Meep Installation

From AbInitio

Jump to: navigation, search
Meep
Download
Release notes
FAQ
Meep manual
Introduction
Installation
Tutorial
Reference
C++ Tutorial
C++ Reference
Acknowledgements
License and Copyright

Much like MPB, 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 should be possible to install Meep on Windows systems as well, by using a free Unix-compatibility environment such as Cygwin. We haven't tried this ourselves, however, as we don't use Windows.)

For people installing Meep on a parallel supercomputer, a note of caution: most supercomputers have more than one different compiler 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!

Contents

Installation on GNU/Linux

For most GNU/Linux distributions, there should be precompiled packages for most of Meep's prerequisites below, and we highly recommend installing those prerequisites using the available packages for your system whenever possible. Using precompiled packages means that you don't have to worry about how to install things manually, you are using packages which have already been tweaked to work well with your system, and (usually) your packages will be automatically upgraded when you upgrade the rest of your system.

BLAS and LAPACK (possibly as part of a package for Atlas BLAS), Guile, MPI, and HDF5 are all almost certain to be available as precompiled packages. One thing to be careful of is that many distributions split packages into two parts: one main package for the libraries and programs, and a "devel" package for w:header files and other things needed to compile software using those libraries. You will need to install both. So, for example, you will probably need both a guile package (probably installed by default) and a guile-dev or guile-devel package (probably not installed by default), and similarly for HDF5 etcetera. You will probably also want to install a libpng-dev or libpng-devel package in order to compile the h5topng utility in H5utils.

The easiest installation is on Debian GNU/Linux (and Ubuntu), which has precompiled packages for Meep. On Debian, just do:

apt-get install meep h5utils

to install everything. (See also Meep Download.)

Installation on MacOS X

Since MacOS X is, at its heart, a Unix system, one can, in principle compile and install Meep and all its prerequisites just as on any other Unix system. However, life will be much easier if you use the Homebrew package to install most of the prerequisites, since it will handle dependencies and other details for you. (You will need administrator privileges on your Mac.)

The first steps are:

  • Install Xcode, the development/compiler package from Apple, free from the Apple Xcode web page.
  • Install Homebrew: download from the Homebrew web site and follow the instructions there.
  • Run the following commands in the terminal to compile and install Meep prerequisites (this may take a while to complete because it will install lots of other stuff first)
brew doctor
brew install homebrew/science/hdf5 homebrew/science/openblas guile fftw h5utils

Now, install the Harminv, Libctl, MPB, and Meep packages from source. Download Harminv and, in the harminv directory, do:

./configure && make && make install

Use the same commands for Libctl, then MPB, then Meep.

Note: Meep currently does not compile on OSX 10.9, due to conflicts with the latest C++ standard. We hope to fix this with a new release shortly.

You are done, and can now run Meep just by typing meep. You can run make check in the meep directory if you want to perform a self-test.)

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 this software, but they've caused a lot of confusion among our beloved users.)

Most of the software below, including this software, 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 in a non-standard location (and /usr/local is considered non-standard by some proprietary compilers), you will need to tell the compilers where to find the libraries and header files that you dutifully installed. You do this by setting two environment variables:

setenv LDFLAGS "-L/usr/local/lib"
setenv CPPFLAGS "-I/usr/local/include"

Of course, substitute whatever installation directory you used. Do this before you run the configure scripts, etcetera. You may need to include multiple -L and -I flags (separated by spaces) if your machine has stuff installed in several non-standard locations. Bourne shell users (e.g. bash or ksh) should use the "export FOO=bar" syntax instead of csh's "setenv FOO bar", of course.

You might also need to update your PATH so that you can run the executables you installed (although /usr/local/bin is in the default PATH on many systems). e.g. if we installed in our home directory as described above, we would do:

setenv 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. The good news is that, when you run make install for the packages involving shared libraries, the output includes the necessary instructions specific to your system, so pay close attention! It will say something like "add LIBDIR to the <code>foobar environment variable</code>," where LIBDIR will be your library installation directory (e.g. /usr/local/lib) and foobar is some environment variable specific to your system (e.g. LD_LIBRARY_PATH on some systems, including Linux). For example, you might do:

setenv LD_LIBRARY_PATH "/usr/local/lib:$LD_LIBRARY_PATH"

Note that we just add to the library path variable, and don't replace it in case it contains stuff already. If you use Linux and have root privileges, you can instead simply run /sbin/ldconfig, first making sure that a line "/usr/local/lib" (or whatever) is in /etc/ld.so.conf.

