Build From Source


The main effort in installing Meep lies in installing the various prerequisite packages. This requires some understanding of how to install software on Unix systems.

It is also possible to install Meep on Windows systems by using a free Unix-compatibility environment such as Cygwin. For more information, see these step-by-step instructions.

For those installing Meep on a supercomputer, a note of caution: most supercomputers have multiple compilers installed, and different versions of libraries compiled with different compilers. Meep is written in C++, and it is almost impossible to mix C++ code compiled by different compilers — pick one set of compilers by one vendor and stick with it consistently.

Unix Installation Basics

Installation Paths

First, let's review some important information about installing software on Unix systems, especially in regards to installing software in non-standard locations. None of these issues are specific to Meep, but they've caused a lot of confusion among users.

Most of the software below, including Meep, installs under /usr/local by default. That is, libraries go in /usr/local/lib, programs in /usr/local/bin, etc. If you don't have root privileges on your machine, you may need to install somewhere else, e.g. under $HOME/install (the install/ subdirectory of your home directory). Most of the programs below use a GNU-style configure script, which means that all you would do to install there would be:

 ./configure --prefix=$HOME/install

when configuring the program. The directories $HOME/install/lib etc. are created automatically as needed.

Paths for Configuring

There are two further complications. First, if you install dependencies in a non-standard location like $HOME/install/lib, you will need to tell the compilers where to find the libraries and header files that you installed. You do this by passing two variables to ./configure:

./configure LDFLAGS="-L$HOME/install/lib" CPPFLAGS="-I$HOME/install/include"   ...other flags...

Of course, substitute whatever installation directory you used. You may need to include multiple -L and -I flags separated by spaces if your machine has stuff installed in several non-standard locations.

You might also need to update your PATH so that you can run the executables; e.g. if we installed in our home directory as described above, we would do:

export PATH="$HOME/install/bin:$PATH"

Paths for Running (Shared Libraries)

Second, many of the packages installed below (e.g. Guile) are installed as shared libraries. You need to make sure that your runtime linker knows where to find these shared libraries. The bad news is that every operating system does this in a slightly different way. If you installed all of your libraries in a standard location on your operating system (e.g. /usr/lib), then the runtime linker will look there already and you don't need to do anything. Otherwise, if you compile things like libctl and install them into a "nonstandard" location (e.g. in your home directory), you will need to tell the runtime linker where to find them.

There are several ways to do this. Suppose that you installed libraries into the directory $HOME/install/lib. The most robust option is probably to include this path in the linker flags:

./configure LDFLAGS="-L$HOME/install/lib -Wl,-rpath,$HOME/install/lib" ...other flags...

There are also some other ways. If you use Linux, have superuser privileges, and are installing in a system-wide location (not your home directory), you can add the library directory to /etc/ld.so.conf and run /sbin/ldconfig.

On many systems, you can also specify directories to the runtime linker via the LD_LIBRARY_PATH environment variable. In particular, by export LD_LIBRARY_PATH="$HOME/install/lib:$LD_LIBRARY_PATH"; you can add this to your .profile file (depending on your shell) to make it run every time you run your shell. On MacOS, a security feature called System Integrity Protection causes the value of LD_LIBRARY_PATH to be ignored, so using environment variables won't work there.

Fun with Fortran

Meep, along with many of the libraries it calls, is written in C or C++, but it also calls libraries such as BLAS and LAPACK (see below) that are usually compiled from Fortran. This can cause some added difficulty because of the various linking schemes used by Fortran compilers. The configure script attempts to detect the Fortran linking scheme automatically, but in order for this to work you must use the same Fortran compiler and options with Meep as were used to compile BLAS/LAPACK.

By default, Meep looks for a vendor Fortran compiler first (f77, xlf, etcetera) and then looks for GNU g77. In order to manually specify a Fortran compiler foobar you would configure it with ./configure F77=foobar ....

If, when you compiled BLAS/LAPACK, you used compiler options that alter the linking scheme (e.g. g77's -fcase-upper or -fno-underscoring), you will need to pass the same flags to Meep via ./configure FFLAGS=...flags... ....

Picking a Compiler

It is often important to be consistent about which compiler you employ. This is especially true for C++ software. To specify a particular C compiler foo, configure with ./configure CC=foo; to specify a particular C++ compiler foo++, configure with ./configure CXX=foo++; to specify a particular Fortran compiler foo90, configure with ./configure F77=foo90.

Linux and BSD Binary Packages

If you are installing on your personal Linux or BSD machine, then precompiled binary packages are likely to be available for many of these packages, and may even have been included with your system. On Debian systems, the packages are in .deb format and the built-in apt-get program can fetch them from a central repository. On Red Hat, SuSE, and most other Linux-based systems, binary packages are in RPM format. OpenBSD has its "ports" system, and so on.

