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1 jfenwick 2289 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2     %
3 jfenwick 2548 % Copyright (c) 2003-2009 by University of Queensland
4 jfenwick 2289 % 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 caltinay 2536 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 caltinay 2538 \Sec{sec:deps} describes the dependencies, while \Sec{sec:compilesrc} gives the compile instructions.
19 jfenwick 2529
20 caltinay 2547 If you would prefer to build all the dependecies from source in the escript-support packages please see \Chap{chap:allsrc}.
21 jfenwick 2289 \esfinley is known to compile and run on the following systems:
22     \begin{itemize}
23 caltinay 2547 \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 caltinay 2536 \item \winxp using the Visual C compiler (we do not specifically discuss Windows builds in this guide).
27 jfenwick 2289 \end{itemize}
28    
29     \section{External dependencies}
30 jfenwick 2529 \label{sec:deps}
31 jfenwick 2289 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 caltinay 2536 The advantage of using existing packages is that they are more likely to work together properly.
35 jfenwick 2289 You must take greater care if downloading sources separately.
36    
37     \begin{itemize}
38 caltinay 2547 \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 jfenwick 2289 \end{itemize}
47    
48 caltinay 2547 The version numbers given here are not strict requirements, more recent (and in some cases older) versions are very likely to work.
49 jfenwick 2289 The following packages should be sufficient (but not necessarily minimal) for Debian 5.0 (``Lenny''):
50 jfenwick 2512 python-dev, libboost1.35-dev, scons, python-numpy, g++.
51 jfenwick 2289
52 caltinay 2536 These packages may be required for some of the optional capabilities of the system:
53 jfenwick 2289
54     \begin{itemize}
55     \item netcdf-3.6.2 (\url{http://www.unidata.ucar.edu/software/netcdf}) \\-
56 caltinay 2547 Used to save data sets in binary form for checkpoint/restart (must be compiled with -fPIC)
57 caltinay 2536 \item vtk-5.0.4 (\url{http://www.vtk.org}) \\-
58 caltinay 2547 Used to save VTK files for visualization
59 jfenwick 2289 \begin{itemize}
60 caltinay 2536 \item cmake-2.4.6 (\url{http://www.cmake.org}) \\-
61 caltinay 2547 Required to build VTK
62 caltinay 2536 \item mesa-7.0.3 (\url{http://www.mesa3d.org})\\-
63 caltinay 2547 Free OpenGL replacement used by VTK
64 jfenwick 2289 \end{itemize}
65 caltinay 2536 \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 caltinay 2547 Parallelization with \mpi
69 caltinay 2536 \item parmetis-3.1 (\url{http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview}) \\-
70 caltinay 2547 Optimization of the stiffness matrix
71 caltinay 2536 \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 jfenwick 2289 \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 caltinay 2547 Mesh generation and viewing
79 jfenwick 2289 \begin{itemize}
80 caltinay 2536 \item fltk-1.1.9 (\url{http://www.fltk.org}) \\-
81 caltinay 2547 Required to build gmsh
82 caltinay 2536 \item gsl-1.10 (\url{http://www.gnu.org/software/gsl}) \\-
83 caltinay 2547 Required to build gmsh
84 caltinay 2536 \end{itemize}
85 caltinay 2547 \item triangle-1.6 (\url{http://www.cs.cmu.edu/~quake/triangle.html}) \\-
86     Two-dimensional mesh generator and Delaunay triangulator.
87 jfenwick 2289 \end{itemize}
88    
89     Packages for visualization:
90     \begin{itemize}
91     \item mayavi-1.5 (\url{http://mayavi.sourceforge.net}) \\-
92 caltinay 2547 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 jfenwick 2289 \end{itemize}
96    
97 jfenwick 2324 \section{Compilation}\label{sec:compilesrc}
98 jfenwick 2529 Throughout this section we will assume that the source code is uncompressed in a directory called \filename{escript.d}.
99 jfenwick 2289 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     Unless specified otherwise, all paths will be relative to the top level of the source.
103 caltinay 2536 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).
104 jfenwick 2289 As a starting point use one of the following:
105     \begin{itemize}
106     \item \filename{scons/linux_options_example.py} (\linux desktop)
107     \item \filename{scons/mac_options_example.py} (\macosx desktop)
108     \item \filename{ice_options_example.py} (SGI ICE 8200)
109     \item \filename{winxp_options_example.py} (\winxp)
110     \end{itemize}
111    
112     To actually compile (if you have $n$ processors, then you can use \texttt{scons -j$n$} instead):
113    
114     \begin{shellCode}
115 jfenwick 2529 cd escript.d
116 jfenwick 2289 scons
117     \end{shellCode}
118    
119     As part of its output, scons will tell you the name of the options file it used as well as a list of features
120     and whether they are enabled for your build.
121    
122     If you require debug versions of the libraries, use:
123     \begin{shellCode}
124     scons usedebug=yes
125     \end{shellCode}
126 caltinay 2536 A note about scons: if you recompile later with different options (e.g. leaving out usedebug), scons will revert
127 jfenwick 2289 to its default values. If you wish to make a change more permanent, then modify your options file.
