[CIG-LONG] compiling gale from repository on mac 10.6.8
Robert Gray
graywacke at gmail.com
Thu Mar 22 07:29:32 PDT 2012
Here's the associated config.log file.
Cheers,
Rob
file /Users/robgray/Gale-2.0.0_source/config/config.py,line 66:
Configure(confdir = .sconf_temp)
Configuring using:
config/scons/scons.py --config=force -f SConfigure
--petsc-dir=/opt/local/lib/petsc --hdf5-dir=/opt/local
file /Users/robgray/Gale-2.0.0_source/config/cxx.py,line 11:
Configure(confdir = .sconf_temp)
scons: Configure: Checking whether the C++ compiler works
.sconf_temp/conftest_0.cpp <-
|
|int main()
|{
| return 0;
|}
|
g++ -o .sconf_temp/conftest_0.o -c .sconf_temp/conftest_0.cpp
scons: Configure: yes
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library None...
.sconf_temp/conftest_1.cpp <-
|
|
|#include "libxml/parser.h"
|
|int
|main() {
|
|return 0;
|}
|
g++ -o .sconf_temp/conftest_1.o -c -g -DDEBUG .sconf_temp/conftest_1.cpp
.sconf_temp/conftest_1.cpp:3:27: error: libxml/parser.h: No such file or
directory
scons: Configure: no
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library None...
.sconf_temp/conftest_2.cpp <-
|
|
|#include "libxml/parser.h"
|
|int
|main() {
|
|return 0;
|}
|
g++ -o .sconf_temp/conftest_2.o -c -g -DDEBUG -I/usr/include/libxml2
.sconf_temp/conftest_2.cpp
g++ -o .sconf_temp/conftest_2 .sconf_temp/conftest_2.o -lxml2
scons: Configure: yes
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for MPI_Finalize() in C++ library None...
.sconf_temp/conftest_3.cpp <-
|
|
|#include "mpi.h"
|
|int
|main() {
| MPI_Finalize();
|return 0;
|}
|
mpicxx -o .sconf_temp/conftest_3.o -c -g -DDEBUG -DHAVE_LIBXML2
-I/usr/include/libxml2 .sconf_temp/conftest_3.cpp
mpicxx -o .sconf_temp/conftest_3 .sconf_temp/conftest_3.o -lxml2
scons: Configure: yes
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for C++ library None...
.sconf_temp/conftest_4.cpp <-
|
|
|#include "hdf5.h"
|
|int
|main() {
|
|return 0;
|}
|
mpicxx -o .sconf_temp/conftest_4.o -c -g -DDEBUG -DHAVE_LIBXML2 -DHAVE_MPI
-I/usr/include/libxml2 -I/opt/local/include .sconf_temp/conftest_4.cpp
mpicxx -o .sconf_temp/conftest_4 .sconf_temp/conftest_4.o -L/opt/local/lib
-lhdf5 -lxml2
scons: Configure: yes
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec']
Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Looked in: ['/opt/local/lib/petsc/lib']
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for PetscInitialize(NULL, NULL, NULL, NULL);..
in C++ library None...
.sconf_temp/conftest_5.cpp <-
|
|
|#include "mpi.h"
|#include "petsc.h"
|#include "petscvec.h"
|#include "petscmat.h"
|#include "petscksp.h"
|#include "petscsnes.h"
|
|int
|main() {
| PetscInitialize(NULL, NULL, NULL, NULL);
|PetscFinalize();
|return 0;
|}
|
mpicxx -o .sconf_temp/conftest_5.o -c -g -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -O -DDEBUG -DHAVE_LIBXML2
-DHAVE_MPI -DHAVE_HDF5 -I/usr/include/libxml2 -I/opt/local/include
-I/opt/local/lib/petsc/include -I/opt/local/include/openmpi
.sconf_temp/conftest_5.cpp
mpicxx -o .sconf_temp/conftest_5 -Wl,-multiply_defined,suppress
-Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs
-Wl,-search_paths_first .sconf_temp/conftest_5.o -L/opt/local/lib
-L/opt/local/lib/petsc/lib -lpetsc -lhdf5 -lxml2
Undefined symbols:
"_XMaskEvent", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
_Xi_wait_map in libpetsc.a(wmap.c.o)
"_XGetWMName", referenced from:
_PetscDrawSetTitle_X in libpetsc.a(xops.c.o)
_XiSetWindowLabel in libpetsc.a(xinit.c.o)
"_XDrawLine", referenced from:
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawLine_X in libpetsc.a(xops.c.o)
"_XCreateColormap", referenced from:
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
"_XListFontsWithInfo", referenced from:
_XiInitFonts in libpetsc.a(text.c.o)
_XiInitFonts in libpetsc.a(text.c.o)
"_XAllocNamedColor", referenced from:
_PetscDrawSetUpColormap_Shared in libpetsc.a(xcolor.c.o)
"_XChangeGC", referenced from:
_XiLoadFont in libpetsc.a(text.c.o)
"_XFreeFontInfo", referenced from:
_XiInitFonts in libpetsc.a(text.c.o)
_XiInitFonts in libpetsc.a(text.c.o)
_XiLoadFont in libpetsc.a(text.c.o)
"_XSetWindowColormap", referenced from:
_XiSetColormap in libpetsc.a(xcolor.c.o)
"_XCheckTypedEvent", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
"_XFillArc", referenced from:
_PetscDrawEllipse_X in libpetsc.a(xops.c.o)
"_XResizeWindow", referenced from:
_PetscDrawResizeWindow_X in libpetsc.a(xops.c.o)
"_XFlush", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawFlush_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedClear_X in libpetsc.a(xops.c.o)
"_XGetGeometry", referenced from:
_PetscDrawResizeWindow_X in libpetsc.a(xops.c.o)
_PetscDrawCheckResizedWindow_X in libpetsc.a(xops.c.o)
_XiQuickWindowFromWindow in libpetsc.a(xinit.c.o)
"_XStoreColor", referenced from:
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
"_XFree", referenced from:
_PetscDrawSetTitle_X in libpetsc.a(xops.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XFreeGC", referenced from:
_PetscDrawRestoreSingleton_X in libpetsc.a(xops.c.o)
_PetscDrawDestroy_X in libpetsc.a(xops.c.o)
"_XQueryPointer", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
"_XDrawString", referenced from:
_PetscDrawStringVertical_X in libpetsc.a(xops.c.o)
_PetscDrawString_X in libpetsc.a(xops.c.o)
_PetscDrawString_X in libpetsc.a(xops.c.o)
"_XGetWindowAttributes", referenced from:
_XiDisplayWindow in libpetsc.a(xinit.c.o)
_XiQuickWindowFromWindow in libpetsc.a(xinit.c.o)
"_XDrawPoint", referenced from:
_PetscDrawPoint_X in libpetsc.a(xops.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
"_XSetForeground", referenced from:
_PetscDrawEllipse_X in libpetsc.a(xops.c.o)
_PetscDrawTriangle_X in libpetsc.a(xops.c.o)
_PetscDrawRectangle_X in libpetsc.a(xops.c.o)
_PetscDrawClear_X in libpetsc.a(xops.c.o)
_PetscDrawStringVertical_X in libpetsc.a(xops.c.o)
_PetscDrawString_X in libpetsc.a(xops.c.o)
_PetscDrawPoint_X in libpetsc.a(xops.c.o)
_PetscDrawArrow_X in libpetsc.a(xops.c.o)
_PetscDrawLine_X in libpetsc.a(xops.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_PetscDrawInterpolatedTriangle_X in libpetsc.a(tone.c.o)
_XiSetToBackground in libpetsc.a(xinit.c.o)
_XiQuickWindowFromWindow in libpetsc.a(xinit.c.o)
_XiQuickWindow in libpetsc.a(xinit.c.o)
"_XSetWMName", referenced from:
_PetscDrawSetTitle_X in libpetsc.a(xops.c.o)
_XiSetWindowLabel in libpetsc.a(xinit.c.o)
"_XMapWindow", referenced from:
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XFillRectangle", referenced from:
_PetscDrawRectangle_X in libpetsc.a(xops.c.o)
_PetscDrawClear_X in libpetsc.a(xops.c.o)
_XiQuickWindow in libpetsc.a(xinit.c.o)
"_XDefineCursor", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
"_XCreateWindow", referenced from:
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XSelectInput", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XSetWindowBackground", referenced from:
_XiQuickWindowFromWindow in libpetsc.a(xinit.c.o)
_XiQuickWindow in libpetsc.a(xinit.c.o)
"_XFillPolygon", referenced from:
_PetscDrawTriangle_X in libpetsc.a(xops.c.o)
"_XUndefineCursor", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
"_XCopyArea", referenced from:
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawFlush_X in libpetsc.a(xops.c.o)
"_XQueryFont", referenced from:
_XiLoadFont in libpetsc.a(text.c.o)
"_XStringListToTextProperty", referenced from:
_XiDisplayWindow in libpetsc.a(xinit.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XSetWMProperties", referenced from:
_XiDisplayWindow in libpetsc.a(xinit.c.o)
"_XSetClipRectangles", referenced from:
_PetscDrawCheckResizedWindow_X in libpetsc.a(xops.c.o)
_PetscDrawSetViewport_X in libpetsc.a(xops.c.o)
"_XLoadFont", referenced from:
_XiLoadFont in libpetsc.a(text.c.o)
"_XCreateGC", referenced from:
_XiSetGC in libpetsc.a(xinit.c.o)
"_XSync", referenced from:
_PetscDrawSetDoubleBuffer_X in libpetsc.a(xops.c.o)
_PetscDrawCheckResizedWindow_X in libpetsc.a(xops.c.o)
_PetscDrawCheckResizedWindow_X in libpetsc.a(xops.c.o)
