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1
2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3 %
4 % Copyright (c) 2003-2008 by University of Queensland
5 % Earth Systems Science Computational Center (ESSCC)
6 % http://www.uq.edu.au/esscc
7 %
8 % Primary Business: Queensland, Australia
9 % Licensed under the Open Software License version 3.0
10 % http://www.opensource.org/licenses/osl-3.0.php
11 %
12 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
13
14 % This file contains material common to all src distributions.
15
16 % The original version of this content came from the esscc twiki page maintained by ksteube
17
18 This chapter describes how to build \esfinley from source assuming that the dependencies are already installed (for example using precompiled packages for your OS).
19 Section~\ref{sec:deps} describes the dependencies, while Section~\ref{sec:compilesrc} gives the compile instructions.
20
21 If you would prefer to build all the dependecies from source in the escript-support packages please see Chapter~\ref{chap:allsrc}
22
23 \esfinley is known to compile and run on the following systems:
24 \begin{itemize}
25 \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.} - \Sec{sec:srclinux}
26 \item \linux using icc on SGI ICE 8200.
27 \item \macosx using gcc - \Sec{sec:srcmac}
28 \item \winxp using the Visual C compiler (we do not specifically discuss Windows builds in this guide).
29 \end{itemize}
30
31 \section{External dependencies}
32 \label{sec:deps}
33 The following external packages are required in order to compile and run \esfinley.
34 Where version numbers are specified, more recent versions can probably be subsituted.
35 You can either try the standard/precompiled packages available for your operating system or you can download and build them from source.
36 The advantage of using existing packages is that they are more likely to work together properly.
37 You must take greater care if downloading sources separately.
38
39 \begin{itemize}
40 \item python-2.5.1 (\url{http://python.org}) \\
41 - Python interpreter (You must compile with shared libraries.)
42 \item numpy 1.1.0 (\url{http://numpy.scipy.org})
43 - Arrays for python.
44 \item boost-1.35 (\url{http://www.boost.org}) \\
45 - Provides an interface between C++ and python.
46 \item scons-0.989.5 (\url{http://www.scons.org/}) \\
47 - a python-based alternative to ``make''.
48 \end{itemize}
49
50 The version numbers given here are not strict requirements, more recent (and in some cases older) versions will still work.
51 The following packages should be sufficient (but not necessarily minimal) for Debian 5.0 (``Lenny''):
52 python-dev, libboost1.35-dev, scons, python-numpy, g++.
53
54
55 These packages may be required for some of the optional capabilities of the system:
56
57 \begin{itemize}
58 \item netcdf-3.6.2 (\url{http://www.unidata.ucar.edu/software/netcdf}) \\-
59 Used to save data sets in binary form for checkpoint/restart (must be compiled with -fPIC).
60 \item vtk-5.0.4 (\url{http://www.vtk.org}) \\-
61 This is used to save VTK files for visualization.
62 \begin{itemize}
63 \item cmake-2.4.6 (\url{http://www.cmake.org}) \\-
64 Required to build VTK.
65 \item mesa-7.0.3 (\url{http://www.mesa3d.org})\\-
66 Free OpenGL replacement used by VTK.
67 \end{itemize}
68 \item netpbm (\url{http://netpbm.sourceforge.com}) \\-
69 Tools for producing movies from images
70 \item mpich2-1.0.7 (\url{http://www.mcs.anl.gov/research/projects/mpich2}) \\-
71 Parallelization with MPI.
72 \item parmetis-3.1 (\url{http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview}) \\-
73 Optimization of the stiffness matrix.
74 \item MKL \\(\url{http://www.intel.com/cd/software/products/asmo-na/eng/307757.htm}) \\-
75 Intel's Math Kernel Library for use with their C compiler.
76 \end{itemize}
77
78 The following packages might be useful for mesh generation:
79 \begin{itemize}
80 \item gmsh-2.2.0 (\url{http://www.geuz.org/gmsh}) \\-
81 Mesh generation and viewing.
82 \begin{itemize}
83 \item fltk-1.1.9 (\url{http://www.fltk.org}) \\-
84 Required to build gmsh
85 \item gsl-1.10 (\url{http://www.gnu.org/software/gsl}) \\-
86 Required to build gmsh
87 \end{itemize}
88 \item triangle-1.6 (\url{http://www.cs.cmu.edu/~quake/triangle.html})
89 \end{itemize}
90
91 Packages for visualization:
92 \begin{itemize}
93 \item mayavi-1.5 (\url{http://mayavi.sourceforge.net}) \\-
94 MayaVi is referenced in our User Guide for viewing VTK files.
95 \item visit-1.11 (\url{https://wci.llnl.gov/codes/visit/}) \\-
96 A featureful visualization system with movie-making capabilities.
97 \end{itemize}
98
99 \section{Compilation}\label{sec:compilesrc}
100 Throughout this section we will assume that the source code is uncompressed in a directory called \filename{escript.d}.
101 You can call the directory anything you like, provided that you make the change before you compile.
102
103 You need to indicate where to find the external dependencies.
104 Unless specified otherwise, all paths will be relative to the top level of the source.
105 To do this, create a file in the \filename{scons} directory called \filename{x_options.py} where ``x'' is the name of your computer (output of the \texttt{hostname} command).
106 As a starting point use one of the following:
107 \begin{itemize}
108 \item \filename{scons/linux_options_example.py} (\linux desktop)
109 \item \filename{scons/mac_options_example.py} (\macosx desktop)
110 \item \filename{ice_options_example.py} (SGI ICE 8200)
111 \item \filename{winxp_options_example.py} (\winxp)
112 \end{itemize}
113
114 To actually compile (if you have $n$ processors, then you can use \texttt{scons -j$n$} instead):
115
116 \begin{shellCode}
117 cd escript.d
118 scons
119 \end{shellCode}
120
121 As part of its output, scons will tell you the name of the options file it used as well as a list of features
122 and whether they are enabled for your build.
