Although I do not think that Valgrind supports mpic++, I have tried to run it. This is what I got, thanks------------------------------------------------------------==18729== Memcheck, a memory error detector==18729== Copyright (C) 2002-2009, and GNU GPL'd, by Julian Seward et al.==18729== Using Valgrind-3.5.0 and LibVEX; rerun with -h for copyright info==18729== Command: ./nsga2b==18729== Parent PID: 18726==18729==--18729----18729-- Valgrind options:--18729-- --tool=memcheck--18729-- --error-limit=no--18729-- --leak-check=full--18729-- --log-file=nsga2b_valg.log--18729-- -v--18729-- Contents of /proc/version:--18729-- Linux version 2.6.18-128.1.1.el5.530g0000 (root@kalamata) (gcc version 4.1.2 20071124 (Red Hat 4.1.2-42)) #1 SMP Tue Mar 17 21:49:24 EDT 2009--18729-- Arch and hwcaps: AMD64, amd64-sse3-cx16--18729-- Page sizes: currently 4096, max supported 4096--18729-- Valgrind library directory: /usr/lib64/valgrind--18729-- Reading syms from /lustre/nsga2b (0x400000)--18729-- warning: DiCfSI 0x0 .. 0x0 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x1 .. 0x3 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x4 .. 0x2a outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x0 .. 0x0 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x1 .. 0x3 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x4 .. 0x2a outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x0 .. 0x0 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x1 .. 0x3 outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0x4 .. 0xb outside segment 0x4438f0 .. 0xd81e77--18729-- warning: DiCfSI 0xc .. 0xaa outside segment 0x4438f0 .. 0xd81e77--18729-- Reading syms from /usr/lib64/valgrind/memcheck-amd64-linux (0x38000000)--18729-- object doesn't have a dynamic symbol table--18729-- Reading syms from /lib64/ld-2.5.so (0x3f75c00000)--18729-- Reading suppressions file: /usr/lib64/valgrind/default.supp--18729-- REDIR: 0x3f75c145d0 (strlen) redirected to 0x3803e767 (vgPlain_amd64_linux_REDIR_FOR_strlen)--18729-- Reading syms from /usr/lib64/valgrind/vgpreload_core-amd64-linux.so (0x4802000)--18729-- Reading syms from /usr/lib64/valgrind/vgpreload_memcheck-amd64-linux.so (0x4a03000)==18729== WARNING: new redirection conflicts with existing -- ignoring it--18729-- new: 0x3f75c145d0 (strlen ) R-> 0x04a06dc0 strlen--18729-- REDIR: 0x3f75c143f0 (index) redirected to 0x4a06c30 (index)--18729-- REDIR: 0x3f75c145a0 (strcmp) redirected to 0x4a06e90 (strcmp)--18729-- Reading syms from /opt/openmpi-1.3.4-gnu/lib/libmpi_cxx.so.0.0.0 (0x4c0a000)--18729-- Reading syms from /opt/openmpi-1.3.4-gnu/lib/libmpi.so.0.0.1 (0x4e2600 --18729-- Reading syms from /opt/openmpi-1.3.4-gnu/lib/libmpi.so.0.0.1 (0x4e26000)--18729-- Reading syms from /opt/openmpi-1.3.4-gnu/lib/libopen-rte.so.0.0.0 (0x5258000)--18729-- Reading syms from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0.0.0 (0x54db000)--18729-- Reading syms from /usr/lib64/librdmacm.so.1.0.0 (0x3f77000000)--18729-- object doesn't have a symbol table--18729-- Reading syms from /usr/lib64/libibverbs.so.1.0.0 (0x3f76400000)--18729-- object doesn't have a symbol table--18729-- Reading syms from /usr/lib64/libdat.so.1.0.2 (0x5778000)--18729-- object doesn't have a symbol table--18729-- Reading syms from /scratch/torque-2.4.2/lib/libtorque.so.2.0.0 (0x5982000)--18729-- Reading syms from /lib64/libdl-2.5.so (0x3f76800000)--18729-- Reading syms from /lib64/libnsl-2.5.so (0x3f7fe00000)--18729-- Reading syms from /lib64/libutil-2.5.so (0x3f84e00000)--18729-- Reading syms from /lib64/libm-2.5.so (0x5c97000)--18729-- Reading syms from /usr/lib64/libstdc++.so.6.0.8 (0x3f7c800000)--18729-- object doesn't have a symbol table--18729-- Reading syms from /lib64/libgcc_s-4.1.2-20080825.so.1 (0x3f7b800000)--18729-- object doesn't have a symbol table--18729-- Reading syms from /lib64/libpthread-2.5.so (0x3f76c00000)--18729-- Reading syms from /lib64/libc-2.5.so (0x3f76000000)--18729-- REDIR: 0x3f7607ae00 (memset) redirected to 0x4a07030 (memset)--18729-- REDIR: 0x3f7607c240 (memcpy) redirected to 0x4a08030 (memcpy)--18729-- REDIR: 0x3f76079f40 (rindex) redirected to 0x4a06ae0 (rindex)--18729-- REDIR: 0x3f76079b50 (strlen) redirected to 0x4a06d80 (strlen)--18729-- REDIR: 0x3f76074dc0 (malloc) redirected to 0x4a05d9a (malloc)--18729-- REDIR: 0x3f76072870 (free) redirected to 0x4a059aa (free)--18729-- REDIR: 0x3f76079e90 (strncpy) redirected to 0x4a081a0 (strncpy)--18729-- REDIR: 0x3f76079dd0 (strncmp) redirected to 0x4a06de0 (strncmp)--18729-- REDIR: 0x3f760749e0 (calloc) redirected to 0x4a05092 (calloc)--18729-- REDIR: 0x3f7c8bd1c0 (operator new(unsigned long)) redirected to 0x4a065ea (operator new(unsigned long))--18729-- REDIR: 0x3f7607b930 (mempcpy) redirected to 0x4a07870 (mempcpy)--18729-- REDIR: 0xffffffffff600400 (???) redirected to 0x3803e75d (vgPlain_amd64_linux_REDIR_FOR_vtime)--18729-- REDIR: 0x3f76079610 (strcpy) redirected to 0x4a082c0 (strcpy)--18729-- REDIR: 0x3f760795d0 (strcmp) redirected to 0x4a06e50 (strcmp)--18729-- REDIR: 0x3f76079c40 (strnlen) redirected to 0x4a06d50 (strnlen)--18729-- REDIR: 0x3f7c8bbf50 (operator delete(void*)) redirected to 0x4a056bc (operator delete(void*))--18729-- REDIR: 0x3f7607a640 (memchr) redirected to 0x4a06f10 (memchr)--18729-- REDIR: 0x3f76079420 (index) redirected to 0x4a06b70 (index)--18729-- REDIR: 0x3f7607ac60 (memmove) redirected to 0x4a07080 (memmove)--18729-- REDIR: 0x3f760752e0 (realloc) redirected to 0x4a05e4b (realloc) --18729-- REDIR: 0x3f76079d30 (strncat) redirected to 0x4a06c60 (strncat)--18729-- REDIR: 0x3f76079260 (strcat) redirected to 0x4a07590 (strcat)--18729-- REDIR: 0x3f7607cea0 (rawmemchr) redirected to 0x4a07110 (rawmemchr)--18729-- REDIR: 0x3f76074ff0 (memalign) redirected to 0x4a04f6c (memalign)--18729-- REDIR: 0xffffffffff600000 (???) redirected to 0x3803e753 (vgPlain_amd64_linux_REDIR_FOR_vgettimeofday)--18729-- REDIR: 0x3f7607cff0 (strchrnul) redirected to 0x4a070e0 (strchrnul)--18729-- REDIR: 0x3f7607bf40 (stpcpy) redirected to 0x4a07b10 (stpcpy)--18729-- Reading syms from /lib64/libnss_files-2.5.so (0x794b000)--18729-- Reading syms from /lib64/libnss_nis-2.5.so (0x7b56000)--18729-- REDIR: 0x3f76075230 (posix_memalign) redirected to 0x4a05047 (posix_memalign)--18729-- Reading syms from /usr/lib64/libdaplcma.so.1.0.2 (0x8762000)--18729-- object doesn't have a symbol table==18729== Invalid write of size 8==18729== at 0x443BEF: initPopPara(population*, std::vector<message_para_to_workersT, std::allocator<message_para_to_workersT> >&, initParaType&, int, int, std::vector<double, std::allocator<double> >&) (main-parallel2.cpp:552)==18729== by 0x44F12E: main (main-parallel2.cpp:204)==18729== Address 0x62c9da0 is 0 bytes after a block of size 0 alloc'd==18729== at 0x4A0666E: operator new(unsigned long) (vg_replace_malloc.c:220)==18729== by 0x4573E4: void std::__uninitialized_fill_n_aux<message_para_to_workersT*, unsigned long, message_para_to_workersT>(message_para_to_workersT*, unsigned long, message_para_to_workersT const&, __false_type) (new_allocator.h:88)==18729== by 0x4576CF: void std::__uninitialized_fill_n_a<message_para_to_workersT*, unsigned long, message_para_to_workersT, message_para_to_workersT>(message_para_to_workersT*, unsigned long, message_para_to_workersT const&, std::allocator<message_para_to_workersT>) (stl_uninitialized.h:218)==18729== by 0x44EE2E: main (stl_vector.h:218)==18729====18729== Invalid read of size 8==18729== at 0x44F13A: main (main-parallel2.cpp:208)==18729== Address 0x62c9d60 is 0 bytes after a block of size 0 alloc'd==18729== at 0x4A0666E: operator new(unsigned long) (vg_replace_malloc.c:220)==18729== by 0x45733D: void std::__uninitialized_fill_n_aux<message_para_to_workersT*, unsigned long, message_para_to_workersT>(message_para_to_workersT*, unsigned long, message_para_to_workersT const&, __false_type) (new_allocator.h:88)==18729== by 0x4576CF: void std::__uninitialized_fill_n_a<message_para_to_workersT*, unsigned long, message_para_to_workersT, message_para_to_workersT>(message_para_to_workersT*, unsigned long, message_para_to_workersT const&, std::allocator<message_para_to_workersT>) (stl_uninitialized.h:218)==18729== by 