[ViewVC] Contents 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, 3 months ago) by gezelter
File size:	6148 byte(s)
Log Message:	Merging trunk changes back to development branch
#	Content
1	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
6	Requirements
7
8	To build OpenMD, you need the following:
9
10	* The source code for the latest release of OpenMD
11	* A C++ compiler
12	* 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