[ViewVC] Annotation of: OpenMD/branches/development/INSTALL

Compiling OpenMD

  OpenMD is written in C++. Compiling is the process of turning this
  C++ into instructions that the computer’s processor can understand.

Requirements

  To build OpenMD, you need the following:

   * The source code for the latest release of OpenMD
   * A C++ compiler
   * CMake 2.6 or newer

  OpenMD uses CMake as its build system. CMake is an open source
  cross-platform build system from KitWare.

  You need to install CMake 2.6 or newer. This is available as a
  binary package from the KitWare website; alternatively, it may be
  available through your package manager (on Linux). If necessary, you
  can also compile it yourself from the source code.

  The following are optional when compiling OpenMD, but if they are not
  available some features will be missing:

   * OpenMPI – A very good implementation of the MPI-2 specification
     for parallel computing.  A version of the MPI library is required
     if you want to run the multi-processor version of OpenMD

   * perl and python - interpreted scripting languages that some of
     the OpenMD utilities use to parse and process data files.

   * qhull – A computational geometry toolbox for computing convex
     hulls and Delaunay triangulations.  qhull is required for the
     LangevinHull integrator and for any of the tools that compute the
     Hull atoms or hull volumes of nanoparticles and clusters.

   * openbabel – a chemical toolbox for converting between different
     data formats.  This is required for building the atom2md program
     which helps prepare initial "metadata" or md files for
     simulations.

   * fftw - a library for computing discrete Fourier transforms.  This
     is required for surface undulation spectra (Hxy in
     staticProps). Get version 3.

   * zlib - required to support reading gzipped trajectory files

  You’ll also likely want to download and compile the following useful
  tools for interacting with the data:

   * Jmol
   * xmgr
   * grace
   * NumPy
   * vmd

  If you are going to be extending or developing OpenMD, you’ll need
  the following tools:

   * antlr – our tool for parsing meta-data files.  You’ll want
     version 2, not 3.  

   * gengetopt - a tool to generate C code to parse the command line
     arguments argc and argv that are part of every C or C++ program


Basic build procedure

  The recommended way to build OpenMD is to use a separate source and
  build directory; for example, openmd-2.0 and build. The first step
  is to create these directories:

  $ tar zxf openmd-2.0.tar.gz   # (this creates openmd-2.0)
  $ mkdir build

  Now you need to run cmake to configure the build. The following will
  configure the build to use all of the default options:

  $ cd build
  $ cmake ../openmd-2.0

  If you need to specify a particular compiler, you can do that with
  environment variables before the cmake line

  $ export CC=/opt/local/lib/openmpi/bin/mpicc
  $ export CXX=/opt/local/lib/openmpi/bin/mpic++
  $ cmake ../openmd-2.0

  If you need to specify an option, use the -D switch to cmake. For
  example, the following line sets the value of CMAKE_INSTALL_PREFIX
  and CMAKE_BUILD_TYPE:

  $ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools -DCMAKE_BUILD_TYPE=DEBUG

  We will discuss various possible options later.

  At this point, it would be a good idea to compile OpenMD:

  $ make

  Have a coffee while the magic happens. If you have a multi-processor
  machine and would prefer an espresso, try a parallel build instead:

  $ make -j4    # parallel build across 4 processors

  And finally, as root (or using sudo) you should install it:

  # make install


Local build

  With the right sort of environment variable magic (see below), you
  can actually use OpenMD straight from the build folder. But life is
  a bit easier if you install it somewhere, either system-wide or
  locally.

  By default, OpenMD is installed in /usr/local on a Unix-like
  system. This requires root access (or sudo). Even if you do have
  root access, you may not want to overwrite an existing installation
  or you may want to avoid conflicts with a version of OpenMD
  installed by your package manager.

  The solution to all of these problems is to do a local install into
  a directory somewhere in your home folder. An additional advantage
  of a local install is that if you ever want to uninstall it, all you
  need to do is delete the installation directory; removing the files
  from a global install is more work.

  To configure cmake to install into ~/Tools/openmd-install, for
  example, you would do the following:

  $ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools/openmd-install

  Then you can run make and make install without needing root access:

  $ make && make install


Troubleshooting build problems

  * CMake caches some variables from run-to-run. How can I wipe the
    cache to start from scratch?

    Delete CMakeCache.txt in the build directory. This is also a very
    useful file to look into if you have any problems.

  * What environment variables affect how OpenMD finds force field and
    data files?

    FORCE_PARAM_PATH - Used to find the location of the data files
                       used for force fields and atom sizes, etc.

    If you get errors about not being able to find some .txt files,
    then you should set this to the name of the folder containing
    files such as Amber.frc and element.txt. These are typically
    installed to /usr/local/openmd/forceFields

Advanced build options 

  * How do I do a debug build?

    -DCMAKE_BUILD_TYPE=Debug does a debug build (gcc -g). To revert to
     a regular build use -DCMAKE_BUILD_TYPE=Release.

  * How do I see what commands cmake is using to build?

    Run Make as follows:

    $ VERBOSE=1 make

  * How do I build the Doxygen documentation?

