pnetcdf 1.2.0 create file issue
David Knaak
knaak at cray.com
Fri May 11 19:50:23 CDT 2012
Jim,
I'm not intimate with pnetcdf but the stack trace entries look a little
strange to me. In particular:
#10
count=0x1527daa0, stride=0x0
#13
start=0x7fffffff3750, count=0x7fffffff3750
Could it be that the high level routine is being called with a bad
argument?
Just a thought.
David
On Fri, May 11, 2012 at 05:37:24PM -0600, Jim Edwards wrote:
> Hi David,
>
> I've updated to the 5.2.5 mpich2 on bluewaters and now get a different problem,
> it happens earlier in the code so I think that this worked in the older
> version, here is a partial stack trace from the core file on 16000 tasks.
> I'll try on Monday to reproduce this on a smaller number of tasks. Can I
> send you more info when I get it?
>
> #0 memcpy () at ../sysdeps/x86_64/memcpy.S:102
> #1 0x0000000000c25b03 in MPIDI_CH3U_Buffer_copy ()
> #2 0x0000000000bc91ae in MPIDI_Isend_self ()
> #3 0x0000000000bc5ef4 in MPID_Isend ()
> #4 0x0000000000be4b2b in PMPI_Isend ()
> #5 0x0000000000b9439a in ADIOI_CRAY_R_Exchange_data ()
> #6 0x0000000000b9503d in ADIOI_CRAY_Read_and_exch ()
> #7 0x0000000000b957ca in ADIOI_CRAY_ReadStridedColl ()
> #8 0x0000000000b7ea69 in MPIOI_File_read_all ()
> #9 0x0000000000b7eab6 in PMPI_File_read_all ()
> #10 0x0000000000b3d7ce in ncmpii_getput_vars (ncp=0x107192b0, varp=0x109ee340,
> start=0x15269910, count=0x1527daa0, stride=0x0,
> buf=0x155f5480, bufcount=245561, datatype=-871890885, rw_flag=1, io_method=
> 1) at ./getput_vars.c:741
> #11 0x0000000000b39804 in ncmpi_get_vara_all (ncid=1, varid=59, start=
> 0x15269910, count=0x1527daa0, buf=0x155f5480,
> bufcount=245561, datatype=-871890885) at ./getput_vara.c:435
> #12 0x0000000000b092c6 in nfmpi_get_vara_all_ (v1=0x33e8dd8, v2=0x33e89a0, v3=
> 0x418d500, v4=0x418c500, v5=0x155f5480,
> v6=0x1e72e10, v7=0x1e72e04) at ./get_vara_allf.c:57
> #13 0x00000000007c0524 in pionfread_mod::read_nfdarray_double (file=..., iobuf=
> 0x155f5480, vardesc=..., iodesc=...,
> start=0x7fffffff3750, count=0x7fffffff3750)
>
>
> On Fri, May 11, 2012 at 5:25 PM, Jim Edwards <jedwards at ucar.edu> wrote:
>
> David,
>
> I will give this a try, thanks.
>
>
> On Fri, May 11, 2012 at 5:15 PM, David Knaak <knaak at cray.com> wrote:
>
> Rob,
>
> I suggested taking the discussion off line to not bother those not
> interested in the Cray specifics. But if you think those on the list
> are either interested, or don't consider it a bother, I can certainly
> use the full list.
>
> All,
>
> In the MPT 5.4.0 release, I made some changes to MPI_File_open to
> improve scalability. Because of these changes and previous changes
> I had made (for added functionality, not because of any bugs), the
> code was getting very messy. In fact, I introduced a bug or 2 with
> these changes. So in 5.4.3, I significantly restructured the code
> for better maintainability, fixed the bugs (that I knew of) and made
> more scalability changes.
>
> Jim,
>
> The NCSA's "ESS" has the 5.4.2 version of Cray's MPI implementation as
> default. The "module list" command output that you included shows:
>
> 3) xt-mpich2/5.4.2
>
> The "module avail xt-mpch2" command shows what other versions are
> available:
>
> h2ologin2 25=>module avail xt-mpich2
> --------------------- /opt/cray/modulefiles ---------------------
> xt-mpich2/5.4.2(default) xt-mpich2/5.4.4 xt-mpich2/5.4.5
>
> Would you switch to 5.4.5, relink, and try again?
>
> h2ologin2 25=>module swap xt-mpich2/5.4.2 xt-mpich2/5.4.5
>
> Thanks.
> David
>
>
> On Fri, May 11, 2012 at 12:54:39PM -0500, Rob Latham wrote:
> > On Fri, May 11, 2012 at 11:46:25AM -0500, David Knaak wrote:
> > > Jim,
> > >
> > > Since you are having this problem on a Cray system, please open a
> Cray
> > > bug report against MPI and I will look at it. We can take further
> > > discussions off line.
> >
> > Oh, howdy David! forgot you were on the list. Thanks for keeping an
> > eye on things.
