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Subject: Re: [OMPI users] Memory allocation error when linking with MPI libraries
From: Nicolas Deladerriere (nicolas.deladerriere_at_[hidden])
Date: 2010-08-08 10:19:37


Yes, I'am using 24G machine on 64 bit Linux OS.
If I compile without wrapper, I did not get any problems.

It seems that when I am linking with openmpi, my program use a kind of
openmpi implemented malloc. Is it possible to switch it off in order ot only
use malloc from libc ?

Nicolas

2010/8/8 Terry Frankcombe <terry_at_[hidden]>

> 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
> >
> > _______________________________________________
> > users mailing list
> > users_at_[hidden]
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
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