On 7 Sep 2010, at 09:44, Cody Permann wrote: > > On Sep 4, 2010, at 10:29 AM, Anna-Lena Gerner wrote: > >> >> Hi everybody, >> >> I installed libMesh on my Mac OS X, and in opt mode everything is just fine. >> There also seem to be no compilation problems in dbg mode. However, in dbg >> mode I get the following runtime error: (./ex4-dbg -d 1 -n 20) >> >> ex4-dbg(73819) malloc: *** error for object 0x1032e6fa0: pointer being freed >> was not allocated >> *** set a breakpoint in malloc_error_break to debug >> >> Program received signal SIGABRT, Aborted. >> 0x00007fff853623d6 in __kill () >> (gdb) bt >> #0 0x00007fff853623d6 in __kill () >> #1 0x00007fff85402972 in abort () >> #2 0x00007fff8531a615 in free () >> #3 0x0000000100026e0a in __gnu_cxx::new_allocator<char>::deallocate >> (this=0x7fff5fbfb5b7, __p=0x1032e6fa0 "") at ext/new_allocator.h:95 >> #4 0x0000000100020a61 in std::string::_Rep::_M_destroy (this=0x1032e6fa0, >> _...@0x7fff5fbfb61f) at basic_string.tcc:449 >> #5 0x000000010001b0e0 in std::string::_Rep::_M_dispose (this=0x1032e6fa0, >> _...@0x7fff5fbfb61f) at basic_string.h:236 >> #6 0x000000010001351b in ~basic_string (this=0x7fff5fbfcad0) at >> basic_string.h:503 >> #7 0x00000001016199c4 in libMesh::PerfLog::get_info_header >> (this=0x7fff5fbfd2f0) at src/utils/perf_log.C:171 >> #8 0x000000010161b356 in libMesh::PerfLog::get_log (this=0x7fff5fbfd2f0) at >> src/utils/perf_log.C:452 >> #9 0x000000010161b450 in libMesh::PerfLog::print_log (this=0x7fff5fbfd2f0) >> at src/utils/perf_log.C:469 >> #10 0x0000000101619481 in ~PerfLog (this=0x7fff5fbfd2f0) at >> src/utils/perf_log.C:61 >> #11 0x000000010000568b in assemble_poisson (e...@0x7fff5fbff570, >> system_na...@0x10350fc18) at ex4.C:290 >> #12 0x00000001015bbb46 in libMesh::System::user_assembly (this=0x10350fb60) >> at src/systems/system.C:1451 >> #13 0x00000001015b30a0 in libMesh::System::assemble (this=0x10350fb60) at >> src/systems/system.C:376 >> #14 0x000000010151c0a8 in libMesh::ImplicitSystem::assemble >> (this=0x10350fb60) at src/systems/implicit_system.C:173 >> #15 0x000000010152a394 in libMesh::LinearImplicitSystem::assemble >> (this=0x10350fb60) at linear_implicit_system.h:100 >> #16 0x0000000101529e55 in libMesh::LinearImplicitSystem::solve >> (this=0x10350fb60) at src/systems/linear_implicit_system.C:86 >> #17 0x000000010000392f in main (argc=6, argv=0x7fff5fbff880) at ex4.C:246 >> >> I use the GCC 4.5 compilers from http://hpc.sourceforge.net/ and installed >> libMesh with the following configure options: >> CC=mpicc CXX=mpicxx ./configure >> --enable-everything >> --enable-slepc >> --with-glpk-include=/opt/local/include >> --with-glpk-lib=/opt/local/lib >> >> (PETSc configure options are: >> --with-fc=0 >> --with-mpi=1 >> --with-mpi-dir=/usr/local >> --with-x11=1 --with-umfpack=1 >> --with-umfpack-include=/opt/local/include/ufsparse >> --with-umfpack-lib=[/opt/local/lib/libamd.a,/opt/local/lib/libcamd.a,/opt/local/lib/libccolamd.a,/opt/local/lib/cholmod.a,/opt/local/lib/libcolamd.a,/opt/local/lib/libumfpack.a]) >> > > with-mpi-dir -> /usr/local - Where are your MPI wrappers coming from? Make > sure that when you compile MPI or install MPI that you use everything from > the hpc.sourceforge.net installation of your GCC compilers. The Mac versions > of the compilers do not play well with the third party version. You may have > some cross linking going on there. If you still can't see the problem, > please give us more info on your MPI installation. >
Hi Cody, For my mpich2 installation I used the following configure options (I attached c.txt for more details): CC=/usr/local/bin/gcc CXX=/usr/local/bin/g++ ./configure --enable-cxx --enable-sharedlibs=osx-gcc --disable-f77 --disable-f90 So I made sure that I used the correct GCC compilers; but is there anything else I have to specify or to take care of? I checked the doc files of my mpich2 installation and noticed that during make there had been the following error (line 2406 in m.txt): /usr/local/bin/gcc -O2 -o /Users/agerner/Software/mpich2-1.2.1p1/src/mpe2/src/slog2sdk/trace_rlog/bin/rlog_print trace_input.o rlogutil.o trace_print.o -shrext .jnilib gcc: .jnilib: No such file or directory gcc: unrecognized option '-shrext' make[7]: *** [/Users/agerner/Software/mpich2-1.2.1p1/src/mpe2/src/slog2sdk/trace_rlog/bin/rlog_print] Error 1 make[6]: *** [ALL] Error 2 make[5]: *** [all] Error 2 make[4]: [all] Error 2 (ignored) Apparently, it looks for the file /Users/agerner/Software/mpich2-1.2.1p1/src/mpe2/src/slog2sdk/trace_rlog/bin/rlog_print, but when I check this directory, there is only a file called rlogprint (without underscore)... Thank you so much for any further hints. -Anna ------------------------------------------------------------------------------ Automate Storage Tiering Simply Optimize IT performance and efficiency through flexible, powerful, automated storage tiering capabilities. View this brief to learn how you can reduce costs and improve performance. http://p.sf.net/sfu/dell-sfdev2dev _______________________________________________ Libmesh-users mailing list Libmesh-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/libmesh-users