    If CMake found the "doxygen" program in your PATH, an optional
    build target called "doc" is created.  If the Doxygen executable
    was not on the PATH, you will need to specify its location with
    -DDOXYGEN_EXECUTABLE=wherever.  To build the documentation, type:

    $ make doc
Revision:	1840
Committed:	Mon Jan 28 15:44:32 2013 UTC (12 years, 9 months ago) by gezelter
File size:	6148 byte(s)
Log Message:	Merging trunk changes back to development branch
#	User	Rev	Content
1	gezelter	1652	Compiling OpenMD
2
3			OpenMD is written in C++. Compiling is the process of turning this
4	gezelter	1655	C++ into instructions that the computer’s processor can understand.
5	gezelter	1652
6			Requirements
7
8			To build OpenMD, you need the following:
9
10			* The source code for the latest release of OpenMD
11	gezelter	1840	* A C++ compiler
12	gezelter	1652	* CMake 2.6 or newer
13
14			OpenMD uses CMake as its build system. CMake is an open source
15			cross-platform build system from KitWare.
16
17			You need to install CMake 2.6 or newer. This is available as a
18			binary package from the KitWare website; alternatively, it may be
19			available through your package manager (on Linux). If necessary, you
20			can also compile it yourself from the source code.
21
22			The following are optional when compiling OpenMD, but if they are not
23			available some features will be missing:
24
25			* OpenMPI – A very good implementation of the MPI-2 specification
26			for parallel computing. A version of the MPI library is required
27			if you want to run the multi-processor version of OpenMD
28
29			* perl and python - interpreted scripting languages that some of
30			the OpenMD utilities use to parse and process data files.
31
32			* qhull – A computational geometry toolbox for computing convex
33			hulls and Delaunay triangulations. qhull is required for the
34			LangevinHull integrator and for any of the tools that compute the
35			Hull atoms or hull volumes of nanoparticles and clusters.
36
37			* openbabel – a chemical toolbox for converting between different
38			data formats. This is required for building the atom2md program
39			which helps prepare initial "metadata" or md files for
40			simulations.
41
42			* fftw - a library for computing discrete Fourier transforms. This
43			is required for surface undulation spectra (Hxy in
44			staticProps). Get version 3.
45
46			* zlib - required to support reading gzipped trajectory files
47
48			You’ll also likely want to download and compile the following useful
49			tools for interacting with the data:
50
51			* Jmol
52			* xmgr
53			* grace
54			* NumPy
55			* vmd
56
57			If you are going to be extending or developing OpenMD, you’ll need
58			the following tools:
59
60			* antlr – our tool for parsing meta-data files. You’ll want
61			version 2, not 3.
62
63			* gengetopt - a tool to generate C code to parse the command line
64			arguments argc and argv that are part of every C or C++ program
65
66
67			Basic build procedure
68
69			The recommended way to build OpenMD is to use a separate source and
70			build directory; for example, openmd-2.0 and build. The first step
71			is to create these directories:
72
73			$ tar zxf openmd-2.0.tar.gz # (this creates openmd-2.0)
74			$ mkdir build
75
76			Now you need to run cmake to configure the build. The following will
77			configure the build to use all of the default options:
78
79			$ cd build
80			$ cmake ../openmd-2.0
81
82			If you need to specify a particular compiler, you can do that with
83			environment variables before the cmake line
84
85			$ export CC=/opt/local/lib/openmpi/bin/mpicc
86			$ export CXX=/opt/local/lib/openmpi/bin/mpic++
87			$ cmake ../openmd-2.0
88
89			If you need to specify an option, use the -D switch to cmake. For
90			example, the following line sets the value of CMAKE_INSTALL_PREFIX
91			and CMAKE_BUILD_TYPE:
92
93			$ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools -DCMAKE_BUILD_TYPE=DEBUG
94
95			We will discuss various possible options later.
96
97			At this point, it would be a good idea to compile OpenMD:
98
99			$ make
100
101			Have a coffee while the magic happens. If you have a multi-processor
102			machine and would prefer an espresso, try a parallel build instead:
103
104			$ make -j4 # parallel build across 4 processors
105
106			And finally, as root (or using sudo) you should install it:
107
108			# make install
109
110
111			Local build
112
113			With the right sort of environment variable magic (see below), you
114			can actually use OpenMD straight from the build folder. But life is
115			a bit easier if you install it somewhere, either system-wide or
116			locally.
117
118			By default, OpenMD is installed in /usr/local on a Unix-like
119			system. This requires root access (or sudo). Even if you do have
120			root access, you may not want to overwrite an existing installation
121			or you may want to avoid conflicts with a version of OpenMD
122			installed by your package manager.
123
124			The solution to all of these problems is to do a local install into
125			a directory somewhere in your home folder. An additional advantage
126			of a local install is that if you ever want to uninstall it, all you
127			need to do is delete the installation directory; removing the files
128			from a global install is more work.
129
130			To configure cmake to install into ~/Tools/openmd-install, for
131			example, you would do the following:
132
133			$ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools/openmd-install
134
135			Then you can run make and make install without needing root access:
136
137			$ make && make install
138
139
140			Troubleshooting build problems
141
142			* CMake caches some variables from run-to-run. How can I wipe the
143			cache to start from scratch?
144
145			Delete CMakeCache.txt in the build directory. This is also a very
146			useful file to look into if you have any problems.
147
148			* What environment variables affect how OpenMD finds force field and
149			data files?
150
151			FORCE_PARAM_PATH - Used to find the location of the data files
152			used for force fields and atom sizes, etc.
153
154			If you get errors about not being able to find some .txt files,
155			then you should set this to the name of the folder containing
156			files such as Amber.frc and element.txt. These are typically
157			installed to /usr/local/openmd/forceFields
158
159			Advanced build options
160
161			* How do I do a debug build?
162
163			-DCMAKE_BUILD_TYPE=Debug does a debug build (gcc -g). To revert to
164			a regular build use -DCMAKE_BUILD_TYPE=Release.
165
166			* How do I see what commands cmake is using to build?
167
168			Run Make as follows:
169
170			$ VERBOSE=1 make
171
172			* How do I build the Doxygen documentation?
173
174			If CMake found the "doxygen" program in your PATH, an optional
175			build target called "doc" is created. If the Doxygen executable
176			was not on the PATH, you will need to specify its location with
177			-DDOXYGEN_EXECUTABLE=wherever. To build the documentation, type:
178
179			$ make doc