Skip to content

Commit

Permalink
finally fixed NULL stride issues
Browse files Browse the repository at this point in the history
  • Loading branch information
@edhartnett
edhartnett committed Jan 30, 2019
1 parent 254b32e commit 04c6110
Show file tree
Hide file tree
Showing 2 changed files with 86 additions and 42 deletions.
126 changes: 85 additions & 41 deletions src/clib/pio_getput_int.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -495,6 +495,8 @@ int PIOc_get_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
char start_present = start ? true : false;
char count_present = count ? true : false;
char stride_present = stride ? true : false;
PIO_Offset one = 1; /* For fake_stride. */
PIO_Offset *fake_stride = &one; /* Needed for NULL stride bug in netcdf-4.6.2. */
int mpierr = MPI_SUCCESS, mpierr2; /* Return code from MPI function codes. */
int ierr; /* Return code. */

Expand Down Expand Up @@ -601,12 +603,29 @@ int PIOc_get_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
check_mpi(file, mpierr, __FILE__, __LINE__);
if ((mpierr = MPI_Bcast(&xtype, 1, MPI_INT, ios->comproot, ios->my_comm)))
check_mpi(file, mpierr, __FILE__, __LINE__);
if ((mpierr = MPI_Bcast(&ndims, 1, MPI_INT, ios->comproot, ios->my_comm)))
check_mpi(file, mpierr, __FILE__, __LINE__);
}

if (ndims)
{
if (!stride_present)
{
LOG((2, "stride not present "));
if (!(fake_stride = malloc(ndims * sizeof(PIO_Offset))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
for (int d = 0; d < ndims; d++)
fake_stride[d] = 1;
}
else
fake_stride = (PIO_Offset *)stride;
}

/* If this is an IO task, then call the netCDF function. */
if (ios->ioproc)
{
LOG((2, "file->iotype = %d xtype = %d file->do_io = %d", file->iotype, xtype, file->do_io));

LOG((2, "file->iotype = %d xtype = %d file->do_io = %d", file->iotype, xtype, file->do_io));
#ifdef _PNETCDF
if (file->iotype == PIO_IOTYPE_PNETCDF)
{
Expand Down Expand Up @@ -653,69 +672,90 @@ int PIOc_get_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
}
#endif /* _PNETCDF */

LOG((2, "duck ndims %d", ndims));
for (int d = 0; d < ndims; d++)
{
LOG((2, "start[%d] %d", d, start[d]));
LOG((2, "count[%d] %d", d, count[d]));
LOG((2, "fake_stride[%d] %d", d, fake_stride[d]));
}

if (file->iotype != PIO_IOTYPE_PNETCDF && file->do_io)
{
switch(xtype)
{
case NC_BYTE:
ierr = nc_get_vars_schar(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_CHAR:
ierr = nc_get_vars_text(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_SHORT:
ierr = nc_get_vars_short(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_INT:
ierr = nc_get_vars_int(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case PIO_LONG_INTERNAL:
ierr = nc_get_vars_long(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_FLOAT:
ierr = nc_get_vars_float(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_DOUBLE:
ierr = nc_get_vars_double(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
#ifdef _NETCDF4
case NC_UBYTE:
ierr = nc_get_vars_uchar(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_USHORT:
ierr = nc_get_vars_ushort(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_UINT:
ierr = nc_get_vars_uint(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_INT64:
LOG((3, "about to call nc_get_vars_longlong"));
ierr = nc_get_vars_longlong(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_UINT64:
ierr = nc_get_vars_ulonglong(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
/* case NC_STRING: */
/* ierr = nc_get_vars_string(file->fh, varid, (size_t *)start, (size_t *)count, */
/* (ptrdiff_t *)stride, (void *)buf); */
/* (ptrdiff_t *)fake_stride, (void *)buf); */
/* break; */
#endif /* _NETCDF4 */
default:
return pio_err(ios, file, PIO_EBADTYPE, __FILE__, __LINE__);
}
}

}

LOG((2, "howdy ndims %d", ndims));
for (int d = 0; d < ndims; d++)
{
LOG((2, "fake_stride[%d] %d", d, fake_stride[d]));
}

