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

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

oecreview from 11518 to present
File size: 10.5 KB

  • proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/python/install.sh

     
    11#!/bin/bash
    2 #wget http://python.org/ftp/python/3.2.2/Python-3.2.2.tgz
     2#wget http://python.org/ftp/python/version/Python-version.tgz
    33
     4#version=3.2.2
     5version=2.7.2
     6
    47#Some cleanup
    58rm -rf install src
    6 rm -rf Python-3.2.2
     9rm -rf Python-$version
    710mkdir install src
    811
    912#exports
    1013export CC
    1114
    1215#Untar and move python into install directory
    13 tar -zxvf  Python-3.2.2.tgz
    14 mv Python-3.2.2/* src
    15 rm -rf Python-3.2.2
     16tar -zxvf  Python-$version.tgz
     17mv Python-$version/* src
     18rm -rf Python-$version
    1619
    1720#Configure doxygen
    1821cd src

  • proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/scipy/install-macosx64.sh

     
    33#1: install numpy
    44#2 install scipy
    55#3 erase
    6 install=1
     6install=2
    77
    88
    99export CC=gcc

  • proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/matlab/install.sh

     
    44rm -rf install
    55
    66#Select or create a new simlink
    7 ln -s /usr/local/pkgs/matlab-7.6/ install
     7#ln -s /usr/local/pkgs/matlab-7.6/ install
    88#ln -s /usr/local/matlab704/ install
    99#ln -s /usr/local/matlab711/ install
    1010#ln -s /usr/local/matlab712/ install
    … …  
    1414#ln -s /Applications/MATLAB_R2008a/ install
    1515#ln -s /Applications/MATLAB_R2009a.app/ install
    1616#ln -s /Applications/MATLAB_R2010a.app/ install
    17 #ln -s /Applications/MATLAB_R2011b.app/ install
     17ln -s /Applications/MATLAB_R2012a.app/ install
    1818#ln -s /Applications/MATLAB*.app/ install

  • proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/boost/install.sh

     
    11#!/bin/bash
    22
     3#Note of caution:  stop after boostrap phase, and run
     4#bjam --debug-configuration, to figure out which paths boost is using to include
     5#python. make sure everyone of these paths is covered by python. If not, just make
     6#symlinks in externalpackages/python to what boost is expecting. Ther is NO WAY
     7#to get the boost library to include python support without doing that.
     8
     9
     10
    311#Some cleanup
    412rm -rf install boost_1_49_0 src
    513mkdir install src

  • proj/ice/larour/issm-uci-clean/trunk-jpl/externalpackages/triangle/install-macosx64.sh

     
    11#!/bin/bash
    22
     3#use matlab?
     4matlab=0
     5
     6
    37#Some cleanup
    48rm -rf install triangle
    59mkdir install
    … …  
    1418cp ../makefile ./
    1519
    1620#Patch triangle.c
    17 patch triangle.c ../triangle.c.patch
     21if [[ $matlab == "1" ]];then
     22        patch triangle.c ../triangle.c.patch.matlab
     23else
     24        patch triangle.c ../triangle.c.patch.python
     25fi
    1826
    1927#Compile triangle
    2028make

  • proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Container/Options.cpp

     
    4242        for (i=istart; i<nrhs; i=i+2){
    4343                if (!mxIsClass(prhs[i],"char")) _error_("Argument %d must be name of option.",i+1);
    4444
    45                 FetchMatlabData(&name,prhs[i]);
     45                FetchData(&name,prhs[i]);
    4646                if (i+1 == nrhs) _error_("Argument %d must exist and be value of option \"%s\".",i+2,name);
    4747
    4848                //_printf_(true,"  Processing option \"%s\" of class \"%s\".\n",name,mxGetClassName(prhs[i+1]));

  • proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/modules.h

     
    115115#endif
    116116#include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h"
    117117#include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h"
     118#include "./TriMeshx/TriMeshx.h"
    118119#include "./UpdateVertexPositionsx/UpdateVertexPositionsx.h"
    119120#include "./UpdateConstraintsx/UpdateConstraintsx.h"
    120121#include "./UpdateDynamicConstraintsx/UpdateDynamicConstraintsx.h"

  • proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/modules/TriMeshx/TriMeshx.cpp

     
    1919
    2020        /*output: */
    2121        double* index=NULL;
     22        Matrix* index_matrix=NULL;
    2223        double* x=NULL;
    2324        double* y=NULL;
    2425        double* segments=NULL;
     26        Matrix* segments_matrix=NULL;
    2527        double* segmentmarkerlist=NULL;
    2628
    2729        /*intermediary: */
    … …  
    8991                 counter++;
    9092                 backcounter=counter;
    9193        }
     94
    9295       
    9396        /*Build regions: */
    9497        in.numberofregions = 0;
    … …  
    123126        /*   neighbor list (n).                                              */
    124127
    125128        sprintf(options,"%s%lf","pQzDq30ia",area); /*replace V by Q to quiet down the logging*/
     129
    126130 
    127131        triangulate(options, &in, &out, NULL);
     132
    128133        /*report(&out, 0, 1, 1, 1, 1, 0);*/
    129134
     135
    130136        /*Allocate index, x and y: */
    131137        index=(double*)xmalloc(3*out.numberoftriangles*sizeof(double));
    132138        x=(double*)xmalloc(out.numberofpoints*sizeof(double));
    … …  
    150156                segmentmarkerlist[i]=(double)out.segmentmarkerlist[i];
    151157        }
    152158
     159
     160
    153161        /*Associate elements with segments: */
    154162        AssociateSegmentToElement(&segments,out.numberofsegments,index,out.numberoftriangles);
    155163
    … …  
    158166                OrderSegments(&segments,out.numberofsegments, index,out.numberoftriangles);
    159167        }
    160168
    161         printf("%i %i %i\n",out.numberoftriangles,out.numberofpoints,out.numberofsegments);
    162169
    163170        /*Output : */
    164         *pindex=new Matrix(index,out.numberoftriangles,3,1);
     171        index_matrix=new Matrix(index,out.numberoftriangles,3,1);
     172        index_matrix->Convert(DENSE_SEQUENTIAL);
     173        *pindex=index_matrix;
     174       
     175        segments_matrix=new Matrix(segments,out.numberofsegments,3,1); segments_matrix->Convert(DENSE_SEQUENTIAL);
     176        *psegments=segments_matrix;
     177
    165178        *px=new Vector(x,out.numberofpoints);
    166179        *py=new Vector(y,out.numberofpoints);
    167         *psegments=new Matrix(segments,out.numberofsegments,3,1);
    168180        *psegmentmarkerlist=new Vector(segmentmarkerlist,out.numberofsegments);
     181
    169182}

