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Subject: Re: [OMPI users] Scalability issue
From: Benjamin Toueg (btoueg_at_[hidden])
Date: 2010-12-05 15:04:23


Hi,

First of all thanks for your insight !

*Do you get a corefile?*
I don't get a core file, but I get a file called _FIL001. It doesn't contain
any debugging symbols. It's most likely a digested version of the input file
given to the executable : ./myexec < inputfile.

*there's no line numbers printed in the stack trace*
I would love to see those, but even if I compile openmpi with -debug
-mem-debug -mem-profile, they don't show up. I recompiled my sources to be
sure to properly link them to the newly debugged version of openmpi. I
assumed I didn't need to compile my own sources with -g option since it
crashes in openmpi itself ? I didn't try to run mpiexec via gdb either, I
guess it wont help since I already get the trace.

*the -fdefault-integer-8 options ought to be highly dangerous*
Thanks for noting. Indeed I had some issues with this option. For instance I
have to declare some arguments as INTEGER*4 like RANK,SIZE,IERR in :
CALL MPI_COMM_RANK(MPI_COMM_WORLD,RANK,IERR)
CALL MPI_COMM_SIZE(MPI_COMM_WORLD,SIZE,IERR)
In your example "call MPI_Send(buf, count, MPI_INTEGER, dest, tag,
MPI_COMM_WORLD, mpierr)" I checked that count is never bigger than 2000 (as
you mentioned it could flip to the negative). However I haven't declared it
as INTEGER*4 and I think I should.
When I said "I had to raise the number of data strucutures to be sent", I
meant that I had to call MPI_SEND many more times, not that buffers were
bigger than before.

I'll get back to you with more info when I'll be able to fix my connexion
problem to the cluster...

