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Add optional force_nofill to skip needsfill #2027

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7994c8e
Add optional force_nofill to skip needsfill
sdbachman Aug 5, 2026
ae4fb25
Merge branch 'main' into needsfill_skip
sdbachman Aug 5, 2026
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20 changes: 17 additions & 3 deletions src/clib/pio.h
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Original file line number Diff line number Diff line change
Expand Up @@ -317,6 +317,11 @@ typedef struct io_desc_t
* everywhere (false) */
bool needsfill;

/** If true, skip the needsfill coverage check and force
* needsfill=false. Set via PIOc_InitDecomp_flags /
* PIOc_InitDecomp_bc_flags (or Fortran force_nofill). */
bool force_nofill;

/** If the map is not monotonically increasing we will need to
* sort it. */
bool needssort;
Expand Down Expand Up @@ -823,10 +828,19 @@ extern "C" {
const PIO_Offset *compmap, int *ioidp, const int *rearr,
const PIO_Offset *iostart, const PIO_Offset *iocount);
int PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int maplen,
const PIO_Offset *compmap, int *ioidp, const int *rearr,
const PIO_Offset *iostart, const PIO_Offset *iocount);
const PIO_Offset *compmap, int *ioidp, const int *rearr,
const PIO_Offset *iostart, const PIO_Offset *iocount);
/** Like PIOc_InitDecomp, but force_nofill!=0 skips the needsfill check. */
int PIOc_InitDecomp_flags(int iosysid, int pio_type, int ndims, const int *gdimlen, int maplen,
const PIO_Offset *compmap, int *ioidp, const int *rearr,
const PIO_Offset *iostart, const PIO_Offset *iocount,
int force_nofill);
int PIOc_InitDecomp_bc(int iosysid, int basetype, int ndims, const int *gdimlen,
const long int *start, const long int *count, int *ioidp);
const long int *start, const long int *count, int *ioidp);
/** Like PIOc_InitDecomp_bc, but force_nofill!=0 skips the needsfill check. */
int PIOc_InitDecomp_bc_flags(int iosysid, int basetype, int ndims, const int *gdimlen,
const long int *start, const long int *count, int *ioidp,
int force_nofill);

/* Init decomposition with 0-based compmap array. */
int PIOc_init_decomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int maplen,
Expand Down
11 changes: 8 additions & 3 deletions src/clib/pio_rearrange.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1141,6 +1141,14 @@ determine_fill(iosystem_desc_t *ios, io_desc_t *iodesc, const int *gdimlen,
pioassert(ios && iodesc && gdimlen && compmap, "invalid input",
__FILE__, __LINE__);

/* Application requested skip of the coverage / hole-fill path. */
if (iodesc->force_nofill)
{
iodesc->needsfill = false;
PLOG((2, "determine_fill: force_nofill set, needsfill forced false"));
return PIO_NOERR;
}

/* Determine size of data space. */
for (int i = 0; i < iodesc->ndims; i++)
totalgridsize *= gdimlen[i];
Expand All @@ -1165,9 +1173,6 @@ determine_fill(iosystem_desc_t *ios, io_desc_t *iodesc, const int *gdimlen,
* total data size then we need fill values. */
iodesc->needsfill = totalllen < totalgridsize;

/* TURN OFF FILL for timing test
iodesc->needsfill=false; */

return PIO_NOERR;
}

Expand Down
56 changes: 48 additions & 8 deletions src/clib/pioc.c
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Original file line number Diff line number Diff line change
Expand Up @@ -500,14 +500,32 @@ int
PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int maplen,
const PIO_Offset *compmap, int *ioidp, const int *rearranger,
const PIO_Offset *iostart, const PIO_Offset *iocount)
{
return PIOc_InitDecomp_flags(iosysid, pio_type, ndims, gdimlen, maplen, compmap,
ioidp, rearranger, iostart, iocount, 0);
}

/**
* Same as PIOc_InitDecomp(), with optional force_nofill.
*
* If force_nofill is non-zero, skip the needsfill coverage check and
* force needsfill=false for this decomposition.
*
* @param force_nofill non-zero to skip needsfill check
*/
int
PIOc_InitDecomp_flags(int iosysid, int pio_type, int ndims, const int *gdimlen, int maplen,
const PIO_Offset *compmap, int *ioidp, const int *rearranger,
const PIO_Offset *iostart, const PIO_Offset *iocount,
int force_nofill)
{
iosystem_desc_t *ios; /* Pointer to io system information. */
io_desc_t *iodesc; /* The IO description. */
int mpierr = MPI_SUCCESS, mpierr2; /* Return code from MPI function calls. */
int ierr; /* Return code. */