If you don't want to type these commands every time you log in, you can put them in your ~/.cshrc file (or ~/.profile, or ~/.bash_profile, depending on your shell).

Fun with Fortran

Our software, 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. Our 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 our software as were used to compile BLAS/LAPACK.

By default, our software 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 our software 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.

GNU/Linux and BSD binary packages

If you are installing on your personal GNU/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 and can be fetched (if they did not come with your system) from places like rpmfind.net. 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 (recommended)

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. (It makes a big difference if you also use MPB, though.)

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 our code and in 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 the BLAS 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:

get 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, I use g77 -O3 -fomit-frame-pointer -funroll-loops, with -malign-double -mcpu=i686 on a Pentium II.) 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 the LAPACK Home Page.

Note that our software 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.)

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

Harminv (recommended)

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

See the Harminv installation instructions.

GNU Guile (recommended)

Guile is required in order to use the ordinary libctl-based front-end to Meep, and is strongly recommended. (If you don't install it, you can only use the C++ interface to Meep.)

GNU 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 Home Page. (Guile is typically included with GNU/Linux systems.)

  • Important: Most Linux distributions come with Guile already installed (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 (e.g. with RPM) that came with your system.
  • Important: Meep currently requires Guile version 1.6 or later. You can see which version of Guile you have by running guile --version.

libctl (recommended)

libctl, which requires Guile, is required to use the ordinary libctl-based front-end to Meep, and is strongly recommended. (If you don't install it, you can only use the C++ interface to Meep.) Meep requires version 3.0 or later of libctl.

Instead of using Guile directly, 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 (parallel machines)

Optionally, Meep is able to run on a distributed-memory parallel machine, and to do this we use the standard MPI message-passing interface. You can learn about MPI from the MPI Home Page. Most commercial supercomputers already have an MPI implementation installed; two free MPI implementations that you can install yourself are MPICH and LAM; a promising new implementation is Open MPI. MPI is not required to compile the ordinary, uniprocessor version of our software.

In order for the MPI version of our libctl/Scheme front-end to run successfully, we have a slightly nonstandard requirement: each process must be able to read from the disk. (This way, Guile can boot for each process and they can all read your control file in parallel.) Many (most?) commercial supercomputers, Linux Beowulf clusters, etcetera, 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 #Meep below, when you configure Meep with MPI support (--with-mpi), it installs itself as meep-mpi.

HDF5 (recommended)

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, developed in the National Center for Supercomputing Applications (NCSA) at the University of Illinois (UIUC, home of the Fighting Illini and alma mater to many of this author's fine relatives). You can get HDF and learn about it on the HDF Home Page.

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 our own 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 our MPB and Meep software so that they can 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 supercomputers 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.

Note: version 1.8 of HDF5 changed the programming interface, breaking older programs like MPB (versions 1.4.x and earlier) and Meep (versions 0.11.x and earlier). As a workaround, if you have HDF5 1.8 or later and would like to compile these versions of MPB and/or Meep, include -DH5_USE_16_API=1 in the CPPFLAGS (see below).

Meep

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

./configure
make
su -c "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 su in the last command switches to root for installation; you can just use make install if you have used --prefix (below) to change the installation directory to something like your home directory. 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-mpi. Requires MPI to be installed, as described above. Does not compile the serial Meep; if you want that, you will have to make distclean and install the uniprocessor Meep separately. 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.
--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.

Meep for developers

If you want to modify the Meep source code, you will want to have a number of additional packages, most importantly:

  • The Git version-control system.

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

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

This gives you a fresh, up-to-date Meep repository in a directory meep. See git-scm.com 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 Meep 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 Scheme/libctl interface to Meep is largely generated by a program called SWIG (Simple Wrapper and Interface Generator). We currently require SWIG version 1.3.25 or later. Moreover, if you are using 1.3.27 or earlier, you must patch the file Source/Modules/guile.cxx with this bug fix.
Personal tools