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Patches to compile OpenFOAM 2.2 on Mac OS X

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Old   May 19, 2013, 17:04
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  #41
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Simone Martini
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Quote:
Have a look at /Users/simomartini/OpenFOAM/OpenFOAM-2.1.0/wmake/rules/darwinIntel64Gcc46 : it should be a symbolic link to the directory darwinIntel64Gcc in the same directory. The patch-program doesn't create this correctly. So if it is a plain file delete it (darwinIntel64Gcc46) and replace it with a symbolic link to the neighbour directory. Or copy the directory
I had the same problem but I solve mine with the help of Bernhard with this solution. Try this solution problably this is your problem.
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Old   May 19, 2013, 20:24
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Quote:
Originally Posted by simone.rowing View Post
I had the same problem but I solve mine with the help of Bernhard with this solution. Try this solution problably this is your problem.
Ok, thanks for your answer. I was doing symlinking wrong. I removed all the files and did:

Code:
cd wmake/rules
ln -s darwinIntel64Gcc/ darwinIntel64Gcc46
this seems to have worked.
Another question: Do i have to set
Code:
 export WM_MPLIB=SYSTEMOPENMPI
?
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Old   May 20, 2013, 03:17
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Done compiling, in the log i still have some errors:

Code:
gccmp-4.6 -m64 -fsignaling-nans  -ftrapping-math  -Wall -O2   -fPIC -Ddarwin dirToString.c -o /Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/wmake/platforms/darwinIntel64Gcc46/dirToString
make: gccmp-4.6: No such file or directory
make: *** [/Users/#########/OpenFOAM/OpenFOAM-2.2.x/wmake/platforms/darwinIntel64Gcc46/dirToString] Error 1
Code:
gccmp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -DSCOTCH_VERSION=6 -DSCOTCH_RELEASE=0 -DSCOTCH_PATCHLEVEL=0 dummysizes.c -o dummysizes -lz -lm 
make[2]: gccmp-4.6: No such file or directory
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [scotch] Error 2
Code:
gccmp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -DSCOTCH_VERSION=6 -DSCOTCH_RELEASE=0 -DSCOTCH_PATCHLEVEL=0 ddummysizes.c -o dummysizes -lz -lm 
make[2]: gccmp-4.6: No such file or directory
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [ptscotch] Error 2
Code:
scotchDecomp.C:132:20: fatal error: scotch.h: No such file or directory
compilation terminated.
make: *** [Make/darwinIntel64Gcc46DPOpt/scotchDecomp.o] Error 1
Code:
ptscotchDecomp.C:126:22: fatal error: ptscotch.h: No such file or directory
compilation terminated.
make: *** [Make/darwinIntel64Gcc46DPOptMACPORTOPENMPI/ptscotchDecomp.o] Error 1
Code:
$SOURCE -o Make/darwinIntel64Gcc46DPOpt/SloanRenumber.o
ld: library not found for -lboost_thread
Code:
SurfaceFeatureExtract.C:85:47: error: wrong number of template arguments (1, should be 3)
/opt/local/include/CGAL/Monge_via_jet_fitting.h:57:9: error: provided for 'template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting'
surfaceFeatureExtract.C:85:70: error: invalid type in declaration before ';' token
surfaceFeatureExtract.C:86:47: error: expected initializer before 'Monge_form'
surfaceFeatureExtract.C:148:9: error: 'Monge_form' was not declared in this scope
surfaceFeatureExtract.C:148:20: error: expected ';' before 'monge_form'
surfaceFeatureExtract.C:164:21: error: 'monge_form' was not declared in this scope
surfaceFeatureExtract.C:146:31: warning: unused variable 'monge_fit' [-Wunused-variable]
surfaceFeatureExtract.C:92:18: warning: unused variable 'd_monge' [-Wunused-variable]

It seems to have problem with scotch/ptscotch compiling. Someone can give me some directions to solve this?
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Old   May 20, 2013, 10:25
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  #44
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Quote:
Originally Posted by tidusuper91 View Post
Done compiling, in the log i still have some errors:

