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Revision 2512 - (hide annotations)
Thu Jul 2 05:34:14 2009 UTC (10 years, 2 months ago) by jfenwick
Original Path: trunk/doc/install/srcommon.tex
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Made the warnings against linking gomp a bit more detailed.
Commented out gomp from the linux sample.
1 jfenwick 2289
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     \esfinley is known to compile and run on the following systems:
19     \begin{itemize}
20 jfenwick 2512 \item \linux under 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}
21 jfenwick 2289 \item \linux under icc on SGI ICE 8200.
22     \item \macosx under gcc - \Sec{sec:srcmac}
23     \end{itemize}
24    
25     \section{External dependencies}
26     The following external packages are required in order to compile and run \esfinley.
27     Where version numbers are specified, more recent versions can probably be subsituted.
28     You can either try the standard/precompiled packages available for your operating system or you can download and build them from source.
29     The advantage of using existing packages is that they will probably all work togther properly.
30     You must take greater care if downloading sources separately.
31    
32     \begin{itemize}
33 jfenwick 2317 \item python-2.5.1 (\url{http://python.org}) \\
34     - Python interpreter (You must compile with shared libraries.)
35 jfenwick 2512 \item numpy 1.1.0 (\url{http://numpy.scipy.org})
36 jfenwick 2289 - Arrays for python.
37 artak 2326 \item boost-1.35 (\url{http://www.boost.org}) \\
38 jfenwick 2289 - Provides an interface between C++ and python.
39 jfenwick 2317 \item scons-0.989.5 (\url{http://www.scons.org/}) \\
40 jfenwick 2289 - a python-based alternative to ``make''.
41     \end{itemize}
42    
43 jfenwick 2317 The version numbers given here are not strict requirements, more recent (and in some cases older) versions will
44     still work.
45 jfenwick 2289 The following packages should be sufficient (but not necessarily minimal) for Debian 5.0 (``Lenny''):
46 jfenwick 2512 python-dev, libboost1.35-dev, scons, python-numpy, g++.
47 jfenwick 2289
48    
49     These packages may be required for some of the optional capabilities of the system.
50    
51     \begin{itemize}
52     \item netcdf-3.6.2 (\url{http://www.unidata.ucar.edu/software/netcdf}) \\-
53     Used to save data sets in binary form for checkpoint/restart (must be compiled with -fPIC).
54     \item vtk-5.0.4 (\url{http://www.vtk.org}) \\-
55     This is used to save VTK files for visualization.
56     \begin{itemize}
57     \item cmake-2.4.6 (\url{http://www.cmake.org}) \\-
58     This is used to build VTK.
59     \item mesa-7.0.3 (\url{http://www.mesa3d.org})\\-
60     Free OpenGL replacement used by VTK.
61     \end{itemize}
62    
63     \item mpich2-1.0.7 (\url{http://www.mcs.anl.gov/research/projects/mpich2}) \\-
64     Parallelization with MPI.
65     \item parmetis-3.1 (\url{http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview}) \\-
66     Optimization of the stiffness matrix.
67 jfenwick 2333 \item MKL \\(\url{http://www.intel.com/cd/software/products/asmo-na/eng/307757.htm}) \\-
68 jfenwick 2289 Intel's Math Kernel Library for use with their c compiler.
69     \end{itemize}
70    
71     The following packages might be useful for mesh generation:
72     \begin{itemize}
73     \item gmsh-2.2.0 (\url{http://www.geuz.org/gmsh}) \\-
74     Mesh generation and viewing.
75     \begin{itemize}
76     \item fltk-1.1.9 (\url{http://www.fltk.org}) \\-
77     This is used to build gmsh
78     \item gsl-1.10 (\url{http://www.gnu.org/software/gsl}) \\-
79     This is used to build gmsh
80     \end{itemize}
81    
82     \item triangle-1.6 (\url{http://www.cs.cmu.edu/~quake/triangle.html})
83     \end{itemize}
84    
85     Packages for visualization:
86     \begin{itemize}
87     \item mayavi-1.5 (\url{http://mayavi.sourceforge.net}) \\-
88     MayaVi is referenced in our User Guide for viewing VTK files.
89     \item visit-1.9 (\url{https://wci.llnl.gov/codes/visit/})
90     \end{itemize}
91    
92 jfenwick 2324 \section{Compilation}\label{sec:compilesrc}
93 jfenwick 2289 Throughout this section we will assume that the source code is uncompressed in a directory called trunk.
94     You can call the directory anything you like, provided that you make the change before you compile.
95    
96     You need to indicate where to find the external dependencies.
97     Unless specified otherwise, all paths will be relative to the top level of the source.
98     To do this, create a file in the \filename{scons} directory called \filename{x_options.py} where ``x'' is the name of your computer.
99     As a starting point use one of the following:
100     \begin{itemize}
101     \item \filename{scons/linux_options_example.py} (\linux desktop)
102     \item \filename{scons/mac_options_example.py} (\macosx desktop)
103     \item \filename{ice_options_example.py} (SGI ICE 8200)
104     \item \filename{winxp_options_example.py} (\winxp)
105     \end{itemize}
106    
107     To actually compile (if you have $n$ processors, then you can use \texttt{scons -j$n$} instead):
108    
109     \begin{shellCode}
110     cd trunk
111     scons
112     \end{shellCode}
113    
114     As part of its output, scons will tell you the name of the options file it used as well as a list of features
115     and whether they are enabled for your build.
