Skip to content

Building M2 from source using Autotools

Jump to bottom Edit New page
Doug Torrance edited this page Jul 15, 2024 · 41 revisions

Quick start

After downloading the dependencies for your system (see below), do the following:

git clone https://github.com/Macaulay2/M2
cd M2/M2
make
cd BUILD
../configure --enable-download
make
sudo make install

Note: On macOS and BSD systems, use gmake instead of make.

Dependencies

Here are some dependencies you may have to install on your system to build Macaulay2:

Arch Linux

sudo pacman -S 4ti2 autoconf automake bison boost cddlib coin-or-csdp eigen fflas-ffpack flex flint gc gcc gcc-fortran gfan git givaro glpk gtest icu libtool libxml2 lrs make mpfi nauty normaliz ntl onetbb patch pkgconf python singular texinfo time topcom which

Note:

  • Add --with-gtest-source-path=/usr/src/googletest to the call to configure so that it can find GoogleTest.
  • cohomCalg, Frobby, Mathic, Mathicgb, Memtailor, MPSolve, and Frobby are not available as packages on Arch Linux and will be downloaded and built. Alternatively, Frobby is available in the Arch User Repository.

Debian/Ubuntu

sudo apt install 4ti2 autoconf automake bison ca-certificates cohomcalg coinor-csdp fflas-ffpack flex g++ gfan gfortran git install-info libboost-dev libboost-regex-dev libboost-stacktrace-dev libcdd-dev libeigen3-dev libffi-dev libflint-dev libfrobby-dev libgc-dev libgdbm-dev libgivaro-dev libglpk-dev libgmp-dev libgtest-dev liblzma-dev libmathic-dev libmathicgb-dev libmemtailor-dev libmpfi-dev libmpfr-dev libmps-dev libnauty-dev libncurses-dev libnormaliz-dev libntl-dev libopenblas-dev libpython3-dev libreadline-dev libsingular-dev libtbb-dev libtool-bin libxml2-dev lrslib make nauty normaliz patch pkgconf python3 singular-data time topcom wget zlib1g-dev

Note:

  • On Ubuntu 18.04 (Bionic Beaver) and Ubuntu 20.04 (Focal Fossa) run the following first, as several of the above dependencies are missing from the official Ubuntu archives: 
    sudo apt install software-properties-common
sudo add-apt-repository ppa:macaulay2/macaulay2

Fedora

sudo dnf install 4ti2 TOPCOM autoconf automake bison boost-devel cddlib-devel cohomCalg csdp-tools diffutils eigen3-devel factory-devel fflas-ffpack-devel flex flint-devel g++ gc-devel gcc-gfortran gdbm-devel gfan git glpk-devel gmp-devel lapack-devel libffi-devel libfrobby-devel libnauty-devel libnormaliz-devel libtool libxml2-devel lrslib-utils make mathic-devel mathicgb-devel memtailor-devel mpfi-devel mpfr-devel mpsolve-devel nauty ncurses-devel normaliz ntl-devel patch python3-devel readline-devel tbb-devel which xz-devel zlib-devel

Note:

  • Add CPPFLAGS=-I/usr/include/frobby to the call to configure so that it can find Frobby.
  • Fedora's GoogleTest package does not include some necessary files, so it will be downloaded and built.

Gentoo

Coming soon

macOS

Coming soon

Red Hat Enterprise Linux

sudo dnf install autoconf automake bison boost-devel diffutils eigen3 flex gc-devel gcc-c++ gcc-gfortran gdbm-devel git glpk-devel gmp-devel lapack-devel libffi-devel libtool libxml2-devel make mpfr-devel ncurses-devel openblas-devel patch python3-devel readline-devel tbb-devel which xz-devel zlib-devel

Note: You must have the EPEL enabled in order to install several of these packages.

SUSE

Coming soon

Getting the source code

The current development version of the source code can be obtained with this command, assuming you have installed git on your machine:

git clone https://github.com/Macaulay2/M2

A directory called M2 which you can move or rename, will be created. By default, the master branch of the M2 repository will be checked out.

The release tags tend to be more stable, and if you compile from one of those, you'll have the same functionality as those who download our binary releases. So, after cloning, you can switch to the tag containing version 1.24.05, for example, with the following command:

git checkout release-1.24.05

Instead of release-1.24.05 you should, of course, use the most recent one.

The following command shows the list of release tags:

git tag | grep release

However, if some time has passed since the most recent release and your system has newer versions of some of Macaulay2's dependencies than were available at the time of the release, you may have more success building the master branch.