Code:
gccmp-4.6 -m64 -fsignaling-nans  -ftrapping-math  -Wall -O2   -fPIC -Ddarwin dirToString.c -o /Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/wmake/platforms/darwinIntel64Gcc46/dirToString
make: gccmp-4.6: No such file or directory
make: *** [/Users/#########/OpenFOAM/OpenFOAM-2.2.x/wmake/platforms/darwinIntel64Gcc46/dirToString] Error 1
That is strange. It should be gcc-mp-4.6. I don't see how the minus go missing (WM_CC is set in etc/settings/profile.sh). Maybe you changed WM_CC somewhere else in an attempt to fix things
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Old   May 21, 2013, 08:29
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Quote:
Originally Posted by gschaider View Post
That is strange. It should be gcc-mp-4.6. I don't see how the minus go missing (WM_CC is set in etc/settings/profile.sh). Maybe you changed WM_CC somewhere else in an attempt to fix things
Ok right. I had mispelled gcc-mp-4.6 in the bashrc file. Now it's correct. Recompiled, still some errors:

Code:
cp: ../bin/d[agm]*: No such file or directory
make: [install] Error 1 (ignored)
Code:
ld: library not found for -lboost_thread
collect2: ld returned 1 exit status
make: *** [/Users/#####/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib] Error 1
Code:
surfaceFeatureExtract.C:85:47: error: wrong number of template arguments (1, should be 3)
/opt/local/include/CGAL/Monge_via_jet_fitting.h:57:9: error: provided for 'template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting'
surfaceFeatureExtract.C:85:78: error: invalid type in declaration before ';' token
surfaceFeatureExtract.C:86:57: error: expected initializer before 'Monge_form'
surfaceFeatureExtract.C:148:9: error: 'Monge_form' was not declared in this scope
surfaceFeatureExtract.C:148:20: error: expected ';' before 'monge_form'
surfaceFeatureExtract.C:164:21: error: 'monge_form' was not declared in this scope
surfaceFeatureExtract.C:146:31: warning: unused variable 'monge_fit' [-Wunused-variable]
surfaceFeatureExtract.C:92:18: warning: unused variable 'd_monge' [-Wunused-variable]
make[2]: *** [Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o] Error 1
make[2]: Target `/Users/######/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureExtract' not remade because of errors.
make[1]: *** [surfaceFeatureExtract] Error 2
Code:
OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceTransformPoints
make[1]: Target `application' not remade because of errors.
make: *** [surface] Error 2
Sorry for my incapacity.
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Old   May 21, 2013, 15:47
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Quote:
Originally Posted by tidusuper91 View Post
Ok right. I had mispelled gcc-mp-4.6 in the bashrc file. Now it's correct. Recompiled, still some errors:

Code:
cp: ../bin/d[agm]*: No such file or directory
make: [install] Error 1 (ignored)
Where would that happen?
Quote:
Originally Posted by tidusuper91 View Post
Code:
ld: library not found for -lboost_thread
collect2: ld returned 1 exit status
make: *** [/Users/#####/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib] Error 1
With my patches if the variable WM_USE_MACPORT is set and the MacPort-verison of boost is installed then it should use the -lboost_thread-mt library.

Anyway: this library is not essential (99% of OF will work without it)
Quote:
Originally Posted by tidusuper91 View Post
Code:
surfaceFeatureExtract.C:85:47: error: wrong number of template arguments (1, should be 3)
/opt/local/include/CGAL/Monge_via_jet_fitting.h:57:9: error: provided for 'template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting'
surfaceFeatureExtract.C:85:78: error: invalid type in declaration before ';' token
surfaceFeatureExtract.C:86:57: error: expected initializer before 'Monge_form'
surfaceFeatureExtract.C:148:9: error: 'Monge_form' was not declared in this scope
surfaceFeatureExtract.C:148:20: error: expected ';' before 'monge_form'
surfaceFeatureExtract.C:164:21: error: 'monge_form' was not declared in this scope
surfaceFeatureExtract.C:146:31: warning: unused variable 'monge_fit' [-Wunused-variable]
surfaceFeatureExtract.C:92:18: warning: unused variable 'd_monge' [-Wunused-variable]
make[2]: *** [Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o] Error 1
make[2]: Target `/Users/######/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureExtract' not remade because of errors.
make[1]: *** [surfaceFeatureExtract] Error 2
Compiler-call would be super-helpful in this case. Anyway: for first experiments in OF this utilitiy is not required.
Quote:
Originally Posted by tidusuper91 View Post
Code:
OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceTransformPoints
make[1]: Target `application' not remade because of errors.
make: *** [surface] Error 2
Sorry for my incapacity.
The last error is just a followup to the others. But I'm not sure.

