source: src/documentation/install.dox@ 47d041

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 47d041 was 750cff, checked in by Frederik Heber <heber@…>, 13 years ago

HUGE: Update on documenation.

  • a general skeleton of the documentation is now in place with all the major components of MoleCuilder explained to some extent.
  • some information has been transfered from TRAC (e.g. install procecure) into this doxygen documentation where it is general and not specific to the situation at our institute.
  • Property mode set to 100644
File size: 4.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/**
9 * \file install.dox
10 *
11 * Created on: Oct 28, 2011
12 * Author: heber
13 */
14
15/**
16 * \page install Installation
17 *
18 * \section install-compiling Compiling the Code
19 *
20 * After you obtained the code, you do the following:
21 *
22 * \code
23 * ./bootstrap
24 * \endcode
25 *
26 * This creates the necessary autoconf and automake files.
27 *
28 * After this,
29 *
30 * \code
31 * mkdir build
32 * cd build
33 * ../configure --prefix=`pwd`
34 * \endcode
35 *
36 * which will run the configure script that checks whether you have a current
37 * version of the following required packages
38 *
39 * -# GNU Scientific Library (specify via LDFLAGS, ...)
40 * -# Qt4 framework (--with-Qt=<dir> or --with-Qt-include-dir, --with-Qt-bin-dir,
41 * --with-Qt-lib-dir and --with-Qt-lib)
42 * -# Boost library 1.40 or newer with program_options and threads (--with-boost=<dir>)
43 * -# CPPUnit framework (--with-cppunit-prefix=<dir>)
44 * -# CodePatterns (--with-codepatterns=<dir>)
45 *
46 * \a --prefix is the argument to tell configure where all program code should go
47 * to (pwd is the unix command for the current working directory). There are
48 * others, see
49 *
50 * \code
51 * ../configure --help
52 * \endcode
53 *
54 * and some enable/disable switches you should check out:
55 *
56 * - \a --enable-ecut - says that the TestRunner, comprising all unit tests in one
57 * exectuable, shall make use of the Eclipse CppUnitTest (ECUT). If this is
58 * started within eclipse with this plugin installed, a shiny interface will tell
59 * you what failed and what not.
60 * - \a --enable-debug - activates many internal asserts, memory debugger and more
61 * (makes code a lot slower but gives information in case something fails)
62 *
63 * \note A note about configure: If one library is found only under some specific path, you
64 * can add CFLAGS, CPPFLAGS, LDFLAGS, ... to the configure call, like this
65 * \code
66 * ../configure --prefix=`pwd` --enable-hydrogen CFLAGS="-Wall -g3" CXXFLAGS="-Wall -g3"
67 * \endcode
68 * which enables all compiler warnings and full debugging of the code without any
69 * optimization. configure saves these variables, too, such that when it is called
70 * to re-configure it will still make use of them from its cache file.
71 *
72 * There are several flags that change the way molecuilder is compiled and probably
73 * make it run faster, more unsafe, ...
74 * -# \a -DLOG_OBSERVER, What the Observers do is logged, the log is printed on exit
75 * -# \a -DNO_MEMDEBUG, MemDebug (memory debugger) is disabled
76 * -# \a -DNO_CACHING, Cachable are short-wired, i.e. always recalculate, this slows
77 * down the code a lot
78 * -# \a -DNDEBUG, include NO_MEMDEBUG, also ASSERTs are not checked, this speeds up
79 * the code by a factor of 5
80 *
81 * \section install-install Installing
82 *
83 * Now, we are ready to compile and install.
84 *
85 * \code
86 * make
87 * make install
88 * \endcode
89 *
90 * \attention If you have a multi-core system, it is highly recommended to use the
91 * \a -j option of make to allow for multiple threads to work on compiling or
92 * checking the codfe simultaneously.
93 *
94 * And if everything went well, you should launch the unit tests and the testsuite
95 * by (see section \ref tests on how to launch the tests individually)
96 *
97 * \code
98 * make check
99 * \endcode
100 *
101 * If everything is OK, you have a working version of MoleCuilder in form of the
102 * executables \b bin/molecuilder and \b bin/molecuildergui.
103 *
104 * If you have to delete all compiled stuff, enter
105 *
106 * \code
107 * make clean
108 * \endcode
109 *
110 * or
111 *
112 * \code
113 * make distclean
114 * \endcode
115 *
116 * which will also delete all autoconf stuff for configure.
117 *
118 * distclean is at times necessary when stuff does not compile and there's
119 * seemingly no logic behind it, i.e. especially when paths of modules have
120 * changed. To recover your configure options, either look at \b config.log in
121 * the build directory or enter
122 *
123 * \code
124 * ./config.status --version
125 * \endcode
126 *
127 * Further useful commands are
128 * -# make clean uninstall: deletes .o-files and removes executable from the given
129 * binary directory
130 * -# make doc: Creates these html pages out of the documented source
131 * -# make check: Runs an extensive set of unit tests and a testsuite which also gives
132 * a good overview on the set of functions.
133 *
134 * \date 2011-10-31
135 */
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