Installation ============ :ref:`O2scl ` Installation Contents --------------------- - :ref:`General notes ` - :ref:`Compiling O₂scl on Mac OSX with Homebrew ` - :ref:`Compiling O₂scl from a release distribution ` - :ref:`Compiling O₂scl from a release on Linux ` - :ref:`Compiling O₂scl from the source code ` - :ref:`Compiling O₂scl on Docker ` - :ref:`Python support ` - :ref:`Compiling O₂scl on Ubuntu with Snap ` - :ref:`Optional linear algebra libraries` - :ref:`Other optional libraries` - :ref:`Range-checking` - :ref:`More configure flags` - :ref:`Generation of documentation` - :ref:`Uninstallation` .. note:: 7/23/22: On OSX, boost multiprecision (used by O₂scl) appears to currently also include libquadmath. .. _install_general: General notes ------------- O₂scl requires Boost, GSL, and the HDF5 libraries (the precise procedure for installing these libraries differs from system to system, but some common cases and useful information is given below). O₂scl is designed to be used with the most recent release version of all of these libraries, but is sometimes compatible with recent older versions. The configure script attempts to add these libraries to LDFLAGS during the installation of O₂scl. In order to compile your code with O₂scl, you will need to include, e.g. ``-lo2scl -lhdf5 -lgsl -lgslcblas -lm``, and you may need to include ``-I`` flags for O₂scl headers and ``-L`` flags for O₂scl libraries. The sections below describe several different ways of installing O₂scl. It is important to ensure that O₂scl is compiled with the same version of the HDF5 libraries that it is linked with when compiling code based on O₂scl. In order to help resolve these version conflicts, the ``acol`` utility (see :ref:`The acol Command Line Utility`) reports the two different HDF5 versions (see ``acol -v``) so that it is easy to check that they are the same. .. _compile_homebrew: Compiling O₂scl on Mac OSX with Homebrew ---------------------------------------- The easiest way to install on Mac OSX is with homebrew. Use:: brew tap awsteiner/science brew install o2scl to install O₂scl. There are a few options for ``brew install``. The option ``--with-check`` performs the build-time tests and the option ``--with-examples`` double checks that the examples can also be compiled and executed. The homebrew recipe for O₂scl uses the Mac OS X compiler clang. Homebrew also supports the installation of the current version directly from the repository using the ``--HEAD`` option to ``brew install``. The homebrew installation includes readline support. The O₂scl homebrew recipes are stored at the https://github.com/awsteiner/homebrew-science repository. By default, a homebrew installation of O₂scl uses the OSX LLVM compiler. However, a homebrew installation of O₂scl will also install ``gcc`` because O₂scl requires ``hdf5``, and the homebrew ``hdf5`` package requires ``gcc``. Python support in the homebrew package does not yet work yet. .. _compile_dist: Compiling O₂scl from a release distribution ------------------------------------------- O₂scl installation is generally similar to that for GNU-style libraries. The file ``INSTALL`` has some details on this procedure. Once the dependencies are installed you should be able to run ``./configure`` and then type ``make`` and ``make install``. More information on the ``configure`` command can also be obtained from ``./configure --help``. On some systems, you may have to add additional flag to the ``CXXFLAGS`` environment variable manually before the ``./configure`` script. The documentation is included in the O₂scl release distribution and automatically installed by ``make install``. .. note:: If you are trying to install O₂scl with a version of HDF5 earlier than 1.12 you will need to compile with ``-DO2SCL_HDF5_PRE_1_12``. O₂scl requires the Boost (v1.74.0 or later) and the GSL libraries (version 2.0 or later). If the ``configure`` script cannot find Boost or GSL, you may have to specify their location for the associated header files in the ``CXXFLAGS`` variable and the associated libraries in the ``LDFLAGS`` environment variable. Running ``./configure --help`` shows some information on this. For example, in a bash shell, you could do something like:: CXX="g++" CXXFLAGS="-I/dir/to/gsl/include" LDFLAGS="-L/dir/to/gsl/libs" ./configure --prefix=="/dir/to/destination_directory Along with GSL, a CBLAS library is also required, and ``./configure`` will look for ``libcblas`` first, and if not found then it will look for ``libgslcblas``. If neither is present, then you may have to manually specify a CBLAS library using the ``LIBS`` and ``LDFLAGS`` environment variables. Compiling with the readline library is optional, but it is assumed to be present by default. After ``make install``, you may test the library with ``make check`` or ``make o2scl-test``. At the end, the phrase ``"All O2scl tests passed"`` indicates that the testing was successful. You may also run ``make o2scl-test`` in the individual subdirectories of the src directory to individually test the classes and functions in that part of O₂scl. After installation, running ``acol -v`` will output several of the installation settings. .. _compile_release: Compiling O₂scl from a release on Linux --------------------------------------- For example, to install O₂scl on Ubuntu, begin by installing