Welcome to GROMACS! *Note*: Detailed, step-by-step installation instructions are available on the website http://www.gromacs.org/Downloads/Installation_Instructions. *Note*: If you want to use CMake for building look at INSTALL.cmake. You will probably have to download and install FFTW the first time you install GROMACS - our configuration script will check it! * SHORT INSTRUCTIONS FOR THE IMPATIENT: GROMACS uses a standard autoconf script and makefiles created by automake, like most GNU programs. This means your normal installation actions are limited to: ./configure make make install That's it! Most compiler flags and required libraries are checked automatically by configure, and it will tell you if something is missing. The default installation location is /usr/local/gromacs (change it with --prefix). * INSTALLING FFTW: The FFTW library has been removed from the distribution since it is not part of our package, but it is very easy to install separately if it is not already present. Download the source code from http://www.fftw.org , or get it from http://www.gromacs.org . Read the FFTW installation instructions for details. In short, to install the single precision library under /usr/local type ./configure --enable-float and then type make make install Note that in contrast to GROMACS, FFTW defaults to double. Even if you don't think you'll need it's a good idea to install the double precision libraries too, once and for all. Clean your build by issuing make distclean and then type ./configure --enable-type-prefix make make install Your double precision FFTW files will have a "d" prefix. (It is possible to compile a crippled GROMACS without FFTW, but we strongly discourage it - check the configure options for details) * FFTW OR OTHER LIBRARIES IN NON-STANDARD LOCATIONS: If you install FFTW in your homedirectory or some other place where it isn't found automatically (not all systems search /usr/local) by the compiler you should set the environment variables before executing configure. Assume we configured and installed FFTW with --prefix=/home/erik/fftw. If your shell is tcsh, you set setenv CPPFLAGS -I/home/erik/fftw/include setenv LDFLAGS -L/home/erik/fftw/lib or, if you are using a bash shell: export CPPFLAGS=-I/home/erik/fftw/include export LDFLAGS=-L/home/erik/fftw/lib ...and then you run the Gromacs configure script. Similarly, if you don't like the compilers configure selects, just set them with the variables CC and/or F77 (MPICC for an MPI compiler). Don't use LDFLAGS to add extra libraries! Put them in LIBS instead, e.g. setenv LIBS "-lstuff" to add libstuff at the linking stage. Once installed, you can link the Gromacs executables to e.g. /usr/local/bin if you want all users to have them in their path. * SPECIAL OPTIONS; FORTRAN, ASSEMBLY AND PARALLEL GROMACS WITH MPI: Typing ./configure --help will give you some options like compiling for parallel runs using MPI. Not all architecture use the fast fortran loops per default, so if you know you have a fast fortan compiler you should check that option. It won't have much effect for modern x86 boxes though, since these use assembly innerloops. To compile the assembly loops you need a reasonably recent version of binutils. The configuration script checks it - pick up a later version at www.gromacs.org if yours is too old. Don't disable the assembly loops unless you absolutely have to... For instance, if you want to compile only the mdrun executable with parallel MPI support: make clean ./configure --enable-mpi make mdrun make install-mdrun If you want to keep your non-mpi mdrun instead of overwriting it, you can append a suffix with --program-suffix="_mpi": If you only want to create the MPI version of the entire package you can just issue the normal make commands. The mdrun-only installation can also be useful to have e.g. a general version of gromacs for analysis in the main binary directory, and then subdirectories with only an optimized mdrun for each cpu. You can find more installation information on the GROMACS homepage if you have any problems, and don't hesitate to contact us if you find any bugs in the configuration. The architecture names have been expanded and are almost identical to the GNU ones, but where it is possible we have added an extra level with more detailed processor specifications to enable higher optimization. If you have a very heterogeneous environment it might be a good idea to compile a full non-optimized version in the main directory, and then just optimized versions of mdrun in the processor subdirectories! * VPATH BUILDS: If you want to do development on several architectures, you should use a version of make that support VPATH (we suggest GNU make) and create a new directory to contain the object files for this architecture (e.g. i686-pc-linux-gnu/obj). Then run configure from this new directory (../../configure) - you might have to make distclean first. This way you keep all your object files (speeds up compiles) and change architecture by switching to a different object directory. * ARE YOU STILL HAVING PROBLEMS? Post it to the GROMACS mailing lists. We read these on a regular basis, and in many cases another user might already be familiar with the task you're trying to perform! Good luck compiling and running! THE GROMACS CREW gromacs@gromacs.org --------------------------------------------------------------------- These are the generic install instructions from autoconf: The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses those values to create a `Makefile' in each directory of the package. It may also create one or more `.h' files containing system-dependent definitions. Finally, it creates a shell script `config.status' that you can run in the future to recreate the current configuration, a file `config.cache' that saves the results of its tests to speed up reconfiguring, and a file `config.log' containing compiler output (useful mainly for debugging `configure'). If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail diffs or instructions to the address given in the `README' so they can be considered for the next release. If at some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.in' is used to create `configure' by a program called `autoconf'. You only need `configure.in' if you want to change it or regenerate `configure' using a newer version of `autoconf'. The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type `./configure' to configure the package for your system. If you're using `csh' on an old version of System V, you might need to type `sh ./configure' instead to prevent `csh' from trying to execute `configure' itself. Running `configure' takes awhile. While running, it prints some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with the package. 