  • proj/ice/larour/issm-uci-clean/trunk-jpl/src/c/Makefile.am

     
    207207                                        ./shared/Elements/GetGlobalDofList.cpp\
    208208                                        ./shared/Elements/GetNumberOfDofs.cpp\
    209209                                        ./shared/String/sharedstring.h\
     210                                        ./shared/Wrapper/wrappershared.h\
     211                                        ./shared/Wrapper/ModuleBoot.cpp\
     212                                        ./shared/Wrapper/ModuleEnd.cpp\
    210213                                        ./toolkits/mpi/mpiincludes.h\
    211214                                        ./toolkits/mpi/patches/mpipatches.h\
    212215                                        ./toolkits/mpi/patches/DetermineLocalSize.cpp\
    … …  
    252255                                        ./modules/VerticesDofx/VerticesDofx.cpp\
    253256                                        ./modules/OutputResultsx/OutputResultsx.h\
    254257                                        ./modules/OutputResultsx/OutputResultsx.cpp\
     258                                        ./modules/TriMeshx/TriMeshx.h\
     259                                        ./modules/TriMeshx/TriMeshx.cpp\
    255260                                        ./modules/InputDuplicatex/InputDuplicatex.h\
    256261                                        ./modules/InputDuplicatex/InputDuplicatex.cpp\
    257262                                        ./modules/InputScalex/InputScalex.h\
    … …  
    692697#}}}
    693698#Matlab sources  {{{1
    694699matlab_sources= ./shared/Matlab/matlabshared.h\
    695                                     ./shared/Matlab/ModuleBoot.cpp\
    696                                     ./shared/Matlab/ModuleEnd.cpp\
    697700                                    ./shared/Matlab/mxGetAssignedField.cpp\
    698                                     ./shared/Matlab/mxGetField.cpp\
    699701                                    ./shared/Matlab/CheckNumMatlabArguments.cpp\
    700702                                    ./toolkits/matlab/matlabincludes.h\
    701703                                    ./toolkits/matlab/MatlabNArrayToNArray.cpp\
    … …  
    707709                                    ./io/Matlab/FetchMatlabData.cpp\
    708710                                    ./io/Matlab/OptionParse.cpp
    709711#}}}
     712#Python sources  {{{1
     713python_sources=     ./io/Python/pythonio.h\
     714                                    ./io/Python/WritePythonData.cpp\
     715                                    ./io/Python/FetchPythonData.cpp
     716#}}}
    710717#Petsc sources  {{{1
    711718petsc_sources= ./toolkits/petsc\
    712719                                        ./toolkits/petsc/patches\
    … …  
    735742                                        ./toolkits/petsc/patches/MatPartition.cpp\
    736743                                        ./toolkits/petsc/patches/MatInvert.cpp\
    737744                                        ./toolkits/petsc/patches/MatMultPatch.cpp\
     745                                        ./toolkits/petsc/patches/ISSMToPetscMatrixType.cpp\
    738746                                        ./toolkits/petsc/patches/ISSMToPetscInsertMode.cpp\
    739747                                        ./toolkits/petsc/patches/ISSMToPetscNormMode.cpp\
    740748                                        ./toolkits/petsc/petscincludes.h\
    … …  
    927935libISSM_a_SOURCES += $(serial_sources)
    928936libISSM_a_SOURCES += $(bamg_sources)
    929937libISSM_a_SOURCES += $(kml_sources)
     938libISSM_a_CXXFLAGS = -fPIC -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_  $(CXXFLAGS) $(CXXOPTFLAGS)
     939
     940if PYTHON
     941libISSM_a_CXXFLAGS+=  -DNPY_NO_DEPRECATED_API
     942libISSM_a_SOURCES += $(python_sources)
     943endif
     944
     945if MATLAB
    930946libISSM_a_SOURCES += $(matlab_sources)
     947endif
    931948
    932 libISSM_a_CXXFLAGS = -fPIC -DMATLAB -D_SERIAL_ -D_GNU_SOURCE -fno-omit-frame-pointer -pthread -D_CPP_ $(CXXFLAGS) $(CXXOPTFLAGS)
    933949endif
    934950#}}}
    935951#ISSM parallel library {{{1

  • proj/ice/larour/issm-uci-clean/trunk-jpl/src/py/model/petscversion.py

     
    2929                        break
    3030               
    3131                if tline[0:21]=="#define _PETSC_MAJOR_":
    32                         PETSC_VERSION=int(tline[23])
     32                        PETSC_VERSION=int(tline[22])
    3333                        break
    3434               
    3535                tline=fid.readline()
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