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1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2 %
3 % Copyright (c) 2003-2009 by University of Queensland
4 % Earth Systems Science Computational Center (ESSCC)
5 % http://www.uq.edu.au/esscc
6 %
7 % Primary Business: Queensland, Australia
8 % Licensed under the Open Software License version 3.0
9 % http://www.opensource.org/licenses/osl-3.0.php
10 %
11 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
12
13 % This file contains material common to all src distributions.
14
15 % The original version of this content came from the esscc twiki page maintained by ksteube
16
17 This chapter describes how to build \esfinley from source assuming that the dependencies are already installed (for example using precompiled packages for your OS).
18 \Sec{sec:deps} describes the dependencies, while \Sec{sec:compilesrc} gives the compile instructions.
19
20 If you would prefer to build all the dependecies from source in the escript-support packages please see \Chap{chap:allsrc}.
21 \esfinley is known to compile and run on the following systems:
22 \begin{itemize}
23 \item \linux using gcc\footnote{There are some problems with \openmp under gcc prior to version 4.3.2. Also do not link the gomp library with gcc 4.3.3 - it causes problems.}
24 \item \linux using icc on SGI ICE 8200
25 \item \macosx using gcc
26 \item \winxp using the Visual C compiler (we do not specifically discuss Windows builds in this guide).
27 \end{itemize}
28
29 \section{External dependencies}
30 \label{sec:deps}
31 The following external packages are required in order to compile and run \esfinley.
32 Where version numbers are specified, more recent versions can probably be subsituted.
33 You can either try the standard/precompiled packages available for your operating system or you can download and build them from source.
34 The advantage of using existing packages is that they are more likely to work together properly.
35 You must take greater care if downloading sources separately.
36
37 \begin{itemize}
38 \item python-2.5.1 (\url{http://python.org}) \\-
39 Python interpreter (you must compile with shared libraries.)
40 \item numpy 1.1.0 (\url{http://numpy.scipy.org}) \\-
41 Arrays for python
42 \item boost-1.35 (\url{http://www.boost.org}) \\-
43 Interface between C++ and Python
44 \item scons-0.989.5 (\url{http://www.scons.org/}) \\-
45 Python-based alternative to ``make''.
46 \end{itemize}
47
48 The version numbers given here are not strict requirements, more recent (and in some cases older) versions are very likely to work.
49 The following packages should be sufficient (but not necessarily minimal) for Debian 5.0 (``Lenny''):
50 python-dev, libboost-python1.35-dev, scons, python-numpy, g++.
51
52 These packages may be required for some of the optional capabilities of the system:
53
54 \begin{itemize}
55 \item netcdf-3.6.2 (\url{http://www.unidata.ucar.edu/software/netcdf}) \\-
56 Used to save data sets in binary form for checkpoint/restart (must be compiled with -fPIC)
57 \item vtk-5.0.4 (\url{http://www.vtk.org}) \\-
58 Used to save VTK files for visualization
59 \begin{itemize}
60 \item cmake-2.4.6 (\url{http://www.cmake.org}) \\-
61 Required to build VTK
62 \item mesa-7.0.3 (\url{http://www.mesa3d.org})\\-
63 Free OpenGL replacement used by VTK
64 \end{itemize}
65 \item netpbm (\url{http://netpbm.sourceforge.com}) \\-
66 Tools for producing movies from images
67 \item mpich2-1.0.7 (\url{http://www.mcs.anl.gov/research/projects/mpich2}) \\-
68 Parallelization with \mpi
69 \item parmetis-3.1 (\url{http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview}) \\-
70 Optimization of the stiffness matrix
71 \item MKL \\(\url{http://www.intel.com/cd/software/products/asmo-na/eng/307757.htm}) \\-
72 Intel's Math Kernel Library for use with their C compiler.
73 \end{itemize}
74
75 The following packages might be useful for mesh generation:
76 \begin{itemize}
77 \item gmsh-2.2.0 (\url{http://www.geuz.org/gmsh}) \\-
78 Mesh generation and viewing
79 \begin{itemize}
80 \item fltk-1.1.9 (\url{http://www.fltk.org}) \\-
81 Required to build gmsh
82 \item gsl-1.10 (\url{http://www.gnu.org/software/gsl}) \\-
83 Required to build gmsh
84 \end{itemize}
85 \item triangle-1.6 (\url{http://www.cs.cmu.edu/~quake/triangle.html}) \\-
86 Two-dimensional mesh generator and Delaunay triangulator.
87 \end{itemize}
88
89 Packages for visualization:
90 \begin{itemize}
91 \item mayavi-1.5 (\url{http://mayavi.sourceforge.net}) \\-
92 MayaVi is referenced in our User's Guide for viewing VTK files
93 \item visit-1.11.2 (\url{https://wci.llnl.gov/codes/visit/}) \\-
94 A featureful visualization system with movie-making capabilities.
95 \end{itemize}
96
97 \section{Compilation}\label{sec:compilesrc}
98 Throughout this section we will assume that the source code is uncompressed in a directory called \filename{escript.d}.
99 You can call the directory anything you like, provided that you make the change before you compile.
100
101 You need to indicate where to find the external dependencies.
102 To do this, create a file in the \filename{escript.d/scons} directory called \filename{x_options.py} where ``x'' is the name of your computer (output of the \texttt{hostname} command).
103 Please note that if your hostname has non-alphanumeric characters in it (eg - ) you need to replace them with underscores.