Thanks,
Benjamin

2010/12/3 Martin Siegert <siegert_at_[hidden]>

> Hi All,
>
> just to expand on this guess ...
>
> On Thu, Dec 02, 2010 at 05:40:53PM -0500, Gus Correa wrote:
> > Hi All
> >
> > I wonder if configuring OpenMPI while
> > forcing the default types to non-default values
> > (-fdefault-integer-8 -fdefault-real-8) might have
> > something to do with the segmentation fault.
> > Would this be effective, i.e., actually make the
> > the sizes of MPI_INTEGER/MPI_INT and MPI_REAL/MPI_FLOAT bigger,
> > or just elusive?
>
> I believe what happens is that this mostly affects the fortran
> wrapper routines and the way Fortran variables are mapped to C:
>
> MPI_INTEGER -> MPI_LONG
> MPI_FLOAT -> MPI_DOUBLE
> MPI_DOUBLE_PRECISION -> MPI_DOUBLE
>
> In that respect I believe that the -fdefault-real-8 option is harmless,
> i.e., it does the expected thing.
> But the -fdefault-integer-8 options ought to be highly dangerous:
> It works for integer variables that are used as "buffer" arguments
> in MPI statements, but I would assume that this does not work for
> "count" and similar arguments.
> Example:
>
> integer, allocatable :: buf(*,*)
> integer i, count, dest, tag, mpierr
>
> i = 32768
> i2 = 2*i
> allocate(buf(i,i2))
> count = i*i2
> buf = 1
> call MPI_Send(buf, count, MPI_INTEGER, dest, tag, MPI_COMM_WORLD, mpierr)
>
> Now count is 2^31 which overflows a 32bit integer.
> The MPI standard requires that count is a 32bit integer, correct?
> Thus while buf gets the type MPI_LONG, count remains an int.
> Is this interpretation correct? If it is, then you are calling
> MPI_Send with a count argument of -2147483648.
> Which could result in a segmentation fault.
>
> Cheers,
> Martin
>
> --
> Martin Siegert
> Head, Research Computing
> WestGrid/ComputeCanada Site Lead
> IT Services phone: 778 782-4691
> Simon Fraser University fax: 778 782-4242
> Burnaby, British Columbia email: siegert_at_[hidden]
> Canada V5A 1S6
>
> > There were some recent discussions here about MPI
> > limiting counts to MPI_INTEGER.
> > Since Benjamin said he "had to raise the number of data structures",
> > which eventually led to the the error,
> > I wonder if he is inadvertently flipping to negative integer
> > side of the 32-bit universe (i.e. >= 2**31), as was reported here by
> > other list subscribers a few times.
> >
> > Anyway, segmentation fault can come from many different places,
> > this is just a guess.
> >
> > Gus Correa
> >
> > Jeff Squyres wrote:
> > >Do you get a corefile?
> > >
> > >It looks like you're calling MPI_RECV in Fortran and then it segv's.
> This is *likely* because you're either passing a bad parameter or your
> buffer isn't big enough. Can you double check all your parameters?
> > >
> > >Unfortunately, there's no line numbers printed in the stack trace, so
> it's not possible to tell exactly where in the ob1 PML it's dying (i.e., so
> we can't see exactly what it's doing to cause the segv).
> > >
> > >
> > >
> > >On Dec 2, 2010, at 9:36 AM, Benjamin Toueg wrote:
> > >
> > >>Hi,
> > >>
> > >>I am using DRAGON, a neutronic simulation code in FORTRAN77 that has
> its own datastructures. I added a module to send these data structures
> thanks to MPI_SEND / MPI_RECEIVE, and everything worked perfectly for a
> while.
> > >>
> > >>Then I had to raise the number of data structures to be sent up to a
> point where my cluster has this bug :
> > >>*** Process received signal ***
> > >>Signal: Segmentation fault (11)
> > >>Signal code: Address not mapped (1)
> > >>Failing at address: 0x2c2579fc0
> > >>[ 0] /lib/libpthread.so.0 [0x7f52d2930410]
> > >>[ 1] /home/toueg/openmpi/lib/openmpi/mca_pml_ob1.so [0x7f52d153fe03]
> > >>[ 2] /home/toueg/openmpi/lib/libmpi.so.0(PMPI_Recv+0x2d2)
> [0x7f52d3504a1e]
> > >>[ 3] /home/toueg/openmpi/lib/libmpi_f77.so.0(pmpi_recv_+0x10e)
> [0x7f52d36cf9c6]
> > >>
> > >>How can I make this error more explicit ?
> > >>
> > >>I use the following configuration of openmpi-1.4.3 :
> > >>./configure --enable-debug --prefix=/home/toueg/openmpi CXX=g++ CC=gcc
> F77=gfortran FC=gfortran FLAGS="-m64 -fdefault-integer-8 -fdefault-real-8
> -fdefault-double-8" FCFLAGS="-m64 -fdefault-integer-8 -fdefault-real-8
> -fdefault-double-8" --disable-mpi-f90
> > >>
> > >>Here is the output of mpif77 -v :
> > >>mpif77 for 1.2.7 (release) of : 2005/11/04 11:54:51
> > >>Driving: f77 -L/usr/lib/mpich-mpd/lib -v -lmpich-p4mpd -lpthread -lrt
> -lfrtbegin -lg2c -lm -shared-libgcc
> > >>Lecture des spécification à partir de
> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/specs
> > >>Configuré avec: ../src/configure -v --enable-languages=c,c++,f77,pascal
> --prefix=/usr --libexecdir=/usr/lib
> --with-gxx-include-dir=/usr/include/c++/3.4 --enable-shared
> --with-system-zlib --enable-nls --without-included-gettext
> --program-suffix=-3.4 --enable-__cxa_atexit --enable-clocale=gnu
> --enable-libstdcxx-debug x86_64-linux-gnu
> > >>Modèle de thread: posix
> > >>version gcc 3.4.6 (Debian 3.4.6-5)
> > >> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/collect2 --eh-frame-hdr -m
> elf_x86_64 -dynamic-linker /lib64/ld-linux-x86-64.so.2
> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib/crt1.o
> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib/crti.o
> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/crtbegin.o -L/usr/lib/mpich-mpd/lib
> -L/usr/lib/gcc/x86_64-linux-gnu/3.4.6 -L/usr/lib/gcc/x86_64-linux-gnu/3.4.6
> -L/usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib
> -L/usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../.. -L/lib/../lib
> -L/usr/lib/../lib -lmpich-p4mpd -lpthread -lrt -lfrtbegin -lg2c -lm -lgcc_s
> -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/3.4.6/crtend.o
> /usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib/crtn.o
> >
> >>/usr/lib/gcc/x86_64-linux-gnu/3.4.6/../../../../lib/libfrtbegin.a(frtbegin.o):
> dans la fonction â–’ main â–’:
> > >>(.text+0x1e): référence indéfinie vers ▒ MAIN__ ▒
> > >>collect2: ld a retourné 1 code d'état d'exécution
> > >>
> > >>Thanks,
> > >>Benjamin
> > >>
> > >>_______________________________________________
> > >>users mailing list
> > >>users_at_[hidden]
> > >>http://www.open-mpi.org/mailman/listinfo.cgi/users
> > >
> > >
> >
> > _______________________________________________
> > users mailing list
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> > http://www.open-mpi.org/mailman/listinfo.cgi/users
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