128    
129    
130     You can install the binaries/libraries in a different location with:
131     \begin{shellCode}
132     scons prefix=some_dir
133     \end{shellCode}
134    
135     You can test your build using
136     \begin{shellCode}
137     scons all_tests
138     \end{shellCode}
139 caltinay 2536 Grab a coffee or two while the tests compile and run.
140     An alternative method is available for performing tests on \openmp and \mpi builds.
141 jfenwick 2289
142     \subsection{Compilation with \openmp}
143 caltinay 2536 You will need to consult your compiler documentation for the precise switches to use to enable \openmp features.
144 jfenwick 2289 Once you know the options, modify the omp_optim, omp_debug and omp_libs variables in your options.py file.
145    
146 caltinay 2536 For example, for gcc compilers which support \openmp use:
147 jfenwick 2289 \begin{shellCode}
148     omp_optim = '-fopenmp'
149     omp_debug = '-fopenmp'
150     omp_libs = ['gomp']
151     \end{shellCode}
152 caltinay 2536 Depending on your version, the last change may not be required.
153     If you're unsure try without the gomp library first and add it if you get linker errors.
154 jfenwick 2289
155     Then recompile.
156     \begin{shellCode}
157     scons useopenmp=yes
158     \end{shellCode}
159    
160 caltinay 2536 You can test your build, e.g. using 4 threads by issuing
161 gross 2363 \begin{shellCode}
162     export ESCRIPT_NUM_THREADS=4
163     scons all_tests
164     \end{shellCode}
165    
166 caltinay 2536 \subsection{Compilation with \mpi}
167     You will need to have \mpi installed on your system.
168 jfenwick 2289 There are a number of implementations so we do not provide any specific advice here.
169     You will need to modify the following variables in your options file.
170     \begin{itemize}
171 caltinay 2536 \item \texttt{mpi_flavour} \\
172     which \mpi implementation is used. Valid values are
173     \begin{itemize}
174     \item[\texttt{MPT}] SGI MPI implementation \\
175     \url{http://techpubs.sgi.com/library/manuals/3000/007-3687-010/pdf/007-3687-010.pdf}
176     \item[\texttt{MPICH2}] Argonne's MPICH version 2 implementation \\
177     \url{http://www.mcs.anl.gov/research/projects/mpi/mpich2/}
178     \item[\texttt{MPICH}] Argonne's MPICH implementation \\
179     \url{http://www.mcs.anl.gov/research/projects/mpi/mpich1/}
180     \item[\texttt{OPENMPI}] Open MPI \\
181     \url{http://www.open-mpi.org/}
182     \item[\texttt{INTELMPI}] Intel's MPI \\
183     \url{http://software.intel.com/en-us/intel-mpi-library/}
184     \end{itemize}
185 jfenwick 2289 \item \texttt{mpi_path} \\
186     where to find \filename{mpi.h}
187 caltinay 2536 \item \texttt{mpi_lib_path} \\
188     where to find libraries for \mpi
189     \item \texttt{mpi_libs} \\
190 jfenwick 2289 which libraries to link to.
191     \end{itemize}
192    
193 jfenwick 2290 Then compile with:
194     \begin{shellCode}
195     scons usempi=yes
196     \end{shellCode}
197    
198     As with debug and openmp, you can make this a more permanent setting by modifying your options file.
199    
200 caltinay 2536 To test your build using 6 processors enter:
201 gross 2363 \begin{shellCode}
202     export ESCRIPT_NUM_NODES=6
203 gross 2370 scons usempi=yes all_tests
204 gross 2363 \end{shellCode}
205 caltinay 2536 and on 6 processors with 4 threads each using
206 gross 2363 \begin{shellCode}
207     export ESCRIPT_NUM_THREADS=4
208     export ESCRIPT_NUM_NODES=6
209 gross 2370 scons usempi=yes all_tests
210 gross 2363 \end{shellCode}
211     Alternatively, you can give a hostfile
212     \begin{shellCode}
213     export ESCRIPT_NUM_THREADS=4
214     export ESCRIPT_HOSTFILE=myhostfile
215 gross 2370 scons usempi=yes all_tests
216 gross 2363 \end{shellCode}
217 caltinay 2536 Note that depending on your \mpi flavour it may be required to start a daemon before running the tests under \mpi.
218 gross 2363
219    
220 jfenwick 2289 \subsection{Difficulties}
221    
222 caltinay 2536 %This is copied from Ken's notes on the old Twiki page
223 jfenwick 2289 \subsubsection{``Bad magic number''}
224 caltinay 2547 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).
225 jfenwick 2289
226 caltinay 2536 It is also possible that incompatible libraries were used when compiling \esfinley.
227     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.
228     Another case is when Boost or Numarray was compiled against the wrong Python library.
229     To avoid these problems both builder and user must ensure they are using the same python libraries.
230 jfenwick 2512
231 caltinay 2536 \subsubsection{\openmp builds segfault running examples}
232 jfenwick 2512
233     One known cause for this is linking the \filename{gomp} library with escript built using gcc 4.3.3.
234 caltinay 2536 While you need the \texttt{-fopenmp} switch you should not need to link \filename{gomp}.
235    

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