Anyway: you tried to run a basic tutorial (blockMesh, setFields, interFoam) and does that work?
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Old   May 21, 2013, 17:42
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Thanks for your very precious help. Anyway,
i run an incompressible tutorial and it seems to work.

This is for the not found directory. It seems to happen in the scotch directory in Thirdparty folder

Code:
cd libscotchmetis ; make                                                                scotch && make install)
make CC="gcc-mp-4.6" SCOTCHLIB=ptscotch                        \
                    libscotchmetis.dylib
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_order.c -o metis_graph_order.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_order_f.c -o metis_graph_order_f.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_part.c -o metis_graph_part.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_part_f.c -o metis_graph_part_f.o
gcc-mp-4.6 -dynamiclib -undefined dynamic_lookup -o libscotchmetis.dylib metis_graph_order.o metis_graph_order_f.o metis_graph_part.o metis_graph_part_f.o
echo libscotchmetis.dylib
libscotchmetis.dylib
make CC="gcc-mp-4.6" SCOTCHLIB=ptscotch                        \
                    libscotchmetis.dylib
make[2]: `libscotchmetis.dylib' is up to date.
cp metis.h ../../include
cp libscotchmetis.dylib ../../lib
+ make prefix=/Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0 libdir=/Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib install
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/include
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share/man
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share/man/man1
cp -f ../bin/[agm]* /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp -f ../bin/d[agm]* /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp: ../bin/d[agm]*: No such file or directory
This for the surfaceFeatureConvert.C

Code:
Making dependency list for source file surfaceFeatureConvert.C
SOURCE=surfaceFeatureConvert.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOpt/surfaceFeatureConvert.o
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport -lPstream Make/darwinIntel64Gcc46DPOpt/surfaceFeatureConvert.o -L/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib \
         -lmeshTools -ledgeMesh -lOpenFOAM -ldl   -lpthread -lm -o /Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureConvert
+ '[' -n /opt/local ']'
+ echo

+ echo 'Compiling surfaceFeatureExtract with CGAL curvature support'
Compiling surfaceFeatureExtract with CGAL curvature support
+ echo

+ '[' -n 1 ']'
+ THREAD_EXTENSION=-mt
+ wmake 'ENABLE_CURVATURE=-DENABLE_CURVATURE            EXE_FROUNDING_MATH=-frounding-math            USE_F2C=-DCGAL_USE_F2C            CGAL_LIBDIR=-L/opt/local/lib            LAPACK_LIB=-llapack            BLAS_LIB=-lblas            CGAL_LIB=-lCGAL            CGAL_BOOST_LIB=-lboost_thread-mt            CGAL_MPFR_LIB=-lmpfr'
Making dependency list for source file surfaceFeatureExtract.C
SOURCE=surfaceFeatureExtract.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -DENABLE_CURVATURE -frounding-math -DCGAL_USE_F2C -Wno-old-style-cast -I/opt/local/include -I/opt/local/include -I/opt/local/include -I/opt/local/include -ICGALPolyhedron -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/triSurface/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/surfMesh/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o
surfaceFeatureExtract.C: In function 'Foam::scalarField calcCurvature(const Foam::triSurface&)':
surfaceFeatureExtract.C:85:47: error: wrong number of template arguments (1, should be 3)
/opt/local/include/CGAL/Monge_via_jet_fitting.h:57:9: error: provided for 'template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting'
surfaceFeatureExtract.C:85:78: error: invalid type in declaration before ';' token
surfaceFeatureExtract.C:86:57: error: expected initializer before 'Monge_form'
surfaceFeatureExtract.C:148:9: error: 'Monge_form' was not declared in this scope
surfaceFeatureExtract.C:148:20: error: expected ';' before 'monge_form'
surfaceFeatureExtract.C:164:21: error: 'monge_form' was not declared in this scope
surfaceFeatureExtract.C:146:31: warning: unused variable 'monge_fit' [-Wunused-variable]
surfaceFeatureExtract.C:92:18: warning: unused variable 'd_monge' [-Wunused-variable]
make[2]: *** [Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o] Error 1
make[2]: Target `/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureExtract' not remade because of errors.
make[1]: *** [surfaceFeatureExtract] Error 2
WM_USE_MACPORTS is set to 1.

