Hm I just did:make METHOD=devel firstTest
and I got:
Program received signal SIGINT, Interrupt.
0x90ff5980 in __gnu_debug::_Safe_iterator_base::_M_detach ()
(gdb) quit
The program is running. Exit anyway? (y or n) y
EIGHT-THREE-NINETY-EIGHT:karen karenlee$ rm firstTest
EIGHT-THREE-NINETY-EIGHT:karen karenlee$ make METHOD=devel firstTest
echo `../libmesh/contrib/bin/libmesh-config --ldflags`
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/lib/i386-apple-darwin9.8.0_devel/libmesh.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/liblaspack.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libmetis.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libsfcurves.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libgzstream.dylib
-lz
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libgmv.dylib
-Wl,-rpath,/opt/local/lib/vtk-5.2 -L/opt/local/lib/vtk-5.2 -lvtkIO
-lvtkCommon -lvtkFiltering
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libtetgen.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libtriangle.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libexodusii.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libnetcdf.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libnemesis.dylib
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libHilbert.dylib
-Wl,-rpath,/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/lib/i386-apple-darwin9.8.0_devel
-Wl,-rpath,/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel
-L/usr/X11/lib -L/opt/local/lib -L/usr/X11/lib -L/opt/local/lib
-Wl,-rpath,/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/lib/i386-apple-darwin9.8.0_devel
-Wl,-rpath,/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel
g++ -g -o firstTest `../libmesh/contrib/bin/libmesh-config --include`
`../libmesh/contrib/bin/libmesh-config --cxxflags` firstTest.cxx
`../libmesh/contrib/bin/libmesh-config --ldflags`
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/lib/i386-apple-darwin9.8.0_devel/libmesh.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/liblaspack.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libmetis.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libsfcurves.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libgzstream.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libgmv.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libtetgen.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libtriangle.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libexodusii.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libnetcdf.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libnemesis.dylib:
No such file or directory
i686-apple-darwin9-g++-4.0.1:
/Users/karenlee/Documents/Code/libmesh-0.6.4/libmesh/contrib/lib/i386-apple-darwin9.8.0_devel/libHilbert.dylib:
No such file or directory
firstTest.cxx: In function ‘void assemble_poisson(EquationSystems&, const
std::string&)’:
firstTest.cxx:199: warning: unused variable ‘qface_point’
firstTest.cxx:138: warning: unused variable ‘q_point’
make: *** [firstTest] Error 1
The relevant part of my Makefile is as follows:
LIBMESH_CONFIG = ../libmesh/contrib/bin/libmesh-config
CPPFLAGS = `$(LIBMESH_CONFIG) --include`
CXXFLAGS = `$(LIBMESH_CONFIG) --cxxflags`
LDFLAGS =
LIBS = `$(LIBMESH_CONFIG) --ldflags`
PROGS = firstTest
all: $(PROGS)
firstTest: firstTest.cxx
echo $(LIBS)
g++ -g -o $@ $(CPPFLAGS) $(CXXFLAGS) firstTest.cxx $(LDFLAGS)
$(LIBS)
clean:
rm -f $(PROGS)
Thanks,
Karen
On Tue, Mar 9, 2010 at 5:52 PM, Karen Lee <[email protected]> wrote:
> I see. Let me try that... I'm looking at example 4, which does not involve
> reading in a mesh. Is there a way I can parallelize even the read-in?
>
> Thanks,
> Karen
>
>
> On Tue, Mar 9, 2010 at 5:50 PM, Roy Stogner <[email protected]>wrote:
>
>>
>>
>> On Tue, 9 Mar 2010, Karen Lee wrote:
>>
>> Thanks! Looks like I was just missing some entries of my MeshData since I
>>> was combining 2 node files...
>>>
>>> I'm in gdb mode and it has taken 50 min and it seems that the mesh is
>>> still not completely read in yet. Got stalled
>>> here:
>>> (gdb) n
>>> found the tetgen files to read
>>> read in nodes and elements
>>> n
>>> n
>>> n
>>> n
>>>
>>> after I pressed n to see if it was actually already done. Is this normal?
>>> (1.7M points and 11M elements...
>>>
>>
>> Probably. METHOD=dbg turns on a ton of debugging tests, including the
>> GLIBCXX tests, and last time I checked one of those tests turned some
>> basic std::set operations from O(log(N)) to O(N log(N)). This is
>> obviously a problem when N is in the millions...
>>
>> Try METHOD=devel, if you're trying to debug problems that only crop up
>> on large runs. You won't get the vector bounds-checking, which is a
>> shame, but you'll at least still be running all the libmesh_assert()
>> tests, and it'll run much faster.
>> ---
>> Roy
>>
>
>
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