4. Type `make install' to install the programs and any data files and documentation. 5. You can remove the program binaries and object files from the source code directory by typing `make clean'. To also remove the files that `configure' created (so you can compile the package for a different kind of computer), type `make distclean'. There is also a `make maintainer-clean' target, but that is intended mainly for the package's developers. If you use it, you may have to get all sorts of other programs in order to regenerate files that came with the distribution. Compilers and Options ===================== Some systems require unusual options for compilation or linking that the `configure' script does not know about. You can give `configure' initial values for variables by setting them in the environment. Using a Bourne-compatible shell, you can do that on the command line like this: CC=c89 CFLAGS=-O2 LIBS=-lposix ./configure Or on systems that have the `env' program, you can do it like this: env CPPFLAGS=-I/usr/local/include LDFLAGS=-s ./configure Compiling For Multiple Architectures ==================================== You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their own directory. To do this, you must use a version of `make' that supports the `VPATH' variable, such as GNU `make'. `cd' to the directory where you want the object files and executables to go and run the `configure' script. `configure' automatically checks for the source code in the directory that `configure' is in and in `..'. If you have to use a `make' that does not supports the `VPATH' variable, you have to compile the package for one architecture at a time in the source code directory. After you have installed the package for one architecture, use `make distclean' before reconfiguring for another architecture. Installation Names ================== By default, `make install' will install the package's files in `/usr/local/bin', `/usr/local/man', etc. You can specify an installation prefix other than `/usr/local' by giving `configure' the option `--prefix=PATH'. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you give `configure' the option `--exec-prefix=PATH', the package will use PATH as the prefix for installing programs and libraries. Documentation and other data files will still use the regular prefix. In addition, if you use an unusual directory layout you can give options like `--bindir=PATH' to specify different values for particular kinds of files. Run `configure --help' for a list of the directories you can set and what kinds of files go in them. If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving `configure' the option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. Optional Features ================= Some packages pay attention to `--enable-FEATURE' options to `configure', where FEATURE indicates an optional part of the package. They may also pay attention to `--with-PACKAGE' options, where PACKAGE is something like `gnu-as' or `x' (for the X Window System). The `README' should mention any `--enable-' and `--with-' options that the package recognizes. For packages that use the X Window System, `configure' can usually find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. Specifying the System Type ========================== There may be some features `configure' can not figure out automatically, but needs to determine by the type of host the package will run on. Usually `configure' can figure that out, but if it prints a message saying it can not guess the host type, give it the `--host=TYPE' option. TYPE can either be a short name for the system type, such as `sun4', or a canonical name with three fields: CPU-COMPANY-SYSTEM See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the host type. If you are building compiler tools for cross-compiling, you can also use the `--target=TYPE' option to select the type of system they will produce code for and the `--build=TYPE' option to select the type of system on which you are compiling the package. Sharing Defaults ================ If you want to set default values for `configure' scripts to share, you can create a site shell script called `config.site' that gives default values for variables like `CC', `cache_file', and `prefix'. `configure' looks for `PREFIX/share/config.site' if it exists, then `PREFIX/etc/config.site' if it exists. Or, you can set the `CONFIG_SITE' environment variable to the location of the site script. A warning: not all `configure' scripts look for a site script. Operation Controls ================== `configure' recognizes the following options to control how it operates. `--cache-file=FILE' Use and save the results of the tests in FILE instead of `./config.cache'. Set FILE to `/dev/null' to disable caching, for debugging `configure'. `--help' Print a summary of the options to `configure', and exit. `--quiet' `--silent' `-q' Do not print messages saying which checks are being made. To suppress all normal output, redirect it to `/dev/null' (any error messages will still be shown). `--srcdir=DIR' Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. `--version' Print the version of Autoconf used to generate the `configure' script, and exit. `configure' also accepts some other, not widely useful, options.