PS: In the previus post you would be able to download my log file, if you needed it.
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Old   May 22, 2013, 06:34
Default
  #48
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Bernhard Gschaider
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Quote:
Originally Posted by tidusuper91 View Post
Thanks for your very precious help. Anyway,
i run an incompressible tutorial and it seems to work.

This is for the not found directory. It seems to happen in the scotch directory in Thirdparty folder

Code:
cd libscotchmetis ; make                                                                scotch && make install)
make CC="gcc-mp-4.6" SCOTCHLIB=ptscotch                        \
                    libscotchmetis.dylib
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_order.c -o metis_graph_order.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_order_f.c -o metis_graph_order_f.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_part.c -o metis_graph_part.o
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DCOMMON_TIMING_OLD -fPIC -I../../include -I../libscotch -c metis_graph_part_f.c -o metis_graph_part_f.o
gcc-mp-4.6 -dynamiclib -undefined dynamic_lookup -o libscotchmetis.dylib metis_graph_order.o metis_graph_order_f.o metis_graph_part.o metis_graph_part_f.o
echo libscotchmetis.dylib
libscotchmetis.dylib
make CC="gcc-mp-4.6" SCOTCHLIB=ptscotch                        \
                    libscotchmetis.dylib
make[2]: `libscotchmetis.dylib' is up to date.
cp metis.h ../../include
cp libscotchmetis.dylib ../../lib
+ make prefix=/Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0 libdir=/Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib install
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/include
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share/man
mkdir /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/share/man/man1
cp -f ../bin/[agm]* /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp -f ../bin/d[agm]* /Users/rubendibattista/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp: ../bin/d[agm]*: No such file or directory
Hm. But the libraries get correctly created. So I wouldn't put too much thought into it

Quote:
Originally Posted by tidusuper91 View Post
This for the surfaceFeatureConvert.C

Code:
Making dependency list for source file surfaceFeatureConvert.C
SOURCE=surfaceFeatureConvert.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOpt/surfaceFeatureConvert.o
g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -lpthread -L/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-macport -lPstream Make/darwinIntel64Gcc46DPOpt/surfaceFeatureConvert.o -L/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib \
         -lmeshTools -ledgeMesh -lOpenFOAM -ldl   -lpthread -lm -o /Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureConvert
+ '[' -n /opt/local ']'
+ echo

+ echo 'Compiling surfaceFeatureExtract with CGAL curvature support'
Compiling surfaceFeatureExtract with CGAL curvature support
+ echo

+ '[' -n 1 ']'
+ THREAD_EXTENSION=-mt
+ wmake 'ENABLE_CURVATURE=-DENABLE_CURVATURE            EXE_FROUNDING_MATH=-frounding-math            USE_F2C=-DCGAL_USE_F2C            CGAL_LIBDIR=-L/opt/local/lib            LAPACK_LIB=-llapack            BLAS_LIB=-lblas            CGAL_LIB=-lCGAL            CGAL_BOOST_LIB=-lboost_thread-mt            CGAL_MPFR_LIB=-lmpfr'
Making dependency list for source file surfaceFeatureExtract.C
SOURCE=surfaceFeatureExtract.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -DENABLE_CURVATURE -frounding-math -DCGAL_USE_F2C -Wno-old-style-cast -I/opt/local/include -I/opt/local/include -I/opt/local/include -I/opt/local/include -ICGALPolyhedron -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/finiteVolume/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/meshTools/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/edgeMesh/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/triSurface/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/surfMesh/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/sampling/lnInclude -IlnInclude -I. -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OpenFOAM/lnInclude -I/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o
surfaceFeatureExtract.C: In function 'Foam::scalarField calcCurvature(const Foam::triSurface&)':
surfaceFeatureExtract.C:85:47: error: wrong number of template arguments (1, should be 3)
/opt/local/include/CGAL/Monge_via_jet_fitting.h:57:9: error: provided for 'template<class DataKernel, class LocalKernel, class SvdTraits> class CGAL::Monge_via_jet_fitting'
surfaceFeatureExtract.C:85:78: error: invalid type in declaration before ';' token
surfaceFeatureExtract.C:86:57: error: expected initializer before 'Monge_form'
surfaceFeatureExtract.C:148:9: error: 'Monge_form' was not declared in this scope
surfaceFeatureExtract.C:148:20: error: expected ';' before 'monge_form'
surfaceFeatureExtract.C:164:21: error: 'monge_form' was not declared in this scope
surfaceFeatureExtract.C:146:31: warning: unused variable 'monge_fit' [-Wunused-variable]
surfaceFeatureExtract.C:92:18: warning: unused variable 'd_monge' [-Wunused-variable]
make[2]: *** [Make/darwinIntel64Gcc46DPOpt/surfaceFeatureExtract.o] Error 1
make[2]: Target `/Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/bin/surfaceFeatureExtract' not remade because of errors.
make[1]: *** [surfaceFeatureExtract] Error 2
WM_USE_MACPORTS is set to 1.