0x44EE2E: main (stl_vector.h:218)==18729== valgrind: m_mallocfree.c:225 (mk_plain_bszB): Assertion 'bszB != 0' failed.valgrind: This is probably caused by your program erroneously writing past theend of a heap block and corrupting heap metadata. If you fix anyinvalid writes reported by Memcheck, this assertion failure will probably go away. Please try that before reporting this as a bug. ==18729== at 0x38029D5C: report_and_quit (m_libcassert.c:145)==18729== by 0x3802A032: vgPlain_assert_fail (m_libcassert.c:217)==18729== by 0x38035645: vgPlain_arena_malloc (m_mallocfree.c:225)==18729== by 0x38002BB5: vgMemCheck_new_block (mc_malloc_wrappers.c:199)==18729== by 0x38002F6B: vgMemCheck___builtin_new (mc_malloc_wrappers.c:246)==18729== by 0x3806070C: do_client_request (scheduler.c:1362)==18729== by 0x38061D30: vgPlain_scheduler (scheduler.c:1061)==18729== by 0x38085E6E: run_a_thread_NORETURN (syswrap-linux.c:91) sched status: running_tid=1 Thread 1: status = VgTs_Runnable==18729== at 0x4A0666E: operator new(unsigned long) (vg_replace_malloc.c:220)==18729== by 0x464506: __gnu_cxx::new_allocator<int>::allocate(unsigned long, void const*) (new_allocator.h:88)==18729== by 0x46452E: std::_Vector_base<int, std::allocator<int> >::_M_allocate(unsigned long) (stl_vector.h:127)==18729== by 0x464560: std::_Vector_base<int, std::allocator<int> >::_Vector_base(unsigned long, std::allocator<int> const&) (stl_vector.h:113)==18729== by 0x464B6A: std::vector<int, std::allocator<int> >::vector(unsigned long, int const&, std::allocator<int> const&) (stl_vector.h:216)==18729== by 0x488F62: Index::Index() (index.cpp:20)==18729== by 0x489147: ReadFile(char const*) (index.cpp:86)==18729== by 0x48941C: ImportIndices() (index.cpp:121)==18729== by 0x445D00: myNeplanTaskScheduler(CNSGA2*, int, int, int, population*, char, int, std::vector<message_para_to_workersT, std::allocator<message_para_to_workersT> >&, ompi_datatype_t*, int&, int&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, std::vector<double, std::allocator<double> >&, int, std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, ompi_datatype_t*, int, ompi_datatype_t*, int) (myNetplanScheduler.cpp:109)==18729== by 0x44F2DF: main (main-parallel2.cpp:216)
Note: see also the FAQ in the source distribution.It contains workarounds to several common problems.In particular, if Valgrind aborted or crashed afteridentifying problems in your program, there's a good chancethat fixing those problems will prevent Valgrind aborting orcrashing, especially if it happened in m_mallocfree.c. ------------------------------------------------------------ > Subject: Re: [OMPI users] OMPI seg fault by a class with weird address. > From: jsquy...@cisco.com > Date: Wed, 16 Mar 2011 06:43:01 -0400 > To: dtustud...@hotmail.com > CC: us...@open-mpi.org > > Did you run with a memory checking debugger like Valgrind? > > Sent from my phone. No type good. > > On Mar 15, 2011, at 8:30 PM, "Jack Bryan" <dtustud...@hotmail.com> wrote: > > > Hi, > > > > I have installed a new open MPI 1.3.4. > > > > But I got more weird errors: > > > > *** glibc detected *** /lustre/nsga2b: malloc(): memory corruption (fast): > > 0x000000001cafc450 *** > > ======= Backtrace: ========= > > /lib64/libc.so.6[0x3c50272aeb] > > /lib64/libc.so.6(__libc_malloc+0x7a)[0x3c5027402a] > > /usr/lib64/libstdc++.so.6(_Znwm+0x1d)[0x3c590bd17d] > > /lustre/jxding/netplan49/nsga2b[0x445bc6] > > /lustre/jxding/netplan49/nsga2b[0x44f43b] > > /lib64/libc.so.6(__libc_start_main+0xf4)[0x3c5021d974] > > /lustre/jxding/netplan49/nsga2b(__gxx_personality_v0+0x499)[0x443909] > > ======= Memory map: ======== > > 00400000-00f33000 r-xp 00000000 6ac:e3210 685016360 > > /lustre/netplan49/nsga2b > > 01132000-0117e000 rwxp 00b32000 6ac:e3210 685016360 > > /lustre/netplan49/nsga2b > > 0117e000-01188000 rwxp 0117e000 00:00 0 > > 1ca11000-1ca78000 rwxp 1ca11000 00:00 0 > > 1ca78000-1ca79000 rwxp 1ca78000 00:00 0 > > 1ca79000-1ca7a000 rwxp 1ca79000 00:00 0 > > 1ca7a000-1cab8000 rwxp 1ca7a000 00:00 0 > > 1cab8000-1cac7000 