source: issm/oecreview/Archive/11932-11945/ISSM-11943-11944.diff@ 11991

Last change on this file since 11991 was 11991, checked in by Eric.Larour, 13 years ago

oecreview from 11518 to present
File size: 10.5 KB
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[11991]1Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh
2===================================================================
3--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 11943)
4+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh (revision 11944)
5@@ -1,18 +1,21 @@
6 #!/bin/bash
7-#wget http://python.org/ftp/python/3.2.2/Python-3.2.2.tgz
8+#wget http://python.org/ftp/python/version/Python-version.tgz
9
10+#version=3.2.2
11+version=2.7.2
12+
13 #Some cleanup
14 rm -rf install src
15-rm -rf Python-3.2.2
16+rm -rf Python-$version
17 mkdir install src
18
19 #exports
20 export CC
21
22 #Untar and move python into install directory
23-tar -zxvf Python-3.2.2.tgz
24-mv Python-3.2.2/* src
25-rm -rf Python-3.2.2
26+tar -zxvf Python-$version.tgz
27+mv Python-$version/* src
28+rm -rf Python-$version
29
30 #Configure doxygen
31 cd src
32Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh
33===================================================================
34--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 11943)
35+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh (revision 11944)
36@@ -3,7 +3,7 @@
37 #1: install numpy
38 #2 install scipy
39 #3 erase
40-install=1
41+install=2
42
43
44 export CC=gcc
45Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh
46===================================================================
47--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11943)
48+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh (revision 11944)
49@@ -4,7 +4,7 @@
50 rm -rf install
51
52 #Select or create a new simlink
53-ln -s /usr/local/pkgs/matlab-7.6/ install
54+#ln -s /usr/local/pkgs/matlab-7.6/ install
55 #ln -s /usr/local/matlab704/ install
56 #ln -s /usr/local/matlab711/ install
57 #ln -s /usr/local/matlab712/ install
58@@ -14,5 +14,5 @@
59 #ln -s /Applications/MATLAB_R2008a/ install
60 #ln -s /Applications/MATLAB_R2009a.app/ install
61 #ln -s /Applications/MATLAB_R2010a.app/ install
62-#ln -s /Applications/MATLAB_R2011b.app/ install
63+ln -s /Applications/MATLAB_R2012a.app/ install
64 #ln -s /Applications/MATLAB*.app/ install
65Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh
66===================================================================
67--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 11943)
68+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh (revision 11944)
69@@ -1,5 +1,13 @@
70 #!/bin/bash
71
72+#Note of caution: stop after boostrap phase, and run
73+#bjam --debug-configuration, to figure out which paths boost is using to include
74+#python. make sure everyone of these paths is covered by python. If not, just make
75+#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
76+#to get the boost library to include python support without doing that.
77+
78+
79+
80 #Some cleanup
81 rm -rf install boost_1_49_0 src
82 mkdir install src
83Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/install-macosx64.sh
84===================================================================
85--- /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/install-macosx64.sh (revision 11943)
86+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/install-macosx64.sh (revision 11944)
87@@ -1,5 +1,9 @@
88 #!/bin/bash
89
90+#use matlab?
91+matlab=0
92+
93+
94 #Some cleanup
95 rm -rf install triangle
96 mkdir install
97@@ -14,7 +18,11 @@
98 cp ../makefile ./
99
100 #Patch triangle.c
101-patch triangle.c ../triangle.c.patch
102+if [[ $matlab == "1" ]];then
103+ patch triangle.c ../triangle.c.patch.matlab
104+else
105+ patch triangle.c ../triangle.c.patch.python
106+fi
107
108 #Compile triangle
109 make
110Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp
111===================================================================
112--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 11943)
113+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp (revision 11944)
114@@ -42,7 +42,7 @@
115 for (i=istart; i<nrhs; i=i+2){
116 if (!mxIsClass(prhs[i],"char")) _error_("Argument %d must be name of option.",i+1);
117
118- FetchMatlabData(&name,prhs[i]);
119+ FetchData(&name,prhs[i]);
120 if (i+1 == nrhs) _error_("Argument %d must exist and be value of option \"%s\".",i+2,name);
121
122 //_printf_(true," Processing option \"%s\" of class \"%s\".\n",name,mxGetClassName(prhs[i+1]));
123Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h
124===================================================================
125--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 11943)
126+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h (revision 11944)
127@@ -115,6 +115,7 @@
128 #endif
129 #include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h"
130 #include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h"
131+#include "./TriMeshx/TriMeshx.h"
132 #include "./UpdateVertexPositionsx/UpdateVertexPositionsx.h"
133 #include "./UpdateConstraintsx/UpdateConstraintsx.h"
134 #include "./UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h"
135Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp
136===================================================================
137--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp (revision 11943)
138+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp (revision 11944)
139@@ -19,9 +19,11 @@
140
141 /*output: */
142 double* index=NULL;
143+ Matrix* index_matrix=NULL;
144 double* x=NULL;
145 double* y=NULL;
146 double* segments=NULL;
147+ Matrix* segments_matrix=NULL;
148 double* segmentmarkerlist=NULL;
149
150 /*intermediary: */
151@@ -89,6 +91,7 @@
152 counter++;
153 backcounter=counter;
154 }
155+
156
157 /*Build regions: */
158 in.numberofregions = 0;
159@@ -123,10 +126,13 @@
160 /* neighbor list (n). */
161
162 sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/
163+
164
165 triangulate(options, &in, &out, NULL);
166+
167 /*report(&out, 0, 1, 1, 1, 1, 0);*/
168
169+
170 /*Allocate index, x and y: */
171 index=(double*)xmalloc(3*out.numberoftriangles*sizeof(double));
172 x=(double*)xmalloc(out.numberofpoints*sizeof(double));
173@@ -150,6 +156,8 @@
174 segmentmarkerlist[i]=(double)out.segmentmarkerlist[i];
175 }
176
177+
178+
179 /*Associate elements with segments: */
180 AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles);
181
182@@ -158,12 +166,17 @@
183 OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles);
184 }
185
186- printf("%i %i %i\n",out.numberoftriangles,out.numberofpoints,out.numberofsegments);
187
188 /*Output : */
189- *pindex=new Matrix(index,out.numberoftriangles,3,1);
190+ index_matrix=new Matrix(index,out.numberoftriangles,3,1);
191+ index_matrix->Convert(DENSE_SEQUENTIAL);
192+ *pindex=index_matrix;
193+
194+ segments_matrix=new Matrix(segments,out.numberofsegments,3,1); segments_matrix->Convert(DENSE_SEQUENTIAL);
195+ *psegments=segments_matrix;
196+
197 *px=new Vector(x,out.numberofpoints);
198 *py=new Vector(y,out.numberofpoints);
199- *psegments=new Matrix(segments,out.numberofsegments,3,1);
200 *psegmentmarkerlist=new Vector(segmentmarkerlist,out.numberofsegments);
201+
202 }
203Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am
204===================================================================
205--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11943)
206+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am (revision 11944)
207@@ -207,6 +207,9 @@
208 ./shared/Elements/GetGlobalDofList.cpp\
209 ./shared/Elements/GetNumberOfDofs.cpp\
210 ./shared/String/sharedstring.h\
211+ ./shared/Wrapper/wrappershared.h\
212+ ./shared/Wrapper/ModuleBoot.cpp\
213+ ./shared/Wrapper/ModuleEnd.cpp\
214 ./toolkits/mpi/mpiincludes.h\
215 ./toolkits/mpi/patches/mpipatches.h\
216 ./toolkits/mpi/patches/DetermineLocalSize.cpp\
217@@ -252,6 +255,8 @@
218 ./modules/VerticesDofx/VerticesDofx.cpp\
219 ./modules/OutputResultsx/OutputResultsx.h\
220 ./modules/OutputResultsx/OutputResultsx.cpp\
221+ ./modules/TriMeshx/TriMeshx.h\
222+ ./modules/TriMeshx/TriMeshx.cpp\
223 ./modules/InputDuplicatex/InputDuplicatex.h\
224 ./modules/InputDuplicatex/InputDuplicatex.cpp\
225 ./modules/InputScalex/InputScalex.h\
226@@ -692,10 +697,7 @@
227 #}}}
228 #Matlab sources {{{1
229 matlab_sources= ./shared/Matlab/matlabshared.h\
230- ./shared/Matlab/ModuleBoot.cpp\
231- ./shared/Matlab/ModuleEnd.cpp\
232 ./shared/Matlab/mxGetAssignedField.cpp\
233- ./shared/Matlab/mxGetField.cpp\
234 ./shared/Matlab/CheckNumMatlabArguments.cpp\
235 ./toolkits/matlab/matlabincludes.h\
236 ./toolkits/matlab/MatlabNArrayToNArray.cpp\
237@@ -707,6 +709,11 @@
238 ./io/Matlab/FetchMatlabData.cpp\
239 ./io/Matlab/OptionParse.cpp
240 #}}}
241+#Python sources {{{1
242+python_sources= ./io/Python/pythonio.h\
243+ ./io/Python/WritePythonData.cpp\
244+ ./io/Python/FetchPythonData.cpp
245+#}}}
246 #Petsc sources {{{1
247 petsc_sources= ./toolkits/petsc\
248 ./toolkits/petsc/patches\
249@@ -735,6 +742,7 @@
250 ./toolkits/petsc/patches/MatPartition.cpp\
251 ./toolkits/petsc/patches/MatInvert.cpp\
252 ./toolkits/petsc/patches/MatMultPatch.cpp\
253+ ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\
254 ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\
255 ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\
256 ./toolkits/petsc/petscincludes.h\
257@@ -927,9 +935,17 @@
258 libISSM_a_SOURCES += $(serial_sources)
259 libISSM_a_SOURCES += $(bamg_sources)
260 libISSM_a_SOURCES += $(kml_sources)
261+libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
262+
263+if PYTHON
264+libISSM_a_CXXFLAGS+= -DNPY_NO_DEPRECATED_API
265+libISSM_a_SOURCES += $(python_sources)
266+endif
267+
268+if MATLAB
269 libISSM_a_SOURCES += $(matlab_sources)
270+endif
271
272-libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
273 endif
274 #}}}
275 #ISSM parallel library {{{1
276Index: /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py
277===================================================================
278--- /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py (revision 11943)
279+++ /proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py (revision 11944)
280@@ -29,7 +29,7 @@
281 break
282
283 if tline[0:21]=="#define _PETSC_MAJOR_":
284- PETSC_VERSION=int(tline[23])
285+ PETSC_VERSION=int(tline[22])
286 break
287
288 tline=fid.readline()
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