Using CMake to install CHARMM CMake is an alternative to install.com for configuring, compiling, and installing CHARMM. This file describes how to use cmake and the configure shell script to build CHARMM. There are two relevant files in the root CHARMM source distribution. The CMakeLists.txt file is read by CMake to configure the source for compilation. The configure file is a shell script wrapper that invokes CMake. The configure script provides a more traditional command line switch interface. Also, if CMake is not available, the script will build and use a cmake binary from the tool/cmake directory. The script ultimately just builds a list of options and invokes CMake with the list. Other methods of using CMake such as the ncurses ccmake GUI and the Qt GUI are untested and unsupported. Support for ccmake may be added in the future. * Workflow / Three Steps to a CMake Install * Configuration / The First Step * Compilation / The Second Step * Installation / The Third and Final Step
Top Workflow There are three steps, configuration, compilation, and installation to create a working install of CHARMM from the source distribution using CMake. The first step, configuration, uses the configure script, or the cmake command directly, to configure the source for compiling. The configuration step occurs in a new empty directory, the build directory. The second step is to compile the source in the build directory by invoking the make command which uses the makefile written by CMake in the configuration step. The third step is to install the binaries and support files into a path prefix designated during configuration by typing 'make install'.
Top Configuration To configure the source prior to compilation, make a new directory. For example, on a GNU/Linux system, I might have the CHARMM source in my home directory under 'charmm'. $ cd ~ $ ls charmm Making a new build directory might look like the following. $ mkdir charmm-build $ ls charmm charmm-build From the new build directory, invoke the configure script with the desired options. $ cd charmm-build $ ../charmm/configure ... To see the currently supported list of options, use the --help option. $ ../charmm/configure --help Usage: configure [--option1] [--option2] ... Options: -a <keyword1,keyword2,...,keywordN>, --add <keyword1,keyword2,...,keywordN> add the keywords to the final pref.dat -c <path to cmake>, --cmake <path to cmake> use <path to cmake> to configure the build -g, --debug include debug symbols in final exec -i, --intel force use of intel compiler suite -l, --lite compile only lite version (very few keywords) -m, --mpi include support for openmpi -o, --openmm include support for OpenMM -p <install path>, --prefix <install path> install CHARMM into the given directory -r <keyword1,keyword2,...,keywordN>, --remove <keyword1,keyword2,...,keywordN> remove the keywords from the final pref.dat For example, to configure compilation using the Intel compiler suite and including debugging symbols: $ ../charmm/configure --intel --debug --prefix=/home/jdoe/charmm-install Please note that you must provide the prefix to successfully complete the final install phase and the prefix must be the full, literal path. Do not use shortcuts such as ~ or .. If the configure script detects the file 'install.com' and the directory 'build' in the current working directory, then the script will run the cmake command from the 'build/cmake' directory creating this directory if necessary. After configuration, in this case, change to the 'build/cmake' directory to run the make command. A relative prefix option will be relative to the 'build/cmake' directory instead of the top-level source directory.
Top Compilation After configuration completes with no errors, invoke make in the build directory. $ make -j3
Top Finally, if compilation completes with no error, invoke 'make install' to install binaries and support files into the user specified prefix directory. The binaries will be installed to <prefix>/bin To run the test cases from the installed <prefix> test directory, give test.com the first argument cmake intead of gnu or em64t. $ cd <prefix>/test $ ./test.com cmake ...