Changeset 11944

Timestamp:

04/05/12 14:54:00 (13 years ago)

Author:

Eric.Larour

Message:

Diverse

Location:

issm/trunk-jpl

Files:

• externalpackages/boost/install.sh (modified) (1 diff)
• externalpackages/matlab/install.sh (modified) (2 diffs)
• externalpackages/python/install.sh (modified) (2 diffs)
• externalpackages/scipy/install-macosx64.sh (modified) (1 diff)
• externalpackages/triangle/install-macosx64.sh (modified) (2 diffs)
• src/c/Container/Options.cpp (modified) (1 diff)
• src/c/Makefile.am (modified) (6 diffs)
• src/c/modules/TriMeshx/TriMeshx.cpp (modified) (5 diffs)
• src/c/modules/modules.h (modified) (1 diff)
• src/py/model/petscversion.py (modified) (1 diff)

issm/trunk-jpl/externalpackages/boost/install.sh

@@ -1 +1 @@
 #!/bin/bash
+
+#Note of caution:  stop after boostrap phase, and run 
+#bjam --debug-configuration, to figure out which paths boost is using to include 
+#python. make sure everyone of these paths is covered by python. If not, just make 
+#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY 
+#to get the boost library to include python support without doing that. 
+
+
 
 #Some cleanup

issm/trunk-jpl/externalpackages/matlab/install.sh

@@ -5 +5 @@
 
 #Select or create a new simlink
-ln -s /usr/local/pkgs/matlab-7.6/ install
+#ln -s /usr/local/pkgs/matlab-7.6/ install
 #ln -s /usr/local/matlab704/ install
 #ln -s /usr/local/matlab711/ install
@@ -15 +15 @@
 #ln -s /Applications/MATLAB_R2009a.app/ install
 #ln -s /Applications/MATLAB_R2010a.app/ install
-#ln -s /Applications/MATLAB_R2011b.app/ install
+ln -s /Applications/MATLAB_R2012a.app/ install
 #ln -s /Applications/MATLAB*.app/ install

issm/trunk-jpl/externalpackages/python/install.sh

@@ -1 +1 @@
 #!/bin/bash
-#wget http://python.org/ftp/python/3.2.2/Python-3.2.2.tgz
+#wget http://python.org/ftp/python/version/Python-version.tgz
+
+#version=3.2.2
+version=2.7.2
 
 #Some cleanup
 rm -rf install src
-rm -rf Python-3.2.2
+rm -rf Python-$version
 mkdir install src
 
@@ -11 +14 @@
 
 #Untar and move python into install directory
-tar -zxvf  Python-3.2.2.tgz
-mv Python-3.2.2/* src
-rm -rf Python-3.2.2
+tar -zxvf  Python-$version.tgz
+mv Python-$version/* src
+rm -rf Python-$version
 
 #Configure doxygen

issm/trunk-jpl/externalpackages/scipy/install-macosx64.sh

@@ -4 +4 @@
 #2 install scipy
 #3 erase
-install=1
+install=2
 
 

issm/trunk-jpl/externalpackages/triangle/install-macosx64.sh

@@ -1 +1 @@
 #!/bin/bash
+
+#use matlab? 
+matlab=0
+
 
 #Some cleanup 
@@ -15 +19 @@
 
 #Patch triangle.c 
-patch triangle.c ../triangle.c.patch
+if [[ $matlab == "1" ]];then
+        patch triangle.c ../triangle.c.patch.matlab
+else
+        patch triangle.c ../triangle.c.patch.python
+fi
 
 #Compile triangle

issm/trunk-jpl/src/c/Container/Options.cpp

@@ -43 +43 @@
                 if (!mxIsClass(prhs[i],"char")) _error_("Argument %d must be name of option.",i+1);
 
-                FetchMatlabData(&name,prhs[i]);
+                FetchData(&name,prhs[i]);
                 if (i+1 == nrhs) _error_("Argument %d must exist and be value of option \"%s\".",i+2,name);
 