123
124 If you require debug versions of the libraries, use:
125 \begin{shellCode}
126 scons usedebug=yes
127 \end{shellCode}
128 A note about scons: if you recompile later with different options (e.g. leaving out usedebug), scons will revert
129 to its default values. If you wish to make a change more permanent, then modify your options file.
130
131
132 You can install the binaries/libraries in a different location with:
133 \begin{shellCode}
134 scons prefix=some_dir
135 \end{shellCode}
136
137 You can test your build using
138 \begin{shellCode}
139 scons all_tests
140 \end{shellCode}
141 Grab a coffee or two while the tests compile and run.
142 An alternative method is available for performing tests on \openmp and \mpi builds.
143
144 \subsection{Compilation with \openmp}
145 You will need to consult your compiler documentation for the precise switches to use to enable \openmp features.
146 Once you know the options, modify the omp_optim, omp_debug and omp_libs variables in your options.py file.
147
148 For example, for gcc compilers which support \openmp use:
149 \begin{shellCode}
150 omp_optim = '-fopenmp'
151 omp_debug = '-fopenmp'
152 omp_libs = ['gomp']
153 \end{shellCode}
154 Depending on your version, the last change may not be required.
155 If you're unsure try without the gomp library first and add it if you get linker errors.
156
157 Then recompile.
158 \begin{shellCode}
159 scons useopenmp=yes
160 \end{shellCode}
161
162 You can test your build, e.g. using 4 threads by issuing
163 \begin{shellCode}
164 export ESCRIPT_NUM_THREADS=4
165 scons all_tests
166 \end{shellCode}
167
168 \subsection{Compilation with \mpi}
169 You will need to have \mpi installed on your system.
170 There are a number of implementations so we do not provide any specific advice here.
171 You will need to modify the following variables in your options file.
172 \begin{itemize}
173 \item \texttt{mpi_flavour} \\
174 which \mpi implementation is used. Valid values are
175 \begin{itemize}
176 \item[\texttt{MPT}] SGI MPI implementation \\
177 \url{http://techpubs.sgi.com/library/manuals/3000/007-3687-010/pdf/007-3687-010.pdf}
178 \item[\texttt{MPICH2}] Argonne's MPICH version 2 implementation \\
179 \url{http://www.mcs.anl.gov/research/projects/mpi/mpich2/}
180 \item[\texttt{MPICH}] Argonne's MPICH implementation \\
181 \url{http://www.mcs.anl.gov/research/projects/mpi/mpich1/}
182 \item[\texttt{OPENMPI}] Open MPI \\
183 \url{http://www.open-mpi.org/}
184 \item[\texttt{INTELMPI}] Intel's MPI \\
185 \url{http://software.intel.com/en-us/intel-mpi-library/}
186 \end{itemize}
187 \item \texttt{mpi_path} \\
188 where to find \filename{mpi.h}
189 \item \texttt{mpi_lib_path} \\
190 where to find libraries for \mpi
191 \item \texttt{mpi_libs} \\
192 which libraries to link to.
193 \end{itemize}
194
195 Then compile with:
196 \begin{shellCode}
197 scons usempi=yes
198 \end{shellCode}
199
200 As with debug and openmp, you can make this a more permanent setting by modifying your options file.
201
202 To test your build using 6 processors enter:
203 \begin{shellCode}
204 export ESCRIPT_NUM_NODES=6
205 scons usempi=yes all_tests
206 \end{shellCode}
207 and on 6 processors with 4 threads each using
208 \begin{shellCode}
209 export ESCRIPT_NUM_THREADS=4
210 export ESCRIPT_NUM_NODES=6
211 scons usempi=yes all_tests
212 \end{shellCode}
213 Alternatively, you can give a hostfile
214 \begin{shellCode}
215 export ESCRIPT_NUM_THREADS=4
216 export ESCRIPT_HOSTFILE=myhostfile
217 scons usempi=yes all_tests
218 \end{shellCode}
219 Note that depending on your \mpi flavour it may be required to start a daemon before running the tests under \mpi.
220
221
222 \subsection{Difficulties}
223
224 %This is copied from Ken's notes on the old Twiki page
225 \subsubsection{``Bad magic number''}
226 Some reasons for this error message include:
227 \begin{itemize}
228 \item Using different versions of python when installing and running escript (Use \texttt{which python} and \texttt{python --version} to check)
229 \item Using different versions of libraries (Make sure \texttt{LD_LIBRARY_PATH} has \filename{x/lib} listed first, where x is the escript install path)
230 \item Using different versions of python modules (Make sure \texttt{PYTHONPATH} has \filename{/trunk/escript} directory listed first)
231 \end{itemize}
232
233 Another error we sometimes see is unsatisfied externals when trying to run a python script. This is usually due to not having \texttt{LD_LIBRARY_PATH} and \texttt{PYTHONPATH} set correctly so that you run with different libraries from the ones the code was compiled against. Check which libraries you are running against with \texttt{ldd lib/libfinley.so} and \texttt{ldd esys/finley/finleycpp.so}.
234
235 It is also possible that incompatible libraries were used when compiling \esfinley.
236 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.
237 Another case is when Boost or Numarray was compiled against the wrong Python library.
238 To avoid these problems both builder and user must ensure they are using the same python libraries.
239
240 \subsubsection{\openmp builds segfault running examples}
241
242 One known cause for this is linking the \filename{gomp} library with escript built using gcc 4.3.3.
243 While you need the \texttt{-fopenmp} switch you should not need to link \filename{gomp}.
244

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