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

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