possible bug in pnetcdf: cdf5 issue

[Jim Edwards]

I'm using mpich2 1.4.1p1  romio: 1.2.6

In your test program the first MPI_File_write works but the second gives:

Error: MPI_File_write (ddtype) Invalid argument, error stack:
MPI_FILE_WRITE(100): Invalid count argument


On Mon, Feb 18, 2013 at 10:52 AM, Wei-keng Liao <wkliao at ece.northwestern.edu
> wrote:

> Hi, Jim,
>
> I tested your codes with 4 MPI processes and got the error below.
> MPI_FILE_WRITE_ALL(105): Invalid count argument
>
> Maybe you are using IBM's MPI-IO? (I am using MPICH.)
>
> Can you try the attached Fortran program? (run on 1 process).
> I got error below.
>
>  Error: MPI_File_write MPI_DOUBLE Invalid argument, error stack:
> MPI_FILE_WRITE(102): Invalid count argument
>  Error: MPI_File_write (ddtype) Invalid argument, error stack:
> MPI_FILE_WRITE(102): Invalid count argument
>
>
>
>
> Wei-keng
>
> On Feb 18, 2013, at 9:00 AM, Jim Edwards wrote:
>
> > Hi Wei-keng,
> >
> > This is just an interface problem and not a hard limit of mpi-io.  For
> example if I run the
> > same case on 4 tasks instead of 8, it works just fine (example attached).
> >
> > If I create an mpi derived type such as for example an
> mpi_type_contiguous I can do the same call as below successfully.
> >
> >   int len = 322437120;
> >     double *buf = (double*) malloc(len * sizeof(double));
> >     int elemtype, err;
> >     err = mpi_type_contiguous(len,mpi_double,elemtype);
> >     ierr = mpi_type_commit(elemtype)
> >     err = MPI_File_write(fh, buf, 1, elemtype, &status);
> >     if (err != MPI_SUCCESS) {
> >         int errorStringLen;
> >         char errorString[MPI_MAX_ERROR_
> > STRING];
> >         MPI_Error_string(err, errorString, &errorStringLen);
> >         printf("Error: MPI_File_write_at() (%s)\n",errorString);
> >     }
> >
> >
> >
> >
> >
> > It seems to me that every operation that pnetcdf can do using start and
> count can be described as an mpi_type_subarray which will both allow
> pnetcdf to avoid this interface limit and save a potentially considerable
> amount of memory.
> >
> > - Jim
> >
> > On Sun, Feb 17, 2013 at 10:10 PM, Wei-keng Liao <
> wkliao at ece.northwestern.edu> wrote:
> > Hi, Jim,
> >
> > In your test program, each process is writing 322437120 or 322437202
> doubles.
> > so, 322437120 * sizeof(double) = 2,579,496,960 which is larger than
> 2^31, max
> > for a signed 4-byte integer. It did cause 4-byte integer overflow in
> PnetCDF.
> > But, even MPI-IO will have a problem with this size.
> >
> > If you try the code fragment below, ROMIO will throw an error class
> > MPI_ERR_ARG, and error string "Invalid count argument".
> >
> >     int len = 322437120;
> >     double *buf = (double*) malloc(len * sizeof(double));
> >
> >     int err = MPI_File_write(fh, buf, len, MPI_DOUBLE, &status);
> >     if (err != MPI_SUCCESS) {
> >         int errorStringLen;
> >         char errorString[MPI_MAX_ERROR_STRING];
> >         MPI_Error_string(err, errorString, &errorStringLen);
> >         printf("Error: MPI_File_write_at() (%s)\n",errorString);
> >     }
> >
> > A possible PnetCDF solution is to detect the overflow and divide a large
> request
> > into multiple, smaller ones, each with a upper bound of 2^31-1 bytes.
> > Or PnetCDF can simply throw an error, like MPI-IO.
> >
> > Any suggestion?
> >
> > Wei-keng
> >
> > On Feb 17, 2013, at 1:34 PM, Jim Edwards wrote:
> >
> > > Found the problem in the test program, a corrected program is
> attached.   This reminds me of another issue - the interface to
> nfmpi_iput_vara is not defined in pnetcdf.mod
> > >
> > > - Jim
> > >
> > > On Sun, Feb 17, 2013 at 11:43 AM, Jim Edwards <jedwards at ucar.edu>
> wrote:
> > > In my larger program I am getting an error:
> > >
> > > PMPI_Type_create_struct(139): Invalid value for blocklen, must be
> non-negative but is -1715470336
> > >
> > > I see a note about this in nonblocking.c:
> > >
> > >     for (j=0; j<reqs[i].varp->ndims; j++)
> > >                 blocklens[i] *= reqs[i].count[j];
> > >             /* Warning! blocklens[i] might overflow */
> > >
> > >
> > > But I tried to distile this into a small testcase and I'm getting a
> different error, I've attached the test program anyway because I can't spot
> any error there and think it must be in pnetcdf.    Also it seems like
> instead of
> > > calling mpi_type_create_struct you should be calling mpi_type_subarray
> which will avoid the problem of blocklens overflowing.
> > >
> > > This test program is written for 8 mpi tasks, but it uses a lot of
> memory so you may need more than one node to run it.
> > >
> > > --
> > > 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
> > > <testpnetcdf5.F90>
> >
> >
> >
> >
> > --
> > Jim Edwards
> >
> >
> > <testpnetcdf5.F90>
>
>
>


-- 

Jim Edwards
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