rwxp 1cab8000 00:00 0 > > 1cac7000-1cacf000 rwxp 1cac7000 00:00 0 > > 1cacf000-1cad0000 rwxp 1cacf000 00:00 0 > > 1cad0000-1cad1000 rwxp 1cad0000 00:00 0 > > 1cad1000-1cad2000 rwxp 1cad1000 00:00 0 > > 1cad2000-1cada000 rwxp 1cad2000 00:00 0 > > 1cada000-1cadc000 rwxp 1cada000 00:00 0 > > 1cadc000-1cae0000 rwxp 1cadc000 00:00 0 > > > > ......................... > > 512600000-3512605000 r-xp 00000000 00:11 12043 > > /usr/lib64/librdmacm.so.1 > > 3512605000-3512804000 ---p 00005000 00:11 12043 > > /usr/lib64/librdmacm.so.1 > > 3512804000-3512805000 rwxp 00004000 00:11 12043 > > /usr/lib64/librdmacm.so.1 > > 3512e00000-3512e0c000 r-xp 00000000 00:11 5545 > > /usr/lib64/libibverbs.so.1 > > 3512e0c000-351300b000 ---p 0000c000 00:11 5545 > > /usr/lib64/libibverbs.so.1 > > 351300b000-351300c000 rwxp 0000b000 00:11 5545 > > /usr/lib64/libibverbs.so.1 > > 3c4f200000-3c4f21c000 r-xp 00000000 00:11 2853 > > /lib64/ld-2.5.so > > 3c4f41b000-3c4f41c000 r-xp 0001b000 00:11 2853 > > /lib64/ld-2.5.so > > 3c4f41c000-3c4f41d000 rwxp 0001c000 00:11 2853 > > /lib64/ld-2.5.so > > 3c50200000-3c5034c000 r-xp 00000000 00:11 897 > > /lib64/libc.so.6 > > 3c5034c000-3c5054c000 ---p 0014c000 00:11 897 > > /lib64/libc.so.6 > > 3c5054c000-3c50550000 r-xp 0014c000 00:11 897 > > /lib64/libc.so.6 > > 3c50550000-3c50551000 rwxp 00150000 00:11 897 > > /lib64/libc.so.6 > > 3c50551000-3c50556000 rwxp 3c50551000 00:00 0 > > 3c50600000-3c50682000 r-xp 00000000 00:11 2924 > > /lib64/libm.so.6 > > 3c50682000-3c50881000 ---p 00082000 00:11 2924 > > /lib64/libm.so.6 > > 3c50881000-3c50882000 r-xp 00081000 00:11 2924 > > /lib64/libm.so.6 > > 3c50882000-3c50883000 rwxp 00082000 00:11 2924 > > /lib64/libm.so.6 > > 3c50a00000-3c50a02000 r-xp 00000000 00:11 923 > > /lib64/libdl.so.2 > > 3c50a02000-3c50c02000 ---p 00002000 00:11 923 > > /lib64/libdl.so.2 > > 3c50c02000-3c50c03000 r-xp 00002000 00:11 923 > > /lib64/libdl.so.2 > > 3c50c03000-3c50c04000 rwxp 00003000 00:11 923 > > /lib64/libdl.so.2 > > 3c50e00000-3c50e16000 r-xp 00000000 00:11 1011 > > /lib64/libpthread.so.0 > > > > ..................... > > 2ae87b05e000-2ae87b075000 r-xp 00000000 6ac:e3210 686492235 > > /lustre/mpi_protocol_091117/openmpi134/lib/libmpi_cxx.so.0.0.0 > > 2ae87b075000-2ae87b274000 ---p 00017000 6ac:e3210 686492235 > > /lustre/mpi_protocol_091117/openmpi134/lib/libmpi_cxx.so.0.0.0 > > 2ae87b274000-2ae87b277000 rwxp 00016000 6ac:e3210 686492235 > > /lustre/mpi_protocol_091117/openmpi134/lib/libmpi_cxx.so.0.0.0 > > > > > > > > fff2fa38000-7fff2fa4e000 rwxp 7ffffffe9000 00:00 0 > > [stack] > > ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 > > [vdso] > > [n332:82320] *** Process received signal *** > > [n332:82320] Signal: Aborted (6) > > [n332:82320] Signal code: (-6) > > [n332:82320] [ 0] /lib64/libpthread.so.0 [0x3c50e0e4c0] > > [n332:82320] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3c50230215] > > [n332:82320] [ 2] /lib64/libc.so.6(abort+0x110) [0x3c50231cc0] > > [n332:82320] [ 3] /lib64/libc.so.6 [0x3c5026a7fb] > > [n332:82320] [ 4] /lib64/libc.so.6 [0x3c50272aeb] > > [n332:82320] [ 5] /lib64/libc.so.6(__libc_malloc+0x7a) [0x3c5027402a] > > [n332:82320] [ 6] /usr/lib64/libstdc++.so.6(_Znwm+0x1d) [0x3c590bd17d] > > [n332:82320] [ 7] /lustre/jxding/netplan49/nsga2b [0x445bc6] > > [n332:82320] [ 8] /lustre/jxding/netplan49/nsga2b [0x44f43b] > > [n332:82320] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c5021d974] > > [n332:82320] [10] /lustre/nsga2b(__gxx_personality_v0+0x499) [0x443909] > > [n332:82320] *** End of error message *** > > =>> PBS: job killed: walltime 117 exceeded limit 90 > > mpirun: killing job... > > > > > > > > > > > Subject: Re: [OMPI users] OMPI seg fault by a class with weird address. > > > From: jsquy...@cisco.com > > > Date: Tue, 15 Mar 2011 12:50:41 -0400 > > > CC: us...@open-mpi.org > > > To: dtustud...