g++ and make (the ``g++`` and ``make`` packages), GSL (the ``libgsl-dev`` package), Boost (the ``libboost-all-dev`` package), GNU readline (the ``libreadline-dev`` package), and HDF5 the ``libhdf5-dev`` package). You can then install O₂scl from one of the release distributions by using the standard GNU ``./configure`` script and then invoking ``make`` and ``make install`` (which often requires ``sudo``). The HDF5 package for Ubuntu and many other Linux systems is installed in ``hdf5/serial/hdf5.h`` instead of ``hdf5.h``, so O₂scl presumes that Linux systems are arranged that way. If HDF5 include statements should not have the ``hdf5/serial/`` prefix, then you can use ``-DO2SCL_HDF5_PLAIN_HEADER``, i.e.:: CXXFLAGS="-DO2SCL_PLAIN_HDF5_HEADER" ./configure to instruct O₂scl to look for them there (for example, on bridges at the PSC). On many systems, one can use a parallel HDF5 library using ``-DO2SCL_HDF5_PLAIN_HEADER`` and a ``-I`` option to select the proper location for the parallel HDF5 header files. Finally, if your version of HDF5 is earlier than 1.12, you will need to let O₂scl know, using:: CXXFLAGS="-DO2SCL_HDF5_PRE_1_12" ./configure Other Linux distributions are similar. For example, in OpenSUSE, you will need to use ``zypper`` to install ``gcc-c++, make, gsl-devel, hdf5-devel, readline-devel``, and ``boost-devel``. Note that if your boost installation is earlier than 1.70, you will need to use the -DO2SCL_OLD_BOOST flag to get all of the tests to run successfully. .. _compile_source: Compiling O₂scl from the source code ------------------------------------ If you want to install from source (without generating the documentation), then you must first install ``g++``, ``make``, ``automake``, ``autoconf``, and ``libtool`` packages. You also need to install all the dependencies described above (see, e.g. the section :ref:`Compiling O₂scl from a release on Linux`). Then you can use something along the lines of:: git clone https://github.com/awsteiner/o2scl cd o2scl autoreconf -i ./configure Then, you will either need to generate the documentation from doxygen using ``make o2scl-doc`` or use ``make blank-doc`` to create blank documentation. Then you can proceed using ``make`` and ``make install`` (which may require ``sudo`` depending on your configuration). For a full installation with parallelism, I typically also install ``libopenmpi-dev`` and then use ``./configure --enable-openmp`` .. _compile_docker: Docker images for O₂scl ----------------------- There are a few docker images for recent versions of O₂scl up at https://hub.docker.com/r/awsteiner/o2scl . These images are based on the experimental docker files which are stored in the ``docker`` subdirectory, and can be found at https://github.com/awsteiner/o2scl/tree/main/docker . .. For those on MacOS, I recommend the guide at https://medium.com/crowdbotics/a-complete-one-by-one-guide-to-install-docker-on-your-mac-os-using-homebrew-e818eb4cfc3 to installing docker (though this may need revision as now docker-machine is deprecated on homebrew). .. _python_support: Python support -------------- O₂scl can be compiled with python support by providing the option ``--enable-python`` when the library is configured. This may also require adjusting CXXFLAGS and LDFLAGS in order to ensure the Python headers and libraries can be found. O₂scl code which uses Python also assumes that numpy was installed, so the headers for the numpy package may need to be specified. For example, using g++ on MacOS may need something of the form:: CXX="g++-13" CXXFLAGS="-I/usr/local/lib/python3.11/site-packages/numpy/core/include `python3-config --includes`" LDFLAGS="`python3-config --ldflags`" ./configure --enable-python Including Python support also requires the installation of O₂sclpy (for example, using \c pip) to ensure that the tests pass successfully. Thus, when including Python support it is best to install O₂scl first, install O₂sclpy second, and then test O₂scl and O₂sclpy last. See also :ref:`Python Integration` for more details. .. _compile_snap: Compiling O₂scl on Ubuntu with Snap ----------------------------------- .. note:: AWS, 6/23/23: The snap package needs some work and I have not had the time to fix it yet. The easiest way to install on Ubuntu is with snap (see https://snapcraft.io/o2scl). Use:: sudo snap install (--edge or --beta) --devmode o2scl The snap installation includes readline support and uses the GSL CBLAS. Using the command-line utility ``acol`` may require you to set the environment variable ``LD_LIBRARY_PATH``. For example, on machines where I use snap to install in my ``.bashrc``, I use:: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/snap/o2scl/current/usr/lib/x86_64-linux-gnu:/snap/o2scl/current/lib/x86_64-linux-gnu Optional linear algebra libraries --------------------------------- O₂scl is fully functional without any additional linear algebra libraries. However, many classes and functions which require linear algebra are faster with either the Eigen (http://eigen.tuxfamily.org) or Armadillo (http://arma.sourceforge.net) libraries. Support for these can be specified in the ``configure`` command with ``--enable-armadillo`` or ``--enable-eigen``. These libraries may require additional ``-I`` or ``-L`` flags to be defined when O₂scl is installed, depending on how your particular system