./configure --prefix=<> --with-gmp=<> --with-givaro=<> CXXFLAGS=-m64
 make
 make install

IML

Now, that was quite involved. If anyone knows a better way to get IML compiled, please let us know.

 ./configure -prefix=<> --with-gmp-lib=<> --with-gmp-include=<> --with-atlas-include=<> --with-atlas-lib=<> CFLAGS=-m64

(Yes, its CFLAGS and _not_ CXXFLAGS) After configuring, do the following:

 cp librepl.a repl
 cd repl/.libs
 ln -s ../librepl.a librepl.a
 echo "!<arch>" > repl/.libs/librepl.a

On a mac, this seems to be necessary since libtool does apparently not work properly (any help on this is welcome) and we have to fool ar (this approach is just mimicked from a working Linux compilation).

 make
 make check
 chmod 755 config/install-sh

(Do not ask...)

 make install

ATLAS

(Used gFortran, downloaded from http://r.research.att.com/tools)

 ../configure --prefix=<>
 make
 make install

Solaris/UNIX

Compilers

g++ 3.3 up to 4.2, SunPro compiler difficult to use due to problem with gmpxx.h

CoCoALib

Build from source

GMP

Distribution package, build from source

BLAS/Lapack

recommneded: SunPerfLib build from sources: ATLAS, netlib.org

LinBox

build from source

ToDo

• configure no longer errors out, but write a warning
• make links to targz'ed libraries available