PLOG((1, "PIOc_InitDecomp iosysid = %d pio_type = %d ndims = %d maplen = %d",
iosysid, pio_type, ndims, maplen));
PLOG((1, "PIOc_InitDecomp_flags iosysid = %d pio_type = %d ndims = %d maplen = %d force_nofill = %d",
iosysid, pio_type, ndims, maplen, force_nofill));

#ifdef USE_MPE
pio_start_mpe_log(DECOMP);
Expand Down Expand Up @@ -566,8 +584,10 @@ PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int ma
mpierr = MPI_Bcast(&iocount_present, 1, MPI_CHAR, ios->compmain, ios->intercomm);
if (iocount_present && !mpierr)
mpierr = MPI_Bcast((PIO_Offset *)iocount, ndims, MPI_OFFSET, ios->compmain, ios->intercomm);
PLOG((2, "PIOc_InitDecomp iosysid = %d pio_type = %d ndims = %d maplen = %d rearranger_present = %d iostart_present = %d "
"iocount_present = %d ", iosysid, pio_type, ndims, maplen, rearranger_present, iostart_present, iocount_present));
if (!mpierr)
mpierr = MPI_Bcast(&force_nofill, 1, MPI_INT, ios->compmain, ios->intercomm);
PLOG((2, "PIOc_InitDecomp_flags iosysid = %d pio_type = %d ndims = %d maplen = %d rearranger_present = %d iostart_present = %d "
"iocount_present = %d force_nofill = %d", iosysid, pio_type, ndims, maplen, rearranger_present, iostart_present, iocount_present, force_nofill));
}

/* Handle MPI errors. */
Expand All @@ -588,6 +608,9 @@ PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int ma
if ((ierr = malloc_iodesc(ios, pio_type, ndims, &iodesc)))
return pio_err(ios, NULL, ierr, __FILE__, __LINE__);

/* Optional: skip needsfill coverage check for this decomp. */
iodesc->force_nofill = (force_nofill != 0);

/* Remember the maplen. */
iodesc->maplen = maplen;

Expand Down Expand Up @@ -648,7 +671,7 @@ PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int ma
iodesc->rearranger = ios->default_rearranger;
else
iodesc->rearranger = *rearranger;
PLOG((2, "iodesc->rearranger = %d", iodesc->rearranger));
PLOG((2, "iodesc->rearranger = %d force_nofill = %d", iodesc->rearranger, iodesc->force_nofill));

/* Is this the subset rearranger? */
if (iodesc->rearranger == PIO_REARR_SUBSET)
Expand Down Expand Up @@ -1166,14 +1189,31 @@ PIOc_init_decomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int m
int
PIOc_InitDecomp_bc(int iosysid, int pio_type, int ndims, const int *gdimlen,
const long int *start, const long int *count, int *ioidp)
{
return PIOc_InitDecomp_bc_flags(iosysid, pio_type, ndims, gdimlen, start, count,
ioidp, 0);
}

/**
* Same as PIOc_InitDecomp_bc(), with optional force_nofill.
*
* If force_nofill is non-zero, skip the needsfill coverage check and
* force needsfill=false for this decomposition.
*
* @param force_nofill non-zero to skip needsfill check
*/
int
PIOc_InitDecomp_bc_flags(int iosysid, int pio_type, int ndims, const int *gdimlen,
const long int *start, const long int *count, int *ioidp,
int force_nofill)
{
iosystem_desc_t *ios;
int n, i, maplen = 1;
PIO_Offset prod[ndims], loc[ndims];
int rearr = PIO_REARR_SUBSET;

PLOG((1, "PIOc_InitDecomp_bc iosysid = %d pio_type = %d ndims = %d"));
PLOG((1, "PIOc_InitDecomp_bc_flags iosysid = %d pio_type = %d ndims = %d force_nofill = %d",
iosysid, pio_type, ndims, force_nofill));

/* Get the info about the io system. */
if (!(ios = pio_get_iosystem_from_id(iosysid)))
Expand Down Expand Up @@ -1219,8 +1259,8 @@ PIOc_InitDecomp_bc(int iosysid, int pio_type, int ndims, const int *gdimlen,
}
}

return PIOc_InitDecomp(iosysid, pio_type, ndims, gdimlen, maplen, compmap, ioidp,
&rearr, NULL, NULL);
return PIOc_InitDecomp_flags(iosysid, pio_type, ndims, gdimlen, maplen, compmap, ioidp,
&rearr, NULL, NULL, force_nofill);
}