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedFlush_X in libpetsc.a(xops.c.o)
_PetscDrawFlush_X in libpetsc.a(xops.c.o)
_PetscDrawSynchronizedClear_X in libpetsc.a(xops.c.o)
"_XAllocColor", referenced from:
_XiFindColor in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_Shared in libpetsc.a(xcolor.c.o)
"_XCloseDisplay", referenced from:
_PetscDrawRestoreSingleton_X in libpetsc.a(xops.c.o)
_PetscDrawXGetDisplaySize_Private in libpetsc.a(xops.c.o)
_PetscDrawDestroy_X in libpetsc.a(xops.c.o)
"_XMatchVisualInfo", referenced from:
_XiSetVisualClass in libpetsc.a(xcolor.c.o)
_XiSetVisualClass in libpetsc.a(xcolor.c.o)
_XiSetVisualClass in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_X in libpetsc.a(xcolor.c.o)
"_XParseColor", referenced from:
_XiFindColor in libpetsc.a(xcolor.c.o)
_PetscDrawSetUpColormap_Private in libpetsc.a(xcolor.c.o)
"_XCreateFontCursor", referenced from:
_PetscDrawGetMouseButton_X in libpetsc.a(xops.c.o)
"_XOpenDisplay", referenced from:
_PetscDrawXGetDisplaySize_Private in libpetsc.a(xops.c.o)
_XiOpenDisplay in libpetsc.a(xinit.c.o)
_PetscDrawSetColormap_X in libpetsc.a(xcolor.c.o)
"_XCreatePixmap", referenced from:
_PetscDrawSetDoubleBuffer_X in libpetsc.a(xops.c.o)
_PetscDrawCheckResizedWindow_X in libpetsc.a(xops.c.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
scons: Configure: no
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec']
Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Looked in: ['/opt/local/lib/petsc/lib']
file /Users/robgray/Gale-2.0.0_source/config/Package.py,line 145:
Configure(confdir = .sconf_temp)
scons: Configure: Checking for PetscInitialize(NULL, NULL, NULL, NULL);..
in C++ library None...
.sconf_temp/conftest_6.cpp <-
|
|
|#include "mpi.h"
|#include "petsc.h"
|#include "petscvec.h"
|#include "petscmat.h"
|#include "petscksp.h"
|#include "petscsnes.h"
|
|int
|main() {
| PetscInitialize(NULL, NULL, NULL, NULL);
|PetscFinalize();
|return 0;
|}
|
mpicxx -o .sconf_temp/conftest_6.o -c -g -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -O -DDEBUG -DHAVE_LIBXML2
-DHAVE_MPI -DHAVE_HDF5 -I/usr/include/libxml2 -I/opt/local/include
-I/opt/local/lib/petsc/include/petsc -I/opt/local/include/openmpi
.sconf_temp/conftest_6.cpp
.sconf_temp/conftest_6.cpp:4:19: error: petsc.h: No such file or directory
.sconf_temp/conftest_6.cpp:5:22: error: petscvec.h: No such file or
directory
.sconf_temp/conftest_6.cpp:6:22: error: petscmat.h: No such file or
directory
.sconf_temp/conftest_6.cpp:7:22: error: petscksp.h: No such file or
directory
.sconf_temp/conftest_6.cpp:8:23: error: petscsnes.h: No such file or
directory
.sconf_temp/conftest_6.cpp: In function 'int main()':
.sconf_temp/conftest_6.cpp:12: error: 'PetscInitialize' was not declared in
this scope
.sconf_temp/conftest_6.cpp:13: error: 'PetscFinalize' was not declared in
this scope
scons: Configure: no
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Looked in: ['/opt/local/lib/petsc/lib64']
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petsc']
Shared missing: ['petsc']
Looked in: ['/opt/local/lib/petsc/lib64']
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Shared missing: ['petscsnes', 'petscksp', 'petscdm', 'petscmat',
'petscvec', 'petsc']
Looked in: ['/opt/local/lib/petsc/lib64']
Failed to find static or shared libraries for 'PETSc'.
Static missing: ['petsc']
Shared missing: ['petsc']
Looked in: ['/opt/local/lib/petsc/lib64']
On Wed, Mar 21, 2012 at 6:15 PM, Robert Gray <graywacke at gmail.com> wrote:
> Hi all,
> I'm trying to compile GALE from the repository on my macbook pro running
> 10.6.8.
> I installed petsc-3.2 with openmpi through macports.
> When I try to compile GALE it doesn't recognize either petsc or openmpi in
> /opt/local/.
> I tried a repository version of Underworld and it recognized both openmpi
> and petsc.
> Has anyone tried this recently on a mac running snow leopard?
> All suggestions are more than welcome.
> Cheers,
> Rob
>
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