pnetcdf 1.2.0 create file issue

David Knaak knaak at cray.com
Mon May 21 09:06:17 CDT 2012


Hi Jim,

Thanks for the additional information.  I'll begin working on it.

David

On Sat, May 19, 2012 at 07:23:24AM -0600, Jim Edwards wrote:
> Hi David,
> 
> I built the pnetcdf 1.3.0-pre1 release on bluewaters and
> ran the nf_test provided with that package.  It exhibits the same issues with
> nfmpi_create and nfmpi_open that I am seeing from the installed
> parallel-netcdf-1.2.0 and my application. 
> I have opened ticket BWDSPCH-298 on bluewaters to track this issue.  
> 
> On Fri, May 11, 2012 at 6:50 PM, David Knaak <knaak at cray.com> wrote:
> 
>     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
>     >
> 
>     --
> 
> 
> 
> 
> --
> Jim Edwards
> 
> CESM Software Engineering Group
> National Center for Atmospheric Research
> Boulder, CO
> 303-497-1842
> 

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