104 For example the options file for \texttt{bob-desktop} would be named \filename{bob_desktop_options.py}.
105
106 From now on all paths will be relative to the top level of the source.
107 As a starting point copy the contents one of the following files :
108 \begin{itemize}
109 \item \filename{scons/linux_options_example.py} (\linux desktop)
110 \item \filename{scons/mac_options_example.py} (\macosx desktop)
111 \item \filename{scons/ice_options_example.py} (SGI ICE 8200)
112 \item \filename{scons/winxp_options_example.py} (\winxp)
113 \end{itemize}
114
115 To actually compile (if you have $n$ processors, then you can use \texttt{scons -j$n$} instead):
116
117 \begin{shellCode}
118 cd escript.d
119 scons
120 \end{shellCode}
121
122 As part of its output, scons will tell you the name of the options file it used as well as a list of features
123 and whether they are enabled for your build.
124
125 If you require debug versions of the libraries, use:
126 \begin{shellCode}
127 scons usedebug=yes
128 \end{shellCode}
129 A note about scons: if you recompile later with different options (e.g. leaving out usedebug), scons will revert
130 to its default values. If you wish to make a change more permanent, then modify your options file.
131
132
133 You can install the binaries/libraries in a different location with:
134 \begin{shellCode}
135 scons prefix=some_dir
136 \end{shellCode}
137
138 You can test your build using
139 \begin{shellCode}
140 scons all_tests
141 \end{shellCode}
142 Grab a coffee or two while the tests compile and run.
143 An alternative method is available for performing tests on \openmp and \mpi builds.
144
145 \subsection{Compilation with \openmp}
146 You will need to consult your compiler documentation for the precise switches to use to enable \openmp features.
147 Once you know the options, modify the omp_optim, omp_debug and omp_libs variables in your options.py file.
148
149 For example, for gcc compilers which support \openmp use:
150 \begin{shellCode}
151 omp_optim = '-fopenmp'
152 omp_debug = '-fopenmp'
153 omp_libs = ['gomp']
154 \end{shellCode}
155 Depending on your version, the last change may not be required.
156 If you're unsure try without the gomp library first and add it if you get linker errors.
157
158 Then recompile.
159 \begin{shellCode}
160 scons useopenmp=yes
161 \end{shellCode}
162
163 You can test your build, e.g. using 4 threads by issuing
164 \begin{shellCode}
165 export ESCRIPT_NUM_THREADS=4
166 scons all_tests
167 \end{shellCode}
168
169 \subsection{Compilation with \mpi}
170 You will need to have \mpi installed on your system.
171 There are a number of implementations so we do not provide any specific advice here.
172 You will need to modify the following variables in your options file.
173 \begin{itemize}
174 \item \texttt{mpi_flavour} \\
175 which \mpi implementation is used. Valid values are
176 \begin{itemize}
177 \item[\texttt{MPT}] SGI MPI implementation \\
178 \url{http://techpubs.sgi.com/library/manuals/3000/007-3687-010/pdf/007-3687-010.pdf}
179 \item[\texttt{MPICH2}] Argonne's MPICH version 2 implementation \\
180 \url{http://www.mcs.anl.gov/research/projects/mpi/mpich2/}
181 \item[\texttt{MPICH}] Argonne's MPICH implementation \\
182 \url{http://www.mcs.anl.gov/research/projects/mpi/mpich1/}
183 \item[\texttt{OPENMPI}] Open MPI \\
184 \url{http://www.open-mpi.org/}
185 \item[\texttt{INTELMPI}] Intel's MPI \\
186 \url{http://software.intel.com/en-us/intel-mpi-library/}
187 \end{itemize}
188 \item \texttt{mpi_path} \\
189 where to find \filename{mpi.h}
190 \item \texttt{mpi_lib_path} \\
191 where to find libraries for \mpi
192 \item \texttt{mpi_libs} \\
193 which libraries to link to.
194 \end{itemize}
195
196 Then compile with:
197 \begin{shellCode}
198 scons usempi=yes
199 \end{shellCode}
200
201 As with debug and openmp, you can make this a more permanent setting by modifying your options file.
202
203 To test your build using 6 processors enter:
204 \begin{shellCode}
205 export ESCRIPT_NUM_NODES=6
206 scons usempi=yes all_tests
207 \end{shellCode}
208 and on 6 processors with 4 threads each using
209 \begin{shellCode}
210 export ESCRIPT_NUM_THREADS=4
211 export ESCRIPT_NUM_NODES=6
212 scons usempi=yes all_tests
213 \end{shellCode}
214 Alternatively, you can give a hostfile
215 \begin{shellCode}
216 export ESCRIPT_NUM_THREADS=4
217 export ESCRIPT_HOSTFILE=myhostfile
218 scons usempi=yes all_tests
219 \end{shellCode}
220 Note that depending on your \mpi flavour it may be required to start a daemon before running the tests under \mpi.
221
222
223 \subsection{Difficulties}
224
225 %This is copied from Ken's notes on the old Twiki page
226 \subsubsection{``Bad magic number''}
227 This error usually indicates that the version of python used to run escript differs from the version used when installing escript (Use \texttt{which python} and \texttt{python --version} to check).
228
229 It is also possible that incompatible libraries were used when compiling \esfinley.
230 For example, if you run with Python2.4 but the software was compiled against Python2.5 then you will get unsatisfied externals or a large error message with a long traceback.
231 Another case is when Boost or Numarray was compiled against the wrong Python library.
232 To avoid these problems both builder and user must ensure they are using the same python libraries.
233
234 \subsubsection{\openmp builds segfault running examples}
235
236 One known cause for this is linking the \filename{gomp} library with escript built using gcc 4.3.3.
237 While you need the \texttt{-fopenmp} switch you should not need to link \filename{gomp}.
238

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