[ViewVC] Contents of: OpenMD/trunk/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 2.8.5 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-2.3 and build. The first step
  is to create these directories:

  $ tar zxf openmd-2.3.tar.gz   # (this creates openmd-2.3)
  $ 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-2.3

  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-2.3

  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-2.3 -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:

  # umask 0022 && make install

  Or:
  
  $ umask 0022
  $ sudo 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-2.3 -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

  * CMake honors user umask for creating directories as of now:
        http://public.kitware.com/Bug/view.php?id=9620
    To get predictable results please set umask explicitly before
    running the make install command.

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:	2079
Committed:	Tue Mar 10 15:20:28 2015 UTC (10 years, 1 month ago) by gezelter
File size:	6435 byte(s)
Log Message:	Updated some of the root-level text files for 2.3 release
#	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 2.8.5 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-2.3 and build. The first step
71	is to create these directories:
72
73	$ tar zxf openmd-2.3.tar.gz # (this creates openmd-2.3)
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-2.3
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-2.3
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-2.3 -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	# umask 0022 && make install
109
110	Or:
111
112	$ umask 0022
113	$ sudo make install
114
115
116	Local build
117
118	With the right sort of environment variable magic (see below), you
119	can actually use OpenMD straight from the build folder. But life is
120	a bit easier if you install it somewhere, either system-wide or
121	locally.
122
123	By default, OpenMD is installed in /usr/local on a Unix-like
124	system. This requires root access (or sudo). Even if you do have
125	root access, you may not want to overwrite an existing installation
126	or you may want to avoid conflicts with a version of OpenMD
127	installed by your package manager.
128
129	The solution to all of these problems is to do a local install into
130	a directory somewhere in your home folder. An additional advantage
131	of a local install is that if you ever want to uninstall it, all you
132	need to do is delete the installation directory; removing the files
133	from a global install is more work.
134
135	To configure cmake to install into ~/Tools/openmd-install, for
136	example, you would do the following:
137
138	$ cmake ../openmd-2.3 -DCMAKE_INSTALL_PREFIX=~/Tools/openmd-install
139
140	Then you can run make and make install without needing root access:
141
142	$ make && make install
143
144
145	Troubleshooting build problems
146
147	* CMake caches some variables from run-to-run. How can I wipe the
148	cache to start from scratch?
149
150	Delete CMakeCache.txt in the build directory. This is also a very
151	useful file to look into if you have any problems.
152
153	* What environment variables affect how OpenMD finds force field and
154	data files?
155
156	FORCE_PARAM_PATH - Used to find the location of the data files
157	used for force fields and atom sizes, etc.
158
159	If you get errors about not being able to find some .txt files,
160	then you should set this to the name of the folder containing
161	files such as Amber.frc and element.txt. These are typically
162	installed to /usr/local/openmd/forceFields
163
164	* CMake honors user umask for creating directories as of now:
165	http://public.kitware.com/Bug/view.php?id=9620
166	To get predictable results please set umask explicitly before
167	running the make install command.
168
169	Advanced build options
170
171	* How do I do a debug build?
172
173	-DCMAKE_BUILD_TYPE=Debug does a debug build (gcc -g). To revert to
174	a regular build use -DCMAKE_BUILD_TYPE=Release.
175
176	* How do I see what commands cmake is using to build?
177
178	Run Make as follows:
179
180	$ VERBOSE=1 make
181
182	* How do I build the Doxygen documentation?
183
184	If CMake found the "doxygen" program in your PATH, an optional
185	build target called "doc" is created. If the Doxygen executable
186	was not on the PATH, you will need to specify its location with
187	-DDOXYGEN_EXECUTABLE=wherever. To build the documentation, type:
188
189	$ make doc