is configured. For example, O₂scl classes which use Armadillo use matrix decompositions so Armadillo must be compiled with LAPACK support, and you may need to specify the location of the LAPACK libraries manually. If you are installing on Mac OS X with homebrew, the options ``--with-eigen`` and ``with-armadillo`` can be used. Other optional libraries ------------------------ As with the linear algebra libraries, these libraries may require additional ``-I`` or ``-L`` flags to be defined when O₂scl is installed, depending on how your particular system is configured. The configure script should automatically add ``-l`` to LDFLAGS during installation, but you will need to also add this flag to your codes which use O₂scl. Readline support (``-lreadline``): The command-line interface class :ref:`cli `, and ``acol`` (see :ref:`The acol Command Line Utility`) can both take advantage of readline support. If the library is configured with ``--disable-readline``, then the readline library is not used. OpenMP support (typically involves the ``-fopenmp`` compiler flag): O₂scl contains a few functions which use multiple threads for faster execution. This support can be included using the ``-enable-openmp`` option to the configure script. On some systems, this will also include explicitly specifying the OpenMP libraries in the ``LDFLAGS`` environment variable. See more information in :ref:`Parallel Programming with O2scl`. FFTW support (``-lfftw3``): O₂scl contains a few functions which require FFTW support, and this can be included if ``--enable-fftw`` is passed to the configure script. Module support, curses support, MFPR support, cubature support, and pugixml support are all experimental. Other optional libraries ------------------------ As with the linear algebra libraries, these libraries may require additional ``-I`` or ``-L`` flags to be defined when O₂scl is installed, depending on how your particular system is configured. The configure script should automatically add ``-l`` to LDFLAGS during installation, but you will need to also add this flag to your codes which use O₂scl. Readline support (``-lreadline``): The command-line interface class :ref:`cli `, and ``acol`` (see :ref:`The acol Command Line Utility`) can both take advantage of readline support. If the library is configured with ``--disable-readline``, then the readline library is not used. OpenMP support (typically involves the ``-fopenmp`` compiler flag): O₂scl contains a few functions which use multiple threads for faster execution. This support can be included using the ``-enable-openmp`` option to the configure script. On some systems, this will also include explicitly specifying the OpenMP libraries in the ``LDFLAGS`` environment variable. See more information in :ref:`Parallel Programming with O2scl`. FFTW support (``-lfftw3``): O₂scl contains a few functions which require FFTW support, and this can be included if ``--enable-fftw`` is passed to the configure script. Module support, curses support, MFPR support, cubature support, and pugixml support are all experimental. Range-checking -------------- Some extra range-checking for vectors and matrices is turned on by default. You can disable range-checking by defining -DO2SCL_NO_RANGE_CHECK, e.g.:: CXXFLAGS="-DO2SCL_NO_RANGE_CHECK" ./configure More configure flags -------------------- There are several warning flags that are useful when configuring and compiling with O₂scl. See the GSL documentation for an excellent discussion, and also see the generic installation documentation in the file ``INSTALL`` in the O₂scl top-level directory. For running ``configure``, for example, if you do not have privileges to write to ``/usr/local``:: CPPFLAGS="-O3 -I/home/asteiner/install/include" \ LDFLAGS="-L/home/asteiner/install/lib" ./configure \ --prefix=/home/asteiner/install In this example, specifying ``-I/home/asteiner/install/include`` and ``-L/home/asteiner/install/lib`` above ensures that the GSL libraries can be found. The ``--prefix=/home/asteiner/install`` argument to ``./configure`` ensures that O₂scl is installed there as well. Generation of documentation --------------------------- The O₂scl documentation is generated with ``doxygen``, ``sphinx``, ``breathe``, and ``alabaster`` and packaged in with every release file. In principle, the documentation can be regenerated by the end-user, but this is not supported and requires several external applications not included in the distribution. The most recent release documentation is available at https://neutronstars.utk.edu/code/o2scl/html/index.html and the current development version documentation is available at https://neutronstars.utk.edu/code/o2scl-dev/html/index.html . The documentation for previous releases is not on the web, but is still stored in the release ``.tar.gz`` file. Uninstallation -------------- While there is no explicit "uninstall" makefile target, there are only a couple places to check. Installation creates directories named ``o2scl`` in the include, doc and shared files directory (which default to ``/usr/local/include``, ``/usr/local/share/doc/``, and ``/usr/local/share``) which can be removed. The ``acol`` command-line utility is installed to ``/usr/local/bin`` . Finally, all of the libraries are named with the prefix ``libo2scl`` and are created by default in ``/usr/local/lib``.