> >
> > the pnetcdf list is pretty low-traffic these days, but we have an
> > awful lot of users in a cray and Lustre environment. If you'd
> rather
> > discuss cray specific stuff elsewhere, I'd understand, but please let
> > us know what you figure out.
> >
> > ==rob
> >
> > > Thanks.
> > > David
> > >
> > > On Fri, May 11, 2012 at 10:03:28AM -0600, Jim Edwards wrote:
> > > >
> > > >
> > > > On Fri, May 11, 2012 at 9:43 AM, Rob Latham <robl at mcs.anl.gov>
> wrote:
> > > >
> > > > On Thu, May 10, 2012 at 03:28:57PM -0600, Jim Edwards wrote:
> > > > > This occurs on the ncsa machine bluewaters. I am using
> pnetcdf1.2.0 and
> > > > > pgi 11.10.0
> > > >
> > > > need one more bit of information: the version of MPT you are
> using.
> > > >
> > > >
> > > > Sorry, what's mpt? MPI?
> > > > Currently Loaded Modulefiles:
> > > > 1) modules/3.2.6.6 9)
> > > > user-paths 17) xpmem/
> 0.1-2.0400.31280.3.1.gem
> > > > 2) xtpe-network-gemini 10) pgi/
> > > > 11.10.0 18) xe-sysroot/4.0.46
> > > > 3) xt-mpich2/5.4.2 11) xt-libsci/
> > > > 11.0.04 19) xt-asyncpe/5.07
> > > > 4) xtpe-interlagos 12) udreg/
> > > > 2.3.1-1.0400.4264.3.1.gem 20) atp/1.4.1
> > > > 5) eswrap/1.0.12 13) ugni/
> > > > 2.3-1.0400.4374.4.88.gem 21) PrgEnv-pgi/4.0.46
> > > > 6) torque/2.5.10 14) pmi/
> > > > 3.0.0-1.0000.8661.28.2807.gem 22) hdf5-parallel/1.8.7
> > > > 7) moab/6.1.5 15) dmapp/
> > > > 3.2.1-1.0400.4255.2.159.gem 23) netcdf-hdf5parallel/4.1.3
> > > > 8) scripts 16) gni-headers/
> > > > 2.1-1.0400.4351.3.1.gem 24) parallel-netcdf/1.2.0
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > > The issue is that calling nfmpi_createfile would sometimes
> result in an
> > > > > error:
> > > > >
> > > > > MPI_File_open : Other I/O error , error stack:
> > > > > (unknown)(): Other I/O error
> > > > > 126: MPI_File_open : Other I/O error , error stack:
> > > > > (unknown)(): Other I/O error
> > > > > Error on create : 502 -32
> > > > >
> > > > > The error appears to be intermittent and I could not get it
> to occur at
> > > > all
> > > > > on a small number of tasks (160) but it occurs with high
> frequency when
> > > > > using a larger number of tasks (>=1600). I traced the
> problem to the
> > > > use
> > > > > of nf_clobber in the mode argument, removing the nf_clobber
> seems to have
> > > > > solved the problem and I think that create implies clobber
> anyway doesn't
> > > > > it?
> > > >
> > > > > Can someone who knows what is going on under the covers
> enlighten me
> > > > > with some understanding of this issue? I suspect that one
> task is
> > > > trying
> > > > > to clobber the file that another has just created or
> something of that
> > > > > nature.
> > > >
> > > > Unfortunately, "under the covers" here means "inside the
> MPI-IO
> > > > library", which we don't have access to.
> > > >
> > > > in the create case we call MPI_File_open with "MPI_MODE_RDWR
> |
> > > > MPI_MODE_CREATE", and if noclobber set, we add
> MPI_MODE_EXCL.
> > > >
> > > > OK, so that's pnetcdf. What's going on in MPI-IO? Well,
> cray's based
> > > > their MPI-IO off of our ROMIO, but I'm not sure which
> version.
> > > >
> > > > Let me cook up a quick MPI-IO-only test case you can run to
> trigger
> > > > this problem and then you can beat cray over the head with
> it.
> > > >
> > > >
> > > >
> > > > Sounds good, thanks.
> > > >
> > > >
> > > > ==rob
> > > >
> > > > --
> > > > Rob Latham
> > > > Mathematics and Computer Science Division
> > > > Argonne National Lab, IL USA
> > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Jim Edwards
> > > >
> > > > CESM Software Engineering Group
> > > > National Center for Atmospheric Research
> > > > Boulder, CO
> > > > 303-497-1842
> > > >
> > >
> >
> > --
> > Rob Latham
> > Mathematics and Computer Science Division
> > Argonne National Lab, IL USA
>
> --
>
>
>
>
> --
> Jim Edwards
>
> CESM Software Engineering Group
> National Center for Atmospheric Research
> Boulder, CO
> 303-497-1842
>
>
>
>
>
> --
> Jim Edwards
>
> CESM Software Engineering Group
> National Center for Atmospheric Research
> Boulder, CO
> 303-497-1842
>
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