Do not compile something from source if an official binary package is available. For one thing, you're just creating pain for yourself. Worse, the binary package may already be installed, in which case installing a different version from source will just cause trouble.

One thing to watch out for is that libraries like LAPACK, Guile, HDF5, etcetera, will often come split up into two or more packages: e.g. a guile package and a guile-devel package. You need to install both of these to compile software using the library.

BLAS and LAPACK

BLAS and LAPACK libraries are required in order to install Harminv. Harminv is not required for Meep, but is strongly recommended for use in resonant-mode computation.

Note also that Meep's usage of BLAS/LAPACK, via Harminv, is not generally performance critical. So, it doesn't matter too much whether you install an especially optimized BLAS library. However, it makes a big difference if you also use MPB.

BLAS

The first thing you must have on your system is a BLAS implementation. "BLAS" stands for "Basic Linear Algebra Subroutines," and is a standard interface for operations like matrix multiplication. It is designed as a building-block for other linear-algebra applications, and is used both directly by LAPACK (see below). By using it, we can take advantage of many highly-optimized implementations of these operations that have been written to the BLAS interface. Note that you will need implementations of BLAS levels 1-3.

You can find more BLAS information, as well as a basic implementation, on its homepage. Once you get things working with the basic BLAS implementation, it might be a good idea to try and find a more optimized BLAS code for your hardware. Vendor-optimized BLAS implementations are available as part of the Intel MKL, HP CXML, IBM ESSL, SGI sgimath, and other libraries. An excellent, high-performance, free-software BLAS implementation is OpenBLAS. Another is ATLAS.

Note that the generic BLAS does not come with a Makefile; compile it with something like:

  wget http://www.netlib.org/blas/blas.tgz
  gunzip blas.tgz
  tar xf blas.tar
  cd BLAS
  f77 -c -O3 *.f   # compile all of the .f files to produce .o files
  ar rv libblas.a *.o    #  combine the .o files into a library
  su -c "cp libblas.a /usr/local/lib"   # switch to root and install

Replace -O3 with your favorite optimization options. On Linux, this could be g77 -O3 -fomit-frame-pointer -funroll-loops -malign-double. Note that MPB looks for the standard BLAS library with -lblas, so the library file should be called libblas.a and reside in a standard directory like /usr/local/lib. See also below for the --with-blas=lib option to MPB's configure script, to manually specify a library location.

LAPACK

LAPACK, the Linear Algebra PACKage, is a standard collection of routines, built on BLAS, for more-complicated (dense) linear algebra operations like matrix inversion and diagonalization. You can download LAPACK from its homepage.

Note that Meep looks for LAPACK by linking with -llapack. This means that the library must be called liblapack.a and be installed in a standard directory like /usr/local/lib. Alternatively, you can specify another directory via the LDFLAGS environment variable as described earlier. See also below for the --with-lapack=lib option to our configure script, to manually specify a library location.

We currently recommend installing OpenBLAS which includes LAPACK so you do not need to install it separately.

Harminv

To use Meep to extract resonant frequencies and decay rates, you must install Harminv which requires BLAS and LAPACK.

See the Harminv installation instructions.

Python

If you have Python on your system, then the Meep compilation scripts automatically build and install the meep Python module, which works with both the serial and parallel (MPI) versions of Meep.

By default, Meep's Python module is installed for the program python on your system. If you want to install using a different Python program, e.g. python3, pass PYTHON=python3 (or similar) to the Meep configure script. An Anaconda (conda) package for Meep is also available on some systems.

Guile

Guile is required in order to use the Scheme interface. If you don't install it, you can only use the C++ and/or Python interfaces.

Guile is an extension/scripting language implementation based on Scheme, and we use it to provide a rich, fully-programmable user interface with minimal effort. It's free, of course, and you can download it from the Guile homepage. Guile is typically included with Linux systems.

  • Important: Most Linux distributions come with Guile already installed. You can check by seeing whether you can run guile --version from the command line. In that case, do not install your own version of Guile from source — having two versions of Guile on the same system will cause problems. However, by default most distributions install only the Guile libraries and not the programming headers — to compile libctl and MPB, you should install the guile-devel or guile-dev package. Note: SWIG does not support the latest version of Guile. However, Meep contains a workaround for newer versions of Guile.

libctl

libctl is required to use the Scheme or the Python interfaces, and is strongly recommended. If you don't install it, you can only use the C++ interface. libctl version 4.0 or later is required.

(If you only want the Python interface, it is possible to install libctl without having Scheme/Guile by configuring libctl with --without-guile.)