@hotmail.com > > > > > > You can: > > > > > > mpirun -np 4 valgrind ./my_application > > > > > > That is, you run 4 copies of valgrind, each with one instance of > > > ./my_application. Then you'll get valgrind reports for your applications. > > > You might want to dig into the valgrind command line options to have it > > > dump the results to files with unique prefixes (e.g., PID and/or > > > hostname) so that you can get a unique report from each process. > > > > > > If you disabled ptmalloc and you're still getting the same error, then it > > > sounds like an application error. Check out and see what valgrind tells > > > you. > > > > > > > > > > > > On Mar 15, 2011, at 11:25 AM, Jack Bryan wrote: > > > > > > > Thanks, > > > > > > > > From http://valgrind.org/docs/manual/mc-manual.html#mc-manual.mpiwrap > > > > > > > > I find that > > > > > > > > "Currently the wrappers are only buildable with mpiccs which are based > > > > on GNU GCC or Intel's C++ Compiler." > > > > > > > > The cluster which I am working on is using GNU Open MPI mpic++. i am > > > > afraid that the Valgrind wrapper can work here. > > > > > > > > I do not have system administrator authorization. > > > > > > > > Are there other mem-checkers (open source) that can do this ? > > > > > > > > thanks > > > > > > > > Jack > > > > > > > > > Subject: Re: [OMPI users] OMPI seg fault by a class with weird > > > > > address. > > > > > From: jsquy...@cisco.com > > > > > Date: Tue, 15 Mar 2011 06:19:53 -0400 > > > > > CC: dtustud...@hotmail.com > > > > > To: us...@open-mpi.org > > > > > > > > > > You may also want to run your program through a memory-checking > > > > > debugger such as valgrind to see if it turns up any other problems. > > > > > > > > > > AFIK, ptmalloc should be fine for use with STL vector allocation. > > > > > > > > > > > > > > > On Mar 15, 2011, at 4:00 AM, Belaid MOA wrote: > > > > > > > > > > > Hi Jack, > > > > > > I may need to see the whole code to decide but my quick look > > > > > > suggest that ptmalloc is causing a problem with STL-vector > > > > > > allocation. ptmalloc is the openMPI internal malloc library. Could > > > > > > you try to build openMPI without memory management (using > > > > > > --without-memory-manager) and let us know the outcome. ptmalloc is > > > > > > not needed if you are not using an RDMA interconnect. > > > > > > > > > > > > With best regards, > > > > > > -Belaid. > > > > > > > > > > > > From: dtustud...@hotmail.com > > > > > > To: belaid_...@hotmail.com; us...@open-mpi.org > > > > > > Subject: RE: [OMPI users] OMPI seg fault by a class with weird > > > > > > address. > > > > > > Date: Tue, 15 Mar 2011 00:30:19 -0600 > > > > > > > > > > > > Hi, > > > > > > > > > > > > Because the code is very long, I just show the calling relationship > > > > > > of functions. > > > > > > > > > > > > main() > > > > > > { > > > > > > scheduler(); > > > > > > > > > > > > } > > > > > > scheduler() > > > > > > { > > > > > > ImportIndices(); > > > > > > } > > > > > > > > > > > > ImportIndices() > > > > > > { > > > > > > Index IdxNode ; > > > > > > IdxNode = ReadFile("fileName"); > > > > > > } > > > > > > > > > > > > Index ReadFile(const char* fileinput) > > > > > > { > > > > > > Index TempIndex; > > > > > > ......... > > > > > > > > > > > > } > > > > > > > > > > > > vector<int> Index::GetPosition() const { return Position; } > > > > > > vector<int> Index::GetColumn() const { return Column; } > > > > > > vector<int> Index::GetYear() const { return Year; } > > > > > > vector<string> Index::GetName() const { return Name; } > > > > > > int Index::GetPosition(const int idx) const { return Position[idx]; > > > > > > } > > > > > > int Index::GetColumn(const int idx) const { return Column[idx]; } > > > > > > int Index::GetYear(const int idx) const { return Year[idx]; } > > > > > > string Index::GetName(const int idx) const { return Name[idx]; } > > > > > > int Index::GetSize() const { return Position.size(); } > > > > > > > > > > > > The sequential code works well, and there is no scheduler(). > > > > > > > > > > > > The parallel code output from gdb: > > > > > > ---------------------------------------------- > > > > > > Breakpoint 1, myNeplanTaskScheduler(CNSGA2 *, int, int, int, ._85 > > > > > > *, char, int, message_para_to_workers_VecT &, MPI_Datatype, int &, > > > > > > int &, std::vector<std::vector<double, std::allocator<double> >, > > > > > > std::allocator<std::vector<double, std::allocator<double> > > > &, > > > > > > std::vector<std::vector<double, std::allocator<double> >, > > > > > > std::allocator<std::vector<double, std::allocator<double> > > > &, > > > > > > std::vector<double, std::allocator<double> > &, int, > > > > > > std::vector<std::vector<double, std::allocator<double> >, > > > > > > std::allocator<std::vector<double, std::allocator<double> > > > &, > > > > > > MPI_Datatype, int, MPI_Datatype, int) (nsga2=0x118c490, > > > > > > popSize=<value optimized out>, nodeSize=<value optimized out>, > > > > > > myRank=<value optimized out>, myChildpop=0x1208d80, genCandTag=65 > > > > > > 'A', > > > > > > generationNum=1, myPopParaVec=std::vector of length 4, capacity 4 = > > > > > > {...}, > > > > > > message_to_master_type=0x7fffffffd540, myT1Flag=@0x7fffffffd68c, > > > > > > myT2Flag=@0x7fffffffd688, > > > > > > resultTaskPackageT1=std::vector of length 4, capacity 4 = {...}, > > > > > > resultTaskPackageT2Pr=std::vector of length 4, capacity 4 = {...}, > > > > > > xdataV=std::vector of length 4, capacity 4 = {...}, objSize=7, > > > > > > resultTaskPackageT12=std::vector of length 4, capacity 4 = {...}, > > > > > > xdata_to_workers_type=0x121c410, myGenerationNum=1, > > > > > > Mpara_to_workers_type=0x121b9b0, nconNum=0) > > > > > > at src/nsga2/myNetplanScheduler.cpp:109 > > > > > > 109 ImportIndices(); > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 2, ImportIndices () at src/index.cpp:120 > > > > > > 120 IdxNode = ReadFile("prepdata/idx_node.csv"); > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 4, ReadFile (fileinput=0xd8663d "prepdata/idx_node.csv") > > > > > > at src/index.cpp:86 > > > > > > 86 Index TempIndex; > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 5, Index::Index (this=0x7fffffffcb80) at src/index.cpp:20 > > > > > > 20 Name(0) {} > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Program received signal SIGSEGV, Segmentation fault. > > > > > > 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc () > > > > > > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0 > > > > > > > > > > > > --------------------------------------- > > > > > > the backtrace output from the above parallel OpenMPI code: > > > > > > > > > > > > (gdb) bt > > > > > > #0 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc () > > > > > > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0 > > > > > > #1 0x00002aaaab3b2bd3 in opal_memory_ptmalloc2_malloc () > > > > > > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0 > > > > > > #2 0x0000003f7c8bd1dd in operator new(unsigned long) () > > > > > > from /usr/lib64/libstdc++.so.6 > > > > > > #3 0x00000000004646a7 in __gnu_cxx::new_allocator<int>::allocate ( > > > > > > this=0x7fffffffcb80, __n=0) > > > > > > at > > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h:88 > > > > > > #4 0x00000000004646cf in std::_Vector_base<int, std::allocator<int> > > > > > > >::_M_allocate (this=0x7fffffffcb80, __n=0) > > > > > > at > > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:127 > > > > > > #5 0x0000000000464701 in std::_Vector_base<int, std::allocator<int> > > > > > > >::_Vector_base (this=0x7fffffffcb80, __n=0, __a=...) > > > > > > at > > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:113 > > > > > > #6 0x0000000000464d0b in std::vector<int, std::allocator<int> > > > > > > >::vector ( > > > > > > this=0x7fffffffcb80, __n=0, __value=@0x7fffffffc968, __a=...) > > > > > > at > > > > > > /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h:216 > > > > > > #7 0x00000000004890d7 in Index::Index (this=0x7fffffffcb80) > > > > > > ---Type <return> to continue, or q <return> to quit--- > > > > > > at src/index.cpp:20 > > > > > > #8 0x000000000048927a in ReadFile (fileinput=0xd8663d > > > > > > "prepdata/idx_node.csv") > > > > > > at src/index.cpp:86 > > > > > > #9 0x0000000000489533 in ImportIndices () at src/index.cpp:120 > > > > > > #10 