/* Free malloced resources. */
if (ndims && !stride_present)
free(fake_stride);

/* Broadcast and check the return code. */
if ((mpierr = MPI_Bcast(&ierr, 1, MPI_INT, ios->ioroot, ios->my_comm)))
return check_mpi(file, mpierr, __FILE__, __LINE__);
Expand Down Expand Up @@ -1012,6 +1052,20 @@ int PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
/* If this is an IO task, then call the netCDF function. */
if (ios->ioproc)
{
if (ndims)
{
if (!stride_present)
{
LOG((2, "stride not present"));
if (!(fake_stride = malloc(ndims * sizeof(PIO_Offset))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
for (int d = 0; d < ndims; d++)
fake_stride[d] = 1;
}
else
fake_stride = (PIO_Offset *)stride;
}

#ifdef _PNETCDF
if (file->iotype == PIO_IOTYPE_PNETCDF)
{
Expand Down Expand Up @@ -1069,17 +1123,6 @@ int PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
var_desc_t *vdesc;
int *request;

if (!stride_present)
{
LOG((2, "stride not present"));
if (!(fake_stride = malloc(ndims * sizeof(PIO_Offset))))
return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
for (int d = 0; d < ndims; d++)
fake_stride[d] = 1;
}
else
fake_stride = (PIO_Offset *)stride;

LOG((2, "PIOc_put_vars_tc calling pnetcdf function"));
/*vdesc = &file->varlist[varid];*/
if ((ierr = get_var_desc(varid, &file->varlist, &vdesc)))
Expand Down Expand Up @@ -1129,9 +1172,6 @@ int PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
flush_output_buffer(file, false, 0);
LOG((2, "PIOc_put_vars_tc flushed output buffer"));

/* Free malloced resources. */
if (!stride_present)
free(fake_stride);
} /* endif ndims == 0 */
}
#endif /* _PNETCDF */
Expand All @@ -1144,63 +1184,67 @@ int PIOc_put_vars_tc(int ncid, int varid, const PIO_Offset *start, const PIO_Off
{
case NC_BYTE:
ierr = nc_put_vars_schar(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_CHAR:
ierr = nc_put_vars_text(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_SHORT:
ierr = nc_put_vars_short(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_INT:
ierr = nc_put_vars_int(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case PIO_LONG_INTERNAL:
ierr = nc_put_vars_long(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_FLOAT:
ierr = nc_put_vars_float(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_DOUBLE:
ierr = nc_put_vars_double(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
#ifdef _NETCDF4
case NC_UBYTE:
ierr = nc_put_vars_uchar(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_USHORT:
ierr = nc_put_vars_ushort(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_UINT:
ierr = nc_put_vars_uint(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_INT64:
ierr = nc_put_vars_longlong(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
case NC_UINT64:
ierr = nc_put_vars_ulonglong(file->fh, varid, (size_t *)start, (size_t *)count,
(ptrdiff_t *)stride, buf);
(ptrdiff_t *)fake_stride, buf);
break;
/* case NC_STRING: */
/* ierr = nc_put_vars_string(file->fh, varid, (size_t *)start, (size_t *)count, */
/* (ptrdiff_t *)stride, (void *)buf); */
/* (ptrdiff_t *)fake_stride, (void *)buf); */
/* break; */
#endif /* _NETCDF4 */
default:
return pio_err(ios, file, PIO_EBADTYPE, __FILE__, __LINE__);
}
LOG((2, "PIOc_put_vars_tc io_rank 0 done with netcdf call, ierr=%d", ierr));
}

/* Free malloced resources. */
if (ndims && !stride_present)
free(fake_stride);
}

/* Broadcast and check the return code. */
Expand Down
2 changes: 1 addition & 1 deletion tests/cunit/Makefile.am
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# Link to our assembled library.
AM_LDFLAGS = ${top_builddir}/src/clib/libpio.la
AM_CPPFLAGS = -I$(top_srcdir)/src/clib

LDADD = ${top_builddir}/src/clib/libpio.la

# Build the tests for make check.
check_PROGRAMS = test_intercomm2 test_async_mpi test_spmd \
Expand Down

0 comments on commit 04c6110

Please sign in to comment.