Instead of using Guile directly in our Scheme interface, we separated much of the user interface code into a package called libctl, in the hope that this might be more generally useful. libctl automatically handles the communication between the program and Guile, converting complicated data structures and so on, to make it even easier to use Guile to control scientific applications. Download libctl from the libctl page, unpack it, and run the usual configure, make, make install sequence. You'll also want to browse the libctl manual, as this will give you a general overview of what the user interface will be like.

If you are not the system administrator of your machine, and/or want to install libctl somewhere else like your home directory, you can do so with the standard --prefix=dir option to configure. The default prefix is /usr/local. In this case, however, you'll need to specify the location of the libctl shared files for the MPB or Meep package, using the --with-libctl=dir/share/libctl option to our configure script.

MPI

Optionally, Meep is able to run on a distributed-memory parallel machine, and to do this we use the standard message-passing interface (MPI). Most supercomputers already have an MPI implementation installed. The recommended implementation is Open MPI. MPI is not required to compile the serial version of Meep.

In order for the MPI version of the Python and Scheme interface to run successfully, we have a slightly nonstandard requirement: each process must be able to read from the disk. This way, Python and Guile can boot for each process and they can all read your simulation file in parallel. Most supercomputers satisfy this requirement. On the other hand, the C++ interface to Meep does not have this requirement.

If you use Meep with MPI, you should compile HDF5 with MPI support as well (see below).

As described below, when you configure Meep with MPI support (--with-mpi), it installs itself as meep (for the Scheme interface), so it overwrites any serial installation. There is no need to have separate serial meep installed, however, because if you run the parallel Meep simply as meep, it runs on a single processor (to launch multiple processes you need mpirun -np 6 meep).

HDF5

Meep outputs its fields and other volumetric data in the HDF5 format, so you must install the HDF5 libraries if you want to visualize the fields.

HDF is a widely-used, free, portable library and file format for multi-dimensional scientific data. There are two incompatible versions of HDF, HDF4 and HDF5 (no, not HDF1 and HDF2). We require the newer version, HDF5, which is supported by a number scientific of visualization tools, including h5utils utilities.

HDF5 includes parallel I/O support under MPI, which can be enabled by configuring it with --enable-parallel. You may also have to set the CC environment variable to mpicc. Unfortunately, the parallel HDF5 library then does not work with serial code, so you have may have to choose one or the other.

We have some hacks in Meep to do parallel I/O even with the serial HDF5 library. These hacks work okay when you are using a small number of processors, but on large HPG clusters we strongly recommend using the parallel HDF5.

Note: If you have a version of HDF5 compiled with MPI parallel I/O support, then you need to use the MPI compilers to link to it, even when you are compiling the serial versions of Meep or MPB. Just use ./configure CC=mpicc CXX=mpic++ or whatever your MPI compilers are when configuring.

Meep

Once you've installed all of the prerequisites, you can install Meep via:

./configure
make
sudo make install

Assuming you've set your LDFLAGS etcetera, the configure script should find all of the libraries you've installed and, with luck, compile successfully. The sudo in the last command uses administrator privileges to install the binaries in standard system directories. Alternatively, you can just use make install if you have used --prefix to change the installation directory to something like your home directory. This is described below. To make sure Meep is working, you can run its test suite via:

make check

The configure script accepts several flags to modify its behavior.

--prefix=dir
           Install into dir/bin, etcetera, as described above.

--with-mpi
           Attempt to compile a parallel version of Meep using MPI; the resulting program will be installed as meep and can be run in either serial or parallel mode (the latter via mpirun). Requires MPI to be installed, as described above. (You should install this instead of the serial Meep.) Note that the configure script attempts to automatically detect how to compile MPI programs, but this may fail if you have an unusual version of MPI or if you have several versions of MPI installed and you want to select a particular one. You can control the version of MPI selected by setting the MPICXX variable to the name of the compiler to use and the MPILIBS variable to any additional libraries that must be linked (e.g., ./configure MPICXX=foompiCC MPILIBS=-lfoo ...).

--with-libctl=dir
           If libctl was installed in a nonstandard location (i.e. neither /usr nor /usr/local), you need to specify the location of the libctl directory, dir. This is either prefix/share/libctl, where prefix is the installation prefix of libctl, or the original libctl source code directory. To configure without the libctl/Guile interface, use --without-libctl.

--without-python
           Disable building the Python API for Meep.

--with-blas=lib
           The configure script automatically attempts to detect accelerated BLAS libraries, like DXML (DEC/Alpha), SCSL and SGIMATH (SGI/MIPS), ESSL (IBM/PowerPC), ATLAS, and PHiPACK. You can, however, force a specific library name to try via --with-blas=lib.

--with-lapack=lib
           Cause the configure script to look for a LAPACK library called lib. The default is to use -llapack.

--enable-debug
           Compile for debugging, adding extra runtime checks and so on.