PS: In the previus post you would be able to download my log file, if you needed it.
This seems to be a problem with the most recent version 4.2 of CGAL (OpenFOAM uses 4.0). I solved it by downgrading to version 4.1 (MacPort allows you to do that).
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Old   May 29, 2013, 07:43
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Sorry for my late response but i was busy with an exam

Anyway, i downgraded cgal and used openmpi from system and i have just two errors:

Code:
cp -f ../bin/[agm]* /Users/######/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp: ../bin/[agm]*: No such file or directory
Code:
darwinIntel64Gcc46DPOpt/SloanRenumber.o
ld: library not found for -lboost_thread
collect2: ld returned 1 exit status
make: *** [/Users/######/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib] Error 1
Boost is installed:
Code:
The following ports are currently installed:
  boost @1.53.0_1+no_single+no_static+python27 (active)
What could you tell me about especially the last error?

Last edited by tidusuper91; May 29, 2013 at 13:35.
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Old   May 29, 2013, 13:40
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EDIT (19:32 29/05/13):

I tried to run the motorbike tutorial

Code:
./Allrun
Running surfaceFeatureExtract on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running blockMesh on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running decomposePar on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running snappyHexMesh in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running patchSummary in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running potentialFoam in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running simpleFoam in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running reconstructParMesh on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running reconstructPar on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
And opening the SnappyHexMesh log

Code:
sudo nano log.snappyHexMesh
I get:

Code:
Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/bin/tools/RunFunctions: line 75: mpirun: command not found
In fact if i do in a terminal:

Code:
mpirun -V
it can't find the command.

If I, differently, do:
Code:
openmpirun -V
I get:

Code:
openmpirun (OpenRTE) 1.7.1

Report bugs to http://www.open-mpi.org/community/help/
so i managed to edit the ~/.alias file including

Code:
alias mpirun='openmpirun'
it works in the terminal but Runfunctions still can't get it.

(Same things appear to happen with paraview. I created an alias in ~/.alias file. It works from outside the OpenFoam image but if i do
Code:
paraFoam

/Users/#####/OpenFOAM/OpenFOAM-2.2.x/bin/paraFoam: line 267: paraview: command not found
it's like it can't recognize aliases inside OpenFoam directory).
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Old   May 29, 2013, 20:14
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  #51
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Quote:
Originally Posted by tidusuper91 View Post
EDIT (19:32 29/05/13):

I tried to run the motorbike tutorial

Code:
./Allrun
Running surfaceFeatureExtract on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running blockMesh on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running decomposePar on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running snappyHexMesh in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running patchSummary in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running potentialFoam in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running simpleFoam in parallel on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike using 6 processes
Running reconstructParMesh on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
Running reconstructPar on /Users/rubendibattista/OpenFOAM/rubendibattista-2.2.x/run/motorbike
And opening the SnappyHexMesh log

Code:
sudo nano log.snappyHexMesh
I get:

Code:
Users/rubendibattista/OpenFOAM/OpenFOAM-2.2.x/bin/tools/RunFunctions: line 75: mpirun: command not found
In fact if i do in a terminal:

Code:
mpirun -V
it can't find the command.

If I, differently, do:
Code:
openmpirun -V
I get:

Code:
openmpirun (OpenRTE) 1.7.1

Report bugs to http://www.open-mpi.org/community/help/
so i managed to edit the ~/.alias file including

Code:
alias mpirun='openmpirun'
it works in the terminal but Runfunctions still can't get it.

