[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,
  machine code.

Requirements

  To build OpenMD, you need the following:

   * The source code for the latest release of OpenMD
   * C++ and C compilers
   * 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:	1652
Committed:	Tue Sep 27 18:18:28 2011 UTC (13 years, 8 months ago) by gezelter
File size:	6169 byte(s)
Log Message:	added an INSTALL file, using svn2cl to get the ChangeLog target
#	User	Rev	Content
1	gezelter	1652	Compiling OpenMD
2
3			OpenMD is written in C++. Compiling is the process of turning this
4			C++ into instructions that the computer’s processor can understand,
5			machine code.
6
7			Requirements
8
9			To build OpenMD, you need the following:
10
11			* The source code for the latest release of OpenMD
12			* C++ and C compilers
13			* CMake 2.6 or newer
14
15			OpenMD uses CMake as its build system. CMake is an open source
16			cross-platform build system from KitWare.
17
18			You need to install CMake 2.6 or newer. This is available as a
19			binary package from the KitWare website; alternatively, it may be
20			available through your package manager (on Linux). If necessary, you
21			can also compile it yourself from the source code.
22
23			The following are optional when compiling OpenMD, but if they are not
24			available some features will be missing:
25
26			* OpenMPI – A very good implementation of the MPI-2 specification
27			for parallel computing. A version of the MPI library is required
28			if you want to run the multi-processor version of OpenMD
29
30			* perl and python - interpreted scripting languages that some of
31			the OpenMD utilities use to parse and process data files.
32
33			* qhull – A computational geometry toolbox for computing convex
34			hulls and Delaunay triangulations. qhull is required for the
35			LangevinHull integrator and for any of the tools that compute the
36			Hull atoms or hull volumes of nanoparticles and clusters.
37
38			* openbabel – a chemical toolbox for converting between different
39			data formats. This is required for building the atom2md program
40			which helps prepare initial "metadata" or md files for
41			simulations.
42
43			* fftw - a library for computing discrete Fourier transforms. This
44			is required for surface undulation spectra (Hxy in
45			staticProps). Get version 3.
46
47			* zlib - required to support reading gzipped trajectory files
48
49			You’ll also likely want to download and compile the following useful
50			tools for interacting with the data:
51
52			* Jmol
53			* xmgr
54			* grace
55			* NumPy
56			* vmd
57
58			If you are going to be extending or developing OpenMD, you’ll need
59			the following tools:
60
61			* antlr – our tool for parsing meta-data files. You’ll want
62			version 2, not 3.
63
64			* gengetopt - a tool to generate C code to parse the command line
65			arguments argc and argv that are part of every C or C++ program
66
67
68			Basic build procedure
69
70			The recommended way to build OpenMD is to use a separate source and
71			build directory; for example, openmd-2.0 and build. The first step
72			is to create these directories:
73
74			$ tar zxf openmd-2.0.tar.gz # (this creates openmd-2.0)
75			$ mkdir build
76
77			Now you need to run cmake to configure the build. The following will
78			configure the build to use all of the default options:
79
80			$ cd build
81			$ cmake ../openmd-2.0
82
83			If you need to specify a particular compiler, you can do that with
84			environment variables before the cmake line
85
86			$ export CC=/opt/local/lib/openmpi/bin/mpicc
87			$ export CXX=/opt/local/lib/openmpi/bin/mpic++
88			$ cmake ../openmd-2.0
89
90			If you need to specify an option, use the -D switch to cmake. For
91			example, the following line sets the value of CMAKE_INSTALL_PREFIX
92			and CMAKE_BUILD_TYPE:
93
94			$ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools -DCMAKE_BUILD_TYPE=DEBUG
95
96			We will discuss various possible options later.
97
98			At this point, it would be a good idea to compile OpenMD:
99
100			$ make
101
102			Have a coffee while the magic happens. If you have a multi-processor
103			machine and would prefer an espresso, try a parallel build instead:
104
105			$ make -j4 # parallel build across 4 processors
106
107			And finally, as root (or using sudo) you should install it:
108
109			# make install
110
111
112			Local build
113
114			With the right sort of environment variable magic (see below), you
115			can actually use OpenMD straight from the build folder. But life is
116			a bit easier if you install it somewhere, either system-wide or
117			locally.
118
119			By default, OpenMD is installed in /usr/local on a Unix-like
120			system. This requires root access (or sudo). Even if you do have
121			root access, you may not want to overwrite an existing installation
122			or you may want to avoid conflicts with a version of OpenMD
123			installed by your package manager.
124
125			The solution to all of these problems is to do a local install into
126			a directory somewhere in your home folder. An additional advantage
127			of a local install is that if you ever want to uninstall it, all you
128			need to do is delete the installation directory; removing the files
129			from a global install is more work.
130
131			To configure cmake to install into ~/Tools/openmd-install, for
132			example, you would do the following:
133
134			$ cmake ../openmd-2.0 -DCMAKE_INSTALL_PREFIX=~/Tools/openmd-install
135
136			Then you can run make and make install without needing root access:
137
138			$ make && make install
139
140
141			Troubleshooting build problems
142
143			* CMake caches some variables from run-to-run. How can I wipe the
144			cache to start from scratch?
145
146			Delete CMakeCache.txt in the build directory. This is also a very
147			useful file to look into if you have any problems.
148
149			* What environment variables affect how OpenMD finds force field and
150			data files?
151
152			FORCE_PARAM_PATH - Used to find the location of the data files
153			used for force fields and atom sizes, etc.
154
155			If you get errors about not being able to find some .txt files,
156			then you should set this to the name of the folder containing
157			files such as Amber.frc and element.txt. These are typically
158			installed to /usr/local/openmd/forceFields
159
160			Advanced build options
161
162			* How do I do a debug build?
163
164			-DCMAKE_BUILD_TYPE=Debug does a debug build (gcc -g). To revert to
165			a regular build use -DCMAKE_BUILD_TYPE=Release.
166
167			* How do I see what commands cmake is using to build?
168
169			Run Make as follows:
170
171			$ VERBOSE=1 make
172
173			* How do I build the Doxygen documentation?
174
175			If CMake found the "doxygen" program in your PATH, an optional
176			build target called "doc" is created. If the Doxygen executable
177			was not on the PATH, you will need to specify its location with
178			-DDOXYGEN_EXECUTABLE=wherever. To build the documentation, type:
179
180			$ make doc