The following commands, run from the top level of this source tree (the parent of the directory this file is in) will download the latest changes to the source code:

git pull
git submodule sync
git submodule update

To obtain the latest, but potentially unstable, changes to the Macaulay2 source code, switch to the development branch:

git checkout development

Building a fat source tarfile to avoid further downloads

It may be desirable when building Macaulay2 on multiple systems to create a "fat" tarfile containing all of our source code as well as all of the source code of the submodules and libraries that might later be used, to prevent later access to the internt to obtain that source code. To achieve that, do the following:

  • Add the option "--recurse-submodules" to the 'git clone' command above. This populates the submodules' subdirectories with their source code.
  • Run : ./configure --enable-download make -C libraries fetch-all make distclean This fetches tar files containing the source code of all the libraries and deposits them in BUILD/tarfiles/.
  • When satisfied with the result, remove our git source repository with rm -rf ../.git Alternatively, tar up just this directory and not its parent directory. Everything needed to build Macaulay2 will be included.

Building with Python support

The "Python" package embeds a Python interpreter inside Macaulay2. For this to work, the Macaulay2 binary needs to be linked against the Python shared library. To do this, add the option "--with-python" to the "configure" command line below. Optionally, you may specify the Python version, e.g., "--with-python=3.10". Otherwise, the system's default version is used.

Make sure that Python header files and shared library are available on your system. On Debian/Ubuntu systems, do this by running "apt install python3-dev".

If the Python shared library is not in a standard location, then add its path to LDFLAGS. For example, if Python has been installed using brew, then add the following to LDFLAGS, replacing X with the appropriate minor version: "-Lbrew --prefix python/Frameworks/Python.framework/Versions/3.X/lib".

Building without libffi support

Use of the "ForeignFunctions" package requires linking the Macaulay2 binary against libffi (https://sourceware.org/libffi/). This has been known to cause issues on Apple silicon machines, and so it is possible to opt out of this feature by adding the "--without-libffi" option to the "configure" command line below.

Compiling Macaulay2

It seems now, for a 64 bit build in a virtual machine with no swap space, using gcc 7, that 1024MB of RAM is not enough, so try something like 1400MB.

Now the directory to be in is the one containing this file in the source distribution -- it is called "M2", and is a subdirectory of the top level directory of the source tree. If you are reading this file on the web, it may be more convenient to switch now to reading it in its location in the source tree.

Begin with this command:

    make

The "make" command above runs the commands "autoconf" and "autoheader", which create the "configure" script and the "include/config.h.in" file, needed in the next steps. Once those files are created, it is not necessary to make them again. The "make" command on your system should be a recent version of GNU make.

Now continue building the program this way:

    ./configure --enable-download --prefix=/foo/bar
    make
    make check                      # optional
    make install

Remember to add any options specified above, in the section for your particular operating system, to the "configure" command line.

Files will then be installed in the following directories:

    /foo/bar/bin
    /foo/bar/share/Macaulay2
    /foo/bar/share/doc/Macaulay2
    /foo/bar/share/man/man1
    /foo/bar/share/emacs/site-lisp
    /foo/bar/lib/Macaulay2

The Macaulay2 program itself will be located at /foo/bar/bin/M2.

Choose an appropriate directory path, instead of /foo/bar, as the installation prefix, or omit the option entirely for installation in /usr/local.

Note: the "make" program in the commands above should be at least version 4. Under Mac OS X, one encounters an old version of "make", so it is better to use the "gmake" program, as provided by "brew", and installed according to the instructions above.

To take advantage of parallelism when running "make", append an option of the form "-jN" to the command line, where "N" is replaced by the number of processors you wish to devote to the task. (Our makefiles are just beginning to take advantage of this.)

To enable the running of the NTL "wizard", which conducts time consuming experiments to optimize the speed of its code, before compiling it, add the option --enable-ntl-wizard to the "configure" command line above.

To use a different prefix, say $HOME/local, for finding libraries and include files installed in a nonstandard location, add the following options to the "configure" command line: LDFLAGS="-L$HOME/local/lib" CPPFLAGS="-I$HOME/local/include" That step is unnecessary if the compiler was compiled from sources and installed with that prefix.

To use a different compiler suite, such as gcc version 4.8.2 as compiled above, add something like the following to the "configure" command line: CC=gcc-4.8.2 CXX=g++-4.8.2 FC=gfortran-4.8.2 That step is unnecessary if the environment variables CC and CXX are set as described above.