0x0000000000445e0e in myNeplanTaskScheduler(CNSGA2 *, int, int, > > > > > > int, ._85 *, char, int, message_para_to_workers_VecT &, > > > > > > MPI_Datatype, int &, int &, std::vector<std::vector<double, > > > > > > std::allocator<double> >, std::allocator<std::vector<double, > > > > > > std::allocator<double> > > > &, std::vector<std::vector<double, > > > > > > std::allocator<double> >, std::allocator<std::vector<double, > > > > > > std::allocator<double> > > > &, std::vector<double, > > > > > > std::allocator<double> > &, int, std::vector<std::vector<double, > > > > > > std::allocator<double> >, std::allocator<std::vector<double, > > > > > > std::allocator<double> > > > &, MPI_Datatype, int, MPI_Datatype, > > > > > > int) (nsga2=0x118c490, > > > > > > popSize=<value optimized out>, nodeSize=<value optimized out>, > > > > > > myRank=<value optimized out>, myChildpop=0x1208d80, genCandTag=65 > > > > > > 'A', > > > > > > generationNum=1, myPopParaVec=std::vector of length 4, capacity 4 = > > > > > > {...}, > > > > > > message_to_master_type=0x7fffffffd540, myT1Flag=@0x7fffffffd68c, > > > > > > myT2Flag=@0x7fffffffd688, > > > > > > resultTaskPackageT1=std::vector of length 4, capacity 4 = {...}, > > > > > > resultTaskPackageT2Pr=std::vector of length 4, capacity 4 = {...}, > > > > > > xdataV=std::vector of length 4, capacity 4 = {...}, objSize=7, > > > > > > resultTaskPackageT12=std::vector of length 4, capacity 4 = {...}, > > > > > > xdata_to_workers_type=0x121c410, myGenerationNum=1, > > > > > > Mpara_to_workers_type=0x121b9b0, nconNum=0) > > > > > > ---Type <return> to continue, or q <return> to quit--- > > > > > > at src/nsga2/myNetplanScheduler.cpp:109 > > > > > > #11 0x000000000044f44b in main (argc=1, argv=0x7fffffffd998) > > > > > > at src/nsga2/main-parallel2.cpp:216 > > > > > > ---------------------------------------------------- > > > > > > > > > > > > What is "opal_memory_ptmalloc2_int_malloc ()" ? > > > > > > > > > > > > The gdb output from sequential code: > > > > > > ------------------------------------- > > > > > > Breakpoint 1, main (argc=<value optimized out>, argv=<value > > > > > > optimized out>) > > > > > > at src/nsga2/main-seq.cpp:32 > > > > > > 32 ImportIndices(); > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 2, ImportIndices () at src/index.cpp:115 > > > > > > 115 IdxNode = ReadFile("prepdata/idx_node.csv"); > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 4, ReadFile (fileinput=0xd6bb9d "prepdata/idx_node.csv") > > > > > > at src/index.cpp:86 > > > > > > 86 Index TempIndex; > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 5, Index::Index (this=0x7fffffffd6d0) at src/index.cpp:20 > > > > > > 20 Name(0) {} > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 4, ReadFile (fileinput=0xd6bbb3 "prepdata/idx_ud.csv") > > > > > > at src/index.cpp:86 > > > > > > 86 Index TempIndex; > > > > > > (gdb) bt > > > > > > #0 ReadFile (fileinput=0xd6bbb3 "prepdata/idx_ud.csv") at > > > > > > src/index.cpp:86 > > > > > > #1 0x0000000000471cc9 in ImportIndices () at src/index.cpp:116 > > > > > > #2 0x000000000043bba6 in main (argc=<value optimized out>, > > > > > > argv=<value optimized out>) at src/nsga2/main-seq.cpp:32 > > > > > > > > > > > > -------------------------------------- > > > > > > thanks > > > > > > > > > > > > > > > > > > From: belaid_...@hotmail.com > > > > > > To: us...@open-mpi.org; dtustud...@hotmail.com > > > > > > Subject: RE: [OMPI users] OMPI seg fault by a class with weird > > > > > > address. > > > > > > Date: Tue, 15 Mar 2011 06:16:35 +0000 > > > > > > > > > > > > Hi Jack, > > > > > > 1- Where is your main function to see how you called your class? > > > > > > 2- I do not see the implementation of GetPosition, GetName, etc.? > > > > > > > > > > > > With best regards, > > > > > > -Belaid. > > > > > > > > > > > > > > > > > > From: dtustud...@hotmail.com > > > > > > To: us...