/**
Expand Down
62 changes: 42 additions & 20 deletions src/flib/piolib_mod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -529,19 +529,23 @@ end subroutine seterrorhandlingiosysid
!! @param compcount The count for the block-cyclic computational
!! decomposition
!! @param iodesc @copydoc iodesc_generate
!! @param force_nofill Optional. If present and .true., skip the
!! needsfill coverage check and force needsfill=false.
!! @author Jim Edwards
!<
subroutine PIO_initdecomp_bc(iosystem,basepiotype,dims,compstart,compcount,iodesc)
subroutine PIO_initdecomp_bc(iosystem,basepiotype,dims,compstart,compcount,iodesc,force_nofill)
type (iosystem_desc_t), intent(inout) :: iosystem
integer(i4), intent(in) :: basepiotype
integer(i4), intent(in) :: dims(:)
integer (kind=PIO_OFFSET_KIND) :: compstart(:)
integer (kind=PIO_OFFSET_KIND) :: compcount(:)
type (IO_desc_t), intent(out) :: iodesc
logical, optional, intent(in) :: force_nofill

interface
integer(C_INT) function PIOc_InitDecomp_bc(iosysid, basetype, ndims, dims, compstart, compcount, ioidp) &
bind(C,name="PIOc_InitDecomp_bc")
integer(C_INT) function PIOc_InitDecomp_bc_flags(iosysid, basetype, ndims, dims, &
compstart, compcount, ioidp, force_nofill) &
bind(C,name="PIOc_InitDecomp_bc_flags")
use iso_c_binding
integer(C_INT), value :: iosysid
integer(C_INT), value :: basetype
Expand All @@ -550,12 +554,14 @@ integer(C_INT) function PIOc_InitDecomp_bc(iosysid, basetype, ndims, dims, comps
integer(C_INT) :: ioidp
integer(C_SIZE_T) :: compstart(*)
integer(C_SIZE_T) :: compcount(*)
end function PIOc_InitDecomp_bc
integer(C_INT), value :: force_nofill
end function PIOc_InitDecomp_bc_flags
end interface
integer :: i, ndims
integer, allocatable :: cdims(:)
integer(PIO_Offset_kind), allocatable :: cstart(:), ccount(:)
integer :: ierr
integer(C_INT) :: c_force_nofill

ndims = size(dims)

Expand All @@ -567,8 +573,13 @@ end function PIOc_InitDecomp_bc
ccount(i) = compcount(ndims-i+1)
end do

ierr = PIOc_InitDecomp_bc(iosystem%iosysid, basepiotype, ndims, cdims, &
cstart, ccount, iodesc%ioid)
c_force_nofill = 0
if (present(force_nofill)) then
if (force_nofill) c_force_nofill = 1
end if

ierr = PIOc_InitDecomp_bc_flags(iosystem%iosysid, basepiotype, ndims, cdims, &
cstart, ccount, iodesc%ioid, c_force_nofill)

deallocate(cstart, ccount, cdims)

Expand Down Expand Up @@ -831,7 +842,7 @@ end subroutine initdecomp_1dof_nf_i8
!! @param iocount The count for the block-cyclic io decomposition
!! @author Jim Edwards
!<
subroutine PIO_initdecomp_dof_i4(iosystem, basepiotype, dims, compdof, iodesc, rearr, iostart, iocount)
subroutine PIO_initdecomp_dof_i4(iosystem, basepiotype, dims, compdof, iodesc, rearr, iostart, iocount, force_nofill)
type (iosystem_desc_t), intent(inout) :: iosystem
integer(i4), intent(in) :: basepiotype
integer(i4), intent(in) :: compdof(:) ! global degrees of freedom for computational decomposition
Expand All @@ -840,21 +851,23 @@ subroutine PIO_initdecomp_dof_i4(iosystem, basepiotype, dims, compdof, iodesc, r
type (io_desc_t), intent(inout) :: iodesc
integer(PIO_OFFSET_KIND), pointer :: internal_compdof(:)
integer(i4), intent(in) :: dims(:)
logical, optional, intent(in) :: force_nofill

allocate(internal_compdof(size(compdof)))
internal_compdof = int(compdof,PIO_OFFSET_KIND)

if(present(iostart) .and. present(iocount) ) then
call pio_initdecomp_dof_i8(iosystem, basepiotype, dims, internal_compdof, iodesc, &
PIO_REARR_SUBSET, iostart, iocount)
PIO_REARR_SUBSET, iostart, iocount, force_nofill=force_nofill)
else
call pio_initdecomp_dof_i8(iosystem, basepiotype, dims, internal_compdof, iodesc, rearr)
call pio_initdecomp_dof_i8(iosystem, basepiotype, dims, internal_compdof, iodesc, rearr, &
force_nofill=force_nofill)
endif
deallocate(internal_compdof)

