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Subject: Re: [OMPI users] Memory allocation error when linking with MPI libraries
From: Terry Frankcombe (terry_at_[hidden])
Date: 2010-08-08 00:58:22


You're trying to do a 6GB allocate. Can your underlying system handle
that? IF you compile without the wrapper, does it work?

I see your executable is using the OMPI memory stuff. IIRC there are
switches to turn that off.

On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
> Hello,
>
> I'am having an sigsegv error when using simple program compiled and
> link with openmpi.
> I have reproduce the problem using really simple fortran code. It
> actually does not even use MPI, but just link with mpi shared
> libraries. (problem does not appear when I do not link with mpi
> libraries)
> % cat allocate.F90
> program test
> implicit none
> integer, dimension(:), allocatable :: z
> integer(kind=8) :: l
>
> write(*,*) "l ?"
> read(*,*) l
>
> ALLOCATE(z(l))
> z(1) = 111
> z(l) = 222
> DEALLOCATE(z)
>
> end program test
>
> I am using openmpi 1.4.2 and gfortran for my tests. Here is the
> compilation :
>
> % ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
> allocate.F90
> gfortran -g -o testallocate allocate.F90
> -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
> -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
> -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
> -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
> -lutil -lm -ldl -pthread
>
> When I am running that test with different length, I sometimes get a
> "Segmentation fault" error. Here are two examples using two specific
> values, but error happens for many other values of length (I did not
> manage to find which values of lenght gives that error)
>
> % ./testallocate
> l ?
> 1600000000
> Segmentation fault
> % ./testallocate
> l ?
> 2000000000
>
> I used debugger with re-compiled version of openmpi using debug flag.
> I got the folowing error in function sYSMALLOc
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaab70b3b3 in sYSMALLOc (nb=6400000016, av=0x2aaaab930200)
> at malloc.c:3239
> 3239 set_head(remainder, remainder_size | PREV_INUSE);
> Current language: auto; currently c
> (gdb) bt
> #0 0x00002aaaab70b3b3 in sYSMALLOc (nb=6400000016,
> av=0x2aaaab930200) at malloc.c:3239
> #1 0x00002aaaab70d0db in opal_memory_ptmalloc2_int_malloc
> (av=0x2aaaab930200, bytes=6400000000) at malloc.c:4322
> #2 0x00002aaaab70b773 in opal_memory_ptmalloc2_malloc
> (bytes=6400000000) at malloc.c:3435
> #3 0x00002aaaab70a665 in opal_memory_ptmalloc2_malloc_hook
> (sz=6400000000, caller=0x2aaaabf8534d) at hooks.c:667
> #4 0x00002aaaabf8534d in _gfortran_internal_free ()
> from /usr/lib64/libgfortran.so.1
> #5 0x0000000000400bcc in MAIN__ () at allocate.F90:11
> #6 0x0000000000400c4e in main ()
> (gdb) display
> (gdb) list
> 3234 if ((unsigned long)(size) >= (unsigned long)(nb +
> MINSIZE)) {
> 3235 remainder_size = size - nb;
> 3236 remainder = chunk_at_offset(p, nb);
> 3237 av->top = remainder;
> 3238 set_head(p, nb | PREV_INUSE | (av != &main_arena ?
> NON_MAIN_ARENA : 0));
> 3239 set_head(remainder, remainder_size | PREV_INUSE);
> 3240 check_malloced_chunk(av, p, nb);
> 3241 return chunk2mem(p);
> 3242 }
> 3243
>
>
> I also did the same test in C and I got the same problem.
>
> Does someone has any idea that could help me understand what's going
> on ?
>
> Regards
> Nicolas
>
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