@open-mpi.org > > > > > > Date: Mon, 14 Mar 2011 19:04:12 -0600 > > > > > > Subject: [OMPI users] OMPI seg fault by a class with weird address. > > > > > > > > > > > > Hi, > > > > > > > > > > > > I got a run-time error of a Open MPI C++ program. > > > > > > > > > > > > The following output is from gdb: > > > > > > > > > > > > -------------------------------------------------------------------------- > > > > > > Program received signal SIGSEGV, Segmentation fault. > > > > > > 0x00002aaaab3b0b81 in opal_memory_ptmalloc2_int_malloc () > > > > > > from /opt/openmpi-1.3.4-gnu/lib/libopen-pal.so.0 > > > > > > > > > > > > At the point > > > > > > > > > > > > Breakpoint 9, Index::Index (this=0x7fffffffcb80) at src/index.cpp:20 > > > > > > 20 Name(0) {} > > > > > > > > > > > > The Index has been called before this point and no problem: > > > > > > ------------------------------------------------------- > > > > > > Breakpoint 9, Index::Index (this=0x117d800) at src/index.cpp:20 > > > > > > 20 Name(0) {} > > > > > > (gdb) c > > > > > > Continuing. > > > > > > > > > > > > Breakpoint 9, Index::Index (this=0x117d860) at src/index.cpp:20 > > > > > > 20 Name(0) {} > > > > > > (gdb) c > > > > > > Continuing. > > > > > > ---------------------------------------------------------------------------- > > > > > > > > > > > > It seems that the 0x7fffffffcb80 address is a problem. > > > > > > > > > > > > But, I donot know the reason and how to remove the bug. > > > > > > > > > > > > Any help is really appreciated. > > > > > > > > > > > > thanks > > > > > > > > > > > > the following is the index definition. > > > > > > > > > > > > --------------------------------------------------------- > > > > > > class Index { > > > > > > public: > > > > > > Index(); > > > > > > Index(const Index& rhs); > > > > > > ~Index(); > > > > > > Index& operator=(const Index& rhs); > > > > > > > > > > > > vector<int> GetPosition() const; > > > > > > vector<int> GetColumn() const; > > > > > > vector<int> GetYear() const; > > > > > > vector<string> GetName() const; > > > > > > int GetPosition(const int idx) const; > > > > > > int GetColumn(const int idx) const; > > > > > > int GetYear(const int idx) const; > > > > > > string GetName(const int idx) const; > > > > > > int GetSize() const; > > > > > > > > > > > > void Add(const int idx, const int col, const string& name); > > > > > > void Add(const int idx, const int col, const int year, const > > > > > > string& name); > > > > > > void Add(const int idx, const Step& col, const string& name); > > > > > > void WriteFile(const char* fileinput) const; > > > > > > > > > > > > private: > > > > > > vector<int> Position; > > > > > > vector<int> Column; > > > > > > vector<int> Year; > > > > > > vector<string> Name; > > > > > > }; > > > > > > // Contructors and destructor for the Index class > > > > > > Index::Index() : > > > > > > Position(0), > > > > > > Column(0), > > > > > > Year(0), > > > > > > Name(0) {} > > > > > > > > > > > > Index::Index(const Index& rhs) : > > > > > > Position(rhs.GetPosition()), > > > > > > Column(rhs.GetColumn()), > > > > > > Year(rhs.GetYear()), > > > > > > Name(rhs.GetName()) {} > > > > > > > > > > > > Index::~Index() {} > > > > > > > > > > > > Index& Index::operator=(const Index& rhs) { > > > > > > Position = rhs.GetPosition(); > > > > > > Column = rhs.GetColumn(), > > > > > > Year = rhs.GetYear(), > > > > > > Name = rhs.GetName(); > > > > > > return *this; > > > > > > } > > > > > > ---------------------------------------------------------- > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ users mailing list > > > > > > us...@open-mpi.org > > > > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > _______________________________________________ > > > > > > users mailing list > > > > > > us...@open-mpi.org > > > > > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > > > > > > > > > > > > -- > > > > > Jeff Squyres > > > > > jsquy...@cisco.com > > > > > For corporate legal information go to: > > > > > http://www.cisco.com/web/about/doing_business/legal/cri/ > > > > > > > > > > > > > > -- > > > Jeff Squyres > > > jsquy...@cisco.com > > > For corporate legal information go to: > > > http://www.cisco.com/web/about/doing_business/legal/cri/ > > >