--enable-shared
           Install the Meep libraries as shared libraries (i.e. dynamically linked) rather than as static libraries. This is off by default because shared libraries require the user to configure their runtime linker paths correctly (see "Paths for Running" above).

--without-hdf5
           Install Meep without support for the HDF5 libraries (this means you won't be able to output fields and so on).

--enable-portable-binary
           By default, Meep's configure script picks compiler flags to optimize Meep as much as possible for the machine you are compiling on. If you wish to run the same compiled executable on other machines, however, you need to tell it not to pick compiler flags that use features specific to your current processor. In this case you should pass --enable-portable-binary to configure. (This option is mainly useful for people creating binary packages for Debian, Fedora, etcetera.)

--with-gcc-arch=arch, --without-gcc-arch
           By default, Meep's configure script tries to guess the gcc -march flag for the system you are compiling on using -mtune instead when --enable-portable-binary is specified. If it guesses wrong, or if you want to specify a different architecture, you can pass it here. If you want to omit -march/-mtune flags entirely, pass --without-gcc-arch.

Building From Source

The following instructions are for building parallel PyMeep from source on Ubuntu 16.04. The parallel version can still be run serially by running a script with just python instead of mpirun -np 4 python. If you really don't want to install MPI and parallel HDF5, just replace libhdf5-openmpi-dev with libhdf5-dev, and remove the --with-mpi, CC=mpicc, and CPP=mpicxx flags. The paths to HDF5 will also need to be adjusted to /usr/lib/x86_64-linux-gnu/hdf5/serial and /usr/include/hdf5/serial. Note that this script builds with Python 3 by default. If you want to use Python 2, just point the PYTHON variable to the appropriate interpreter when calling autogen.sh for building Meep, and use pip instead of pip3.

#!/bin/bash

set -e

RPATH_FLAGS="-Wl,-rpath,/usr/local/lib:/usr/lib/x86_64-linux-gnu/hdf5/openmpi"
MY_LDFLAGS="-L/usr/local/lib -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi ${RPATH_FLAGS}"
MY_CPPFLAGS="-I/usr/local/include -I/usr/include/hdf5/openmpi"

sudo apt-get update
sudo apt-get -y install     \
    libblas-dev             \
    liblapack-dev           \
    libgmp-dev              \
    swig                    \
    libgsl-dev              \
    autoconf                \
    pkg-config              \
    libpng16-dev            \
    git                     \
    guile-2.0-dev           \
    libfftw3-dev            \
    libhdf5-openmpi-dev     \
    hdf5-tools              \
    libpython3.5-dev        \
    python3-numpy           \
    python3-scipy           \
    python3-matplotlib      \
    python3-pip             \

mkdir -p ~/install

cd ~/install
git clone https://github.com/stevengj/harminv.git
cd harminv/
sh autogen.sh --enable-shared
make && sudo make install

cd ~/install
git clone https://github.com/stevengj/libctl.git
cd libctl/
sh autogen.sh --enable-shared
make && sudo make install

cd ~/install
git clone https://github.com/stevengj/h5utils.git
cd h5utils/
sh autogen.sh CC=mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make && sudo make install

cd ~/install
git clone https://github.com/stevengj/mpb.git
cd mpb/
sh autogen.sh --enable-shared CC=mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}" --with-hermitian-eps
make && sudo make install

sudo pip3 install --upgrade pip
pip3 install --user --no-cache-dir mpi4py
export HDF5_MPI="ON"
pip3 install --user --no-binary=h5py h5py

cd ~/install
git clone https://github.com/stevengj/meep.git
cd meep/
sh autogen.sh --enable-shared --with-mpi PYTHON=python3 \
    CC=mpicc CXX=mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make && sudo make install

You may want to add the following line to your .profile so Python can always find the meep package:

export PYTHONPATH=/usr/local/lib/python3.5/site-packages

Meep for Developers

If you want to modify the source code, you will want to have a number of additional packages, most importantly the Git version-control system.

Once you have Git, you can grab the latest development version of Meep with:

 git clone https://github.com/stevengj/meep.git

This gives you a fresh, up-to-date repository in a directory meep. See the Git manual for more information on using Git. Perhaps the most useful command is git pull which you can execute periodically to get any new updates to the development version.

Git will give you an absolutely minimal set of sources; to create a usable directory, you should run:

sh autogen.sh
make

in the meep directory. And subsequently, if you are editing the sources you should include --enable-maintainer-mode whenever you reconfigure. To do this, however, you will need a number of additional packages beyond those listed above:

  • GNU autoconf, automake, and libtool — these are used to create the Makefiles and configure scripts, and to build shared libraries.
  • SWIG — the Python and Scheme interfaces are largely generated by a program called SWIG (Simple Wrapper and Interface Generator).