end subroutine PIO_initdecomp_dof_i4

subroutine PIO_initdecomp_internal(iosystem,basepiotype,dims,maplen, compdof, iodesc, rearr, iostart, iocount)
subroutine PIO_initdecomp_internal(iosystem,basepiotype,dims,maplen, compdof, iodesc, rearr, iostart, iocount, force_nofill)
type (iosystem_desc_t), intent(in) :: iosystem
integer(i4), intent(in) :: basepiotype
integer(i4), intent(in) :: dims(:)
Expand All @@ -863,16 +876,18 @@ subroutine PIO_initdecomp_internal(iosystem,basepiotype,dims,maplen, compdof, io
integer, optional, target :: rearr
integer (PIO_OFFSET_KIND), optional :: iostart(:), iocount(:)
type (io_desc_t), intent(inout) :: iodesc
logical, optional, intent(in) :: force_nofill

integer(c_int) :: ndims
integer(c_int), dimension(:), allocatable, target :: cdims
integer(PIO_OFFSET_KIND), dimension(:), allocatable, target :: cstart, ccount
integer(C_INT) :: c_force_nofill

type(C_PTR) :: crearr
interface
integer(C_INT) function PIOc_InitDecomp(iosysid,basetype,ndims,dims, &
maplen, compmap, ioidp, rearr, iostart, iocount) &
bind(C,name="PIOc_InitDecomp")
integer(C_INT) function PIOc_InitDecomp_flags(iosysid,basetype,ndims,dims, &
maplen, compmap, ioidp, rearr, iostart, iocount, force_nofill) &
bind(C,name="PIOc_InitDecomp_flags")
use iso_c_binding
integer(C_INT), value :: iosysid
integer(C_INT), value :: basetype
Expand All @@ -884,7 +899,8 @@ integer(C_INT) function PIOc_InitDecomp(iosysid,basetype,ndims,dims, &
type(C_PTR), value :: rearr
type(C_PTR), value :: iostart
type(C_PTR), value :: iocount
end function PIOc_InitDecomp
integer(C_INT), value :: force_nofill
end function PIOc_InitDecomp_flags
end interface
integer :: ierr,i

Expand All @@ -900,19 +916,24 @@ end function PIOc_InitDecomp
crearr = C_NULL_PTR
endif

c_force_nofill = 0
if (present(force_nofill)) then
if (force_nofill) c_force_nofill = 1
end if

if(present(iostart) .and. present(iocount)) then
allocate(cstart(ndims), ccount(ndims))
do i=1,ndims
cstart(i) = iostart(ndims-i+1)-1
ccount(i) = iocount(ndims-i+1)
end do

ierr = PIOc_InitDecomp(iosystem%iosysid, basepiotype, ndims, cdims, &
maplen, compdof, iodesc%ioid, crearr, C_LOC(cstart), C_LOC(ccount))
ierr = PIOc_InitDecomp_flags(iosystem%iosysid, basepiotype, ndims, cdims, &
maplen, compdof, iodesc%ioid, crearr, C_LOC(cstart), C_LOC(ccount), c_force_nofill)
deallocate(cstart, ccount)
else
ierr = PIOc_InitDecomp(iosystem%iosysid, basepiotype, ndims, cdims, &
maplen, compdof, iodesc%ioid, crearr, C_NULL_PTR, C_NULL_PTR)
ierr = PIOc_InitDecomp_flags(iosystem%iosysid, basepiotype, ndims, cdims, &
maplen, compdof, iodesc%ioid, crearr, C_NULL_PTR, C_NULL_PTR, c_force_nofill)
end if

deallocate(cdims)
Expand Down Expand Up @@ -1021,14 +1042,15 @@ end subroutine PIO_initdecomp_readonly
!! I8 version of PIO_initdecomp_dof_i4.
!! @author Jim Edwards
subroutine PIO_initdecomp_dof_i8(iosystem, basepiotype, dims, compdof, &
iodesc, rearr, iostart, iocount)
iodesc, rearr, iostart, iocount, force_nofill)
type (iosystem_desc_t), intent(in) :: iosystem
integer(i4), intent(in) :: basepiotype
integer(i4), intent(in) :: dims(:)
integer (PIO_OFFSET_KIND), intent(in) :: compdof(:) ! global degrees of freedom for computational decomposition
integer, optional, target :: rearr
integer (PIO_OFFSET_KIND), optional :: iostart(:), iocount(:)
type (io_desc_t), intent(inout) :: iodesc
logical, optional, intent(in) :: force_nofill
integer :: maplen

#ifdef TIMING
Expand All @@ -1038,7 +1060,7 @@ subroutine PIO_initdecomp_dof_i8(iosystem, basepiotype, dims, compdof, &
maplen = size(compdof)

call PIO_initdecomp_internal(iosystem, basepiotype, dims, maplen, &
compdof, iodesc, rearr, iostart, iocount)
compdof, iodesc, rearr, iostart, iocount, force_nofill)

#ifdef TIMING
call t_stopf("PIO:initdecomp_dof")
Expand Down