issm/trunk-jpl/src/c/Makefile.am

@@ -208 +208 @@
                                         ./shared/Elements/GetNumberOfDofs.cpp\
                                         ./shared/String/sharedstring.h\
+                                        ./shared/Wrapper/wrappershared.h\
+                                        ./shared/Wrapper/ModuleBoot.cpp\
+                                        ./shared/Wrapper/ModuleEnd.cpp\
                                         ./toolkits/mpi/mpiincludes.h\
                                         ./toolkits/mpi/patches/mpipatches.h\
@@ -253 +256 @@
                                         ./modules/OutputResultsx/OutputResultsx.h\
                                         ./modules/OutputResultsx/OutputResultsx.cpp\
+                                        ./modules/TriMeshx/TriMeshx.h\
+                                        ./modules/TriMeshx/TriMeshx.cpp\
                                         ./modules/InputDuplicatex/InputDuplicatex.h\
                                         ./modules/InputDuplicatex/InputDuplicatex.cpp\
@@ -693 +698 @@
 #Matlab sources  {{{1
 matlab_sources= ./shared/Matlab/matlabshared.h\
-                                    ./shared/Matlab/ModuleBoot.cpp\
-                                    ./shared/Matlab/ModuleEnd.cpp\
                                     ./shared/Matlab/mxGetAssignedField.cpp\
-                                    ./shared/Matlab/mxGetField.cpp\
                                     ./shared/Matlab/CheckNumMatlabArguments.cpp\
                                     ./toolkits/matlab/matlabincludes.h\
@@ -707 +709 @@
                                     ./io/Matlab/FetchMatlabData.cpp\
                                     ./io/Matlab/OptionParse.cpp
+#}}}
+#Python sources  {{{1
+python_sources=     ./io/Python/pythonio.h\
+                                    ./io/Python/WritePythonData.cpp\
+                                    ./io/Python/FetchPythonData.cpp
 #}}}
 #Petsc sources  {{{1
@@ -736 +743 @@
                                         ./toolkits/petsc/patches/MatInvert.cpp\
                                         ./toolkits/petsc/patches/MatMultPatch.cpp\
+                                        ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\
                                         ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\
                                         ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\
@@ -928 +936 @@
 libISSM_a_SOURCES += $(bamg_sources)
 libISSM_a_SOURCES += $(kml_sources)
+libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_  $(CXXFLAGS) $(CXXOPTFLAGS) 
+
+if PYTHON
+libISSM_a_CXXFLAGS+=  -DNPY_NO_DEPRECATED_API 
+libISSM_a_SOURCES += $(python_sources)
+endif
+
+if MATLAB
 libISSM_a_SOURCES += $(matlab_sources)
-
-libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS) 
+endif
+
 endif
 #}}}

issm/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp

@@ -20 +20 @@
         /*output: */
         double* index=NULL;
+        Matrix* index_matrix=NULL;
         double* x=NULL;
         double* y=NULL;
         double* segments=NULL;
+        Matrix* segments_matrix=NULL;
         double* segmentmarkerlist=NULL;
 
@@ -90 +92 @@
                  backcounter=counter;
         }
+
         
         /*Build regions: */
@@ -124 +127 @@
 
         sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/
+
   
         triangulate(options, &in, &out, NULL);
+
         /*report(&out, 0, 1, 1, 1, 1, 0);*/
+
 
         /*Allocate index, x and y: */
@@ -151 +157 @@
         }
 
+
+
         /*Associate elements with segments: */
         AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles);
@@ -159 +167 @@
         }
 
-        printf("%i %i %i\n",out.numberoftriangles,out.numberofpoints,out.numberofsegments);
 
         /*Output : */
-        *pindex=new Matrix(index,out.numberoftriangles,3,1);
+        index_matrix=new Matrix(index,out.numberoftriangles,3,1); 
+        index_matrix->Convert(DENSE_SEQUENTIAL);
+        *pindex=index_matrix;
+        
+        segments_matrix=new Matrix(segments,out.numberofsegments,3,1); segments_matrix->Convert(DENSE_SEQUENTIAL);
+        *psegments=segments_matrix;
+
         *px=new Vector(x,out.numberofpoints);
         *py=new Vector(y,out.numberofpoints);
-        *psegments=new Matrix(segments,out.numberofsegments,3,1);
         *psegmentmarkerlist=new Vector(segmentmarkerlist,out.numberofsegments);
+
 }

issm/trunk-jpl/src/c/modules/modules.h

@@ -116 +116 @@
 #include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h"
 #include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h"
+#include "./TriMeshx/TriMeshx.h"
 #include "./UpdateVertexPositionsx/UpdateVertexPositionsx.h"
 #include "./UpdateConstraintsx/UpdateConstraintsx.h"

issm/trunk-jpl/src/py/model/petscversion.py

@@ -30 +30 @@
                 
                 if tline[0:21]=="#define _PETSC_MAJOR_":
-                        PETSC_VERSION=int(tline[23])
+                        PETSC_VERSION=int(tline[22])
                         break