116    
117     If you require debug versions of the libraries, use:
118     \begin{shellCode}
119     scons usedebug=yes
120     \end{shellCode}
121     A note about scons: if you recompile later with different options (eg leaving off usedebug), scons will revert
122     to its default values. If you wish to make a change more permanent, then modify your options file.
123    
124    
125     You can install the binaries/libraries in a different location with:
126     \begin{shellCode}
127     scons prefix=some_dir
128     \end{shellCode}
129    
130     You can test your build using
131     \begin{shellCode}
132     scons all_tests
133     \end{shellCode}
134     An alternative method is available for performing tests on \openmp and MPI builds.
135    
136     \subsection{Compilation with \openmp}
137     You will need to consult your compiler documentation for the precise switches to use to enable OpenMP features.
138     Once you know the options, modify the omp_optim, omp_debug and omp_libs variables in your options.py file.
139    
140     For example, for gcc compilers which support \openmp use.
141     \begin{shellCode}
142     omp_optim = '-fopenmp'
143     omp_debug = '-fopenmp'
144     omp_libs = ['gomp']
145     \end{shellCode}
146     Depending on your version, last change may not be required.
147    
148     Then recompile.
149     \begin{shellCode}
150     scons useopenmp=yes
151     \end{shellCode}
152    
153 gross 2363 You can test your build on for instance 4 threads using
154     \begin{shellCode}
155     export ESCRIPT_NUM_THREADS=4
156     scons all_tests
157     \end{shellCode}
158    
159 jfenwick 2289 \subsection{Compilation with MPI}
160     You will need to have MPI installed on your system.
161     There are a number of implementations so we do not provide any specific advice here.
162     You will need to modify the following variables in your options file.
163     \begin{itemize}
164 gross 2356 \item \texttt{mpi_flavour} \\
165     which MPI implementation is used. Valid values are \begin{itemize}
166     \item[\texttt{MPT}] SGI MPI implementation \\ \url{http://techpubs.sgi.com/library/manuals/3000/007-3687-010/pdf/007-3687-010.pdf}
167 gross 2370 \item[\texttt{MPICH2}] Argonne's MPICH vesrion 2 implementation \\ \url{http://www.mcs.anl.gov/research/projects/mpi/mpich2/}
168 gross 2356 \item[\texttt{MPICH}] Argonne's MPICH implementation \\ \url{http://www.mcs.anl.gov/research/projects/mpi/mpich1/}
169     \item[\texttt{OPENMPI}] Open MPI \url{http://www.open-mpi.org/}
170     \item[\texttt{INTELMPI}] Intel's MPI \url{http://software.intel.com/en-us/intel-mpi-library/}
171     \end{itemize}
172 jfenwick 2289 \item \texttt{mpi_path} \\
173     where to find \filename{mpi.h}
174     \item \texttt{mpi_lib_path} \\
175     where to find libraries for mpi
176     \item \texttt{mpi_libs} \\
177     which libraries to link to.
178     \end{itemize}
179    
180 jfenwick 2290 Then compile with:
181     \begin{shellCode}
182     scons usempi=yes
183     \end{shellCode}
184    
185     As with debug and openmp, you can make this a more permanent setting by modifying your options file.
186    
187 gross 2363 You can test your build on for instance 6 processors using
188     \begin{shellCode}
189     export ESCRIPT_NUM_NODES=6
190 gross 2370 scons usempi=yes all_tests
191 gross 2363 \end{shellCode}
192     and on 6 processors with 4 threads each using
193     \begin{shellCode}
194     export ESCRIPT_NUM_THREADS=4
195     export ESCRIPT_NUM_NODES=6
196 gross 2370 scons usempi=yes all_tests
197 gross 2363 \end{shellCode}
198     Alternatively, you can give a hostfile
199     \begin{shellCode}
200     export ESCRIPT_NUM_THREADS=4
201     export ESCRIPT_HOSTFILE=myhostfile
202 gross 2370 scons usempi=yes all_tests
203 gross 2363 \end{shellCode}
204 jfenwick 2373 Notice that depending on your MPI flavour it may be required to start a daemon before running the tests under MPI.
205 gross 2363
206    
207 jfenwick 2289 \subsection{Difficulties}
208    
209     %This is copied from Ken's notes on teh old Twiki page
210     \subsubsection{``Bad magic number''}
211     Some reasons for this error message include:
212     \begin{itemize}
213     \item Using different versions of python when installing and running escript (Use \texttt{which python} and \texttt{python --version} to check)
214     \item Using different versions of libraries (Make sure \texttt{LD_LIBRARY_PATH} has \filename{/trunk/lib} listed first)
215     \item Using different versions of python modules (Make sure \texttt{PYTHONPATH} has \filename{/trunk/escript} directory listed first)
216     \end{itemize}
217    
218     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}.
219    
220     It is also possible that the person who compiled \esfinley used incompatible libraries. 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. Another case is when Boost or Numarray was compiled against the wrong Python library. To avoid these problems everyone (builder and user) must make certain they are using the same python libraries.
221 jfenwick 2512
222     \subsubsection{OpenMP builds segfault running examples}
223    
224     One known cause for this is linking the \filename{gomp} library with escript built using gcc 4.3.3.
225     While you need the -fomp switch you should not need to link \filename{gomp}.

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