(Same things appear to happen with paraview. I created an alias in ~/.alias file. It works from outside the OpenFoam image but if i do
Code:
paraFoam

/Users/#####/OpenFOAM/OpenFOAM-2.2.x/bin/paraFoam: line 267: paraview: command not found
it's like it can't recognize aliases inside OpenFoam directory).
Welcome to the wonderful world of shell-initializations.

mpirun vs openmpirun: I wouldn't consider that a bug of the Mac-patch but an inflexibility of the RunFunctions. If you really have to run those scripts create a symbolic link somewhere in the PATH named mpirun pointing to openmpirun

paraFoam: I don't know which paraview you're using. I use the Kitware binaries. If my patches find that at /Applications/paraview.app they modify the path correctly. If not you're on your own.
Also do I not support the paraFoam reader but I use the reader built into paraview. Not because the paraFoam reader is bad but because I don't want to spend my time compiling paraview
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Old   May 29, 2013, 20:21
Default
  #52
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Quote:
Originally Posted by tidusuper91 View Post
Sorry for my late response but i was busy with an exam

Anyway, i downgraded cgal and used openmpi from system and i have just two errors:

Code:
cp -f ../bin/[agm]* /Users/######/OpenFOAM/ThirdParty-2.2.x/platforms/darwinIntel64Gcc46/scotch_6.0.0/bin
cp: ../bin/[agm]*: No such file or directory
Code:
darwinIntel64Gcc46DPOpt/SloanRenumber.o
ld: library not found for -lboost_thread
collect2: ld returned 1 exit status
make: *** [/Users/######/OpenFOAM/OpenFOAM-2.2.x/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib] Error 1
Boost is installed:
Code:
The following ports are currently installed:
  boost @1.53.0_1+no_single+no_static+python27 (active)
What could you tell me about especially the last error?
In OF the library is called boost_thread-mt (no idea why). Check in $FOAM_SRC/renumber/Allwmake if you have something like
Code:
if [ -n "$BOOST_ARCH_PATH" ]
then
    if [ -n "$WM_USE_MACPORT" ]
    then
        export BOOST_THREAD_EXTENSION=-mt
    fi

    wmake $makeType SloanRenumber
else
    echo
    echo "Skipping SloanRenumber"
    echo
fi
there. Especially the WM_USE_MACPORT-part. Anyway. I wouldn't spend too much time on this library. It is not something you use every day. Unless you use the renumberMesh-utiltiy on a regular basis
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Old   July 4, 2013, 07:44
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  #53
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Michael
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Dear all,

thanks to Bernhard for the patches for the new recent version. In fact I spent the last half year with OpenFOAM-ext, so I did not need the other branch.
However, today I tried to compile OpenFOAM 2.2.0 source on a MacBook Pro with OS X 10.8.4. I could confirm some traps I ran into as well:

There is some sort of cp in Paraview.app, so I just deleted it, problem solved. If not this will prevent Scotch from compiling. Marked already here:
Patches to compile OpenFOAM 2.2 on Mac OS X

Concerning surfaceFeatureExtract I would be glad if somebody could tell me where to find cgal 4.1. I tried with port to localise it, but it seems that only 4.2 is in the repository. Problem stated here:
Patches to compile OpenFOAM 2.2 on Mac OS X

Then I also had to use an alias for mpirun as stated here: Patches to compile OpenFOAM 2.2 on Mac OS X

Last but not least I followed Patches to compile OpenFOAM 2.2 on Mac OS X and exchanged line 21 to 28 in $FOAM_SRC/renumber/Allwmake

Code:
if [ -n "$BOOST_ARCH_PATH" ]
then
    wmake $makeType SloanRenumber
else
    echo
    echo "Skipping SloanRenumber"
    echo
fi
by

Code:
if [ -n "$BOOST_ARCH_PATH" ]
then
    if [ -n "$WM_USE_MACPORT" ]
    then
        export BOOST_THREAD_EXTENSION=-mt
    fi

    wmake $makeType SloanRenumber
else
    echo
    echo "Skipping SloanRenumber"
    echo
fi
but I still got

Code:
+ export BOOST_THREAD_EXTENSION=-mt
+ BOOST_THREAD_EXTENSION=-mt
+ wmake libso SloanRenumber
ld: library not found for -lboost_thread
collect2: ld returned 1 exit status
make: ***  [/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib]  Error 1
So in the end I added manually -mt in $FOAM_SRC/renumber/SloanRenumber/Make/options in line 9

Code:
    -L$(BOOST_ARCH_PATH)/lib -lboost_thread-mt \
Then it worked just fine:

Code:
+ export BOOST_THREAD_EXTENSION=-mt
+ BOOST_THREAD_EXTENSION=-mt
+ wmake libso SloanRenumber
wmakeLnInclude: linking include files to ./lnInclude
SOURCE=SloanRenumber.C ; ccache g++-mp-4.6 -m64 -fsignaling-nans   -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra  -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2   -DNoRepository -ftemplate-depth-100 -I/opt/local/include  -I/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/src/meshTools/lnInclude  -I/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/src/parallel/decompose/decompositionMethods/lnInclude   -I/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/src/renumber/renumberMethods/lnInclude  -IlnInclude -I.  -I/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/src/OpenFOAM/lnInclude  -I/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/src/OSspecific/POSIX/lnInclude    -fPIC -Ddarwin -c $SOURCE -o  Make/darwinIntel64Gcc46DPOpt/SloanRenumber.o
'/Users/mplagge/OpenFOAM/OpenFOAM-2.2.0/platforms/darwinIntel64Gcc46DPOpt/lib/libSloanRenumber.dylib'  is up to date.
So if anybody of you could let me know about the cgal 4.1 issue I would appreciate it. If I can spare some time I will set up a new manual and maybe we could write some sort of prerequisite check for Mac. Even if it is not that important I would rather have a fully working image. Just in case I ever need it later.

Have a nice day.

Cheers,

Michael
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Old   July 8, 2013, 14:55
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Quote:
Originally Posted by lithos View Post
anybody of you could let me know about the cgal 4.1 issue I would appreciate it. If I can spare some time I will set up a new manual and maybe we could write some sort of prerequisite check for Mac. Even if it is not that important I would rather have a fully working image. Just in case I ever need it later.
I think I made it compile with 4.2 with the attached patch. Wanted to report it to the upstream but I first wanted to verify whether this is a fix to a MacOnly-problem

Bernhard

SurfaceCGALFix.patch
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Old   July 9, 2013, 07:22
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Quote:
Originally Posted by gschaider View Post
I think I made it compile with 4.2 with the attached patch. Wanted to report it to the upstream but I first wanted to verify whether this is a fix to a MacOnly-problem

Bernhard
Dear Bernhard,

thanks a lot for the patch. It worked perfectly.

Cheers,

Michael
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Old   August 9, 2013, 02:24
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My OpenFOAM-2.2.x installation goes fine except for one item. The Allwmake script for third party complains about a missing ../../etc/wmakeFiles/scotch/Makefile.inc.i686_mac_darwin.shlib-OpenFOAM
file. This file doesn't exist.

Any thoughts?
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Old   August 11, 2013, 18:34
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Quote:
Originally Posted by karlvirgil View Post
My OpenFOAM-2.2.x installation goes fine except for one item. The Allwmake script for third party complains about a missing ../../etc/wmakeFiles/scotch/Makefile.inc.i686_mac_darwin.shlib-OpenFOAM
file. This file doesn't exist.

Any thoughts?
It seems to be missing in the first version of the ThirdParty-patch I uploaded but is in the second one
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Old   August 16, 2013, 08:16
Question Compilation errors
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Hi,

I tried to compile the 2.2.1 version. I followed the instructions posted above, but it seems that the compiler does not find the source files:

Code:
could not open file <path of every source file>
and then the compilation stops after a while. The files are of course present in the path above.


Any ideas?
Thank you
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Old   August 18, 2013, 19:10
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Quote:
Originally Posted by dav.dap83 View Post
Hi,

I tried to compile the 2.2.1 version. I followed the instructions posted above, but it seems that the compiler does not find the source files:

Code:
could not open file <path of every source file>
and then the compilation stops after a while. The files are of course present in the path above.


Any ideas?
Thank you
No idea. Have you sourced etc/bashrc before the compilation?
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Old   August 19, 2013, 06:13
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Quote:
Originally Posted by gschaider View Post
No idea. Have you sourced etc/bashrc before the compilation?
Yes, I have.

Perhaps it may be more helpful to upload the log file.
Attached Files
File Type: zip make-part1.log.zip (58.4 KB, 2 views)
File Type: zip make-part2.log.zip (62.3 KB, 1 views)
File Type: zip make-part3.log.zip (53.8 KB, 1 views)
File Type: zip make-part4.log.zip (64.9 KB, 1 views)
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