To specify libraries to link against during configuration, use the LIBS environment variable, as described in documentation for autoconf. For example, to link with libfoo, add the following option to the "configure" command line:

    LIBS=-lfoo

To see descriptions of all the environment variables that influence configuration, run this command and look at the section of the output entitled "Some influential environment variables":

    ./configure --help

The only one of these variables with a nonempty default value is CFLAGS, and its default value is "-g -O2". That will be supplanted if you override it.

To specify a different installation location for the "make install" command you may add an option to the "make install" line, as follows:

    make install prefix=/foo/bar

To make an encapsulated directory tree or distribution tarball suitable for use with the program "epkg" (see https://github.com/DanGrayson/epkg), add the option

    --enable-encap

to the "configure" command above.

The effect is to insert one more component into the path names used at installation time, so that in response to

    make prefix=/foo/bar install

files will be installed in the following directories:

    /foo/bar/Macaulay2-*/bin
    /foo/bar/Macaulay2-*/share/Macaulay2
    /foo/bar/Macaulay2-*/share/doc/Macaulay2
    /foo/bar/Macaulay2-*/share/man/man1
    /foo/bar/Macaulay2-*/share/emacs/site-lisp
    /foo/bar/Macaulay2-*/lib/Macaulay2

Each * above is replaced by the current version number. There will also be a few extra files placed in the directory /foo/bar/Macaulay2-* which instruct epkg how to make appropriate symbolic links to install our program, and how to initialize the dumped data file, if present:

    /foo/bar/Macaulay2-*/encapinfo
    /foo/bar/Macaulay2-*/postinstall
    /foo/bar/Macaulay2-*/preremove

Compiling for multiple machine architectures

By default, Macaulay2 will compile in such a way that it is adapted to the architectural features of the CPU being used to do the compilation. This is especially true for the library mpir, which exploits many of the advanced features of your CPU, determining them by running a small program and uses the output from that to determine which optimization options (of the form '-mtune=' and '-march=') to pass to gcc.

If you expect the Macaulay2 binary you build to run on other machines (for example, if you are making a binary distribution to hand to others), then you must prevent that from happening.

One way to do that is to pass an explicit "build target" to the configure script, as in this example under Mac OS X:

./configure --build=x86_64-apple-darwin

The build target will be provided to the configure scripts of the libraries needed, and, at least in the case of the mpir library, will prevent it from optimizing further.

To find a suitable target, run :

config/config.guess

To combine those two steps, run :

./configure --build=config/config.guess

HTML validation

To validate all our HTML files, run:

make validate-html

This depends on the installation of the validator (the Python utility html5validator, available using pip), so we don't run it automatically.

Rerunning the package examples

Some packages cache their example output in the source code tree, since they depend on the presence of external programs not included with Macaulay2. Here we briefly summarize them and the software they depend on:

gfanInterface StatePolytope need polymake, builds OK
    http://polymake.org/lib/exe/fetch.php/download/polymake-2.13-1.tar.bz2
    (Make 3.81 has a problem with their makefile, so use 4.0)
    Polymake can be installed under Ubuntu with the following command:
         sudo apt-get install polymake

Bertini needs bertini:
    http://www.nd.edu/~sommese/bertini/
which needs gmp and mpfr:
    https://gmplib.org/
    http://www.mpfr.org/

PHCpack needs PHCpack, download the binary:
        http://homepages.math.uic.edu/~jan/download.html

AdjointIdeal ConvexInterface MapleInterface Parametrization need Maple.

ConvexInterface also needs the maple package "convex" installed.  See the 
package documentation for hints about installing it.
	    http://www.math.uwo.ca/~mfranz/convex/files/current/convex.m

Warning messages

-  warning: -jN forced in submake: disabling jobserver mode

   This message can be ignored, if the previous recursive make command
   had -j1 as an option, as -j1 implies the use of just one processor,
   anyway.  (We use -j1 as an option when compiling third party libraries
   whose makefiles are not known to support parallelism.)

Autoconf, autoreconf, libtool, ...

If you get any mysterious error messages involving autoconf, autoreconf, libtool, etc., try running

 make -f Makefile get-tools

in the top level. This command will install versions of those tools known to work with Macaulay2.

Unexpected problems

Suppose you encounter error messages like this one when compiling in libraries/mpir:

   tmp-mul_1.s:94: Error: no such instruction: `mulx (%rsi),%r9,%r8'

Then try adding --build=./config/config.guess to the command line of the 'configure' command. This will tell mpir to build itself using just machine instructions common to all the architectures in the same class as the architecture of your machine, instead of optimizing itself for speed according to your system. Mpir seems overconfident that the assembler on the machine knows about all the machine instructions on the machine.

Homepage | Projects | Packages | Documentation | Events | Google Group

Clone this wiki locally