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!
! Copyright (C) 2015, Northwestern University
! See COPYRIGHT notice in top-level directory.
!
! $Id$
!
! This example shows how to use
! 1. nfmpi_set_fill() to enable fill mode
! 2. nfmpi_def_var_fill() to define the variable's fill value
! 3. nfmpi_inq_var_fill() to inquire the variable's fill mode information
! 4. nfmpi_put_vara_int_all() to write two 2D 4-byte integer array in parallel.
! It first defines a netCDF record variable of size global_nx * NFMPI_UNLIMITED
! where
! global_nx == (nx * number of MPI processes) and
! It then defines a netCDF variable of size global_nx * global_ny where
! global_nx == (nx * number of MPI processes) and
! global_ny == ny
! The data partitioning pattern for both variables are a column-wise
! partitioning across all processes. Each process writes a subarray of size
! nx * ny. Note the description above follows the Fortran array index order.
!
! Example commands for MPI run and outputs from running ncmpidump on the
! NC file produced by this example program:
!
! % mpif77 -O2 -o fill_mode fill_mode.f -lpnetcdf
! % mpiexec -n 4 ./fill_mode /pvfs2/wkliao/testfile.nc
!
! % ncmpidump /pvfs2/wkliao/testfile.nc
! netcdf testfile {
! // file format: CDF-5 (big variables)
! dimensions:
! REC_DIM = UNLIMITED ; // (2 currently)
! X = 20 ;
! Y = 3 ;
! variables:
! int rec_var(REC_DIM, X) ;
! rec_var:_FillValue = -1 ;
! int fix_var(Y, X) ;
! fix_var:_FillValue = -2147483647 ;
! data:
!
! rec_var =
! 0, 0, 0, 0, _, 1, 1, 1, 1, _, 2, 2, 2, 2, _, 3, 3, 3, 3, _,
! 0, 0, 0, 0, _, 1, 1, 1, 1, _, 2, 2, 2, 2, _, 3, 3, 3, 3, _ ;
!
! fix_var =
! 0, 0, 0, 0, _, 1, 1, 1, 1, _, 2, 2, 2, 2, _, 3, 3, 3, 3, _,
! 0, 0, 0, 0, _, 1, 1, 1, 1, _, 2, 2, 2, 2, _, 3, 3, 3, 3, _,
! 0, 0, 0, 0, _, 1, 1, 1, 1, _, 2, 2, 2, 2, _, 3, 3, 3, 3, _ ;
! }
!
subroutine check(err, message)
implicit none
include 'mpif.h'
include 'pnetcdf.inc'
integer err
character message*(*)
! It is a good idea to check returned value for possible error
if (err .NE. NF_NOERR) then
write(6,*) message//' '//nfmpi_strerror(err)
call MPI_Abort(MPI_COMM_WORLD, -1, err)
end if
end ! subroutine check
program main
implicit none
include 'mpif.h'
include 'pnetcdf.inc'
character*256 filename, cmd
integer i, j, err, ierr, nprocs, rank, get_args
integer cmode, ncid, rec_varid, fix_varid, dimid(2)
integer no_fill, fill_value, old_mode
integer*8 nx, ny, global_nx, global_ny, one
integer*8 starts(2), counts(2)
PARAMETER(nx=5, ny=3)
integer buf(nx,ny)
integer*8 malloc_size, sum_size
logical verbose
integer dummy
call MPI_Init(err)
call MPI_Comm_rank(MPI_COMM_WORLD, rank, err)
call MPI_Comm_size(MPI_COMM_WORLD, nprocs, err)
one = 1
! take filename from command-line argument if there is any
if (rank .EQ. 0) then
verbose = .TRUE.
filename = "testfile.nc"
ierr = get_args(2, cmd, filename, verbose, dummy)
endif
call MPI_Bcast(ierr, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, err)
if (ierr .EQ. 0) goto 999
call MPI_Bcast(verbose, 1, MPI_LOGICAL, 0, MPI_COMM_WORLD,
+ err)
call MPI_Bcast(filename, 256, MPI_CHARACTER, 0,
+ MPI_COMM_WORLD, err)
! set parameters
global_nx = nx * nprocs
global_ny = ny
do i=1, ny
do j=1, nx
buf(j,i) = rank
enddo
enddo
! create file, truncate it if exists
cmode = IOR(NF_CLOBBER, NF_64BIT_DATA)
err = nfmpi_create(MPI_COMM_WORLD, filename, cmode,
+ MPI_INFO_NULL, ncid)
call check(err, 'In nfmpi_create: ')
! define dimensions x and y
err = nfmpi_def_dim(ncid, "REC_DIM", NFMPI_UNLIMITED,dimid(2))
call check(err, 'In nfmpi_def_dim REC_DIM: ')
err = nfmpi_def_dim(ncid, "X", global_nx, dimid(1))
call check(err, 'In nfmpi_def_dim X: ')
! define a 2D record variable of integer type
err = nfmpi_def_var(ncid, "rec_var", NF_INT, 2, dimid,
+ rec_varid)
call check(err, 'In nfmpi_def_var: ')
err = nfmpi_def_dim(ncid, "Y", global_ny, dimid(2))
call check(err, 'In nfmpi_def_dim Y: ')
! define a 2D fixed-size variable of integer type
err = nfmpi_def_var(ncid, "fix_var", NF_INT, 2, dimid,
+ fix_varid)
call check(err, 'In nfmpi_def_var: ')
! set the fill mode to NF_FILL for entire file
err = nfmpi_set_fill(ncid, NF_FILL, old_mode)
call check(err, 'In nfmpi_set_fill: ')
if (verbose) then
if (old_mode .EQ. NF_FILL) then
print*,"The old fill mode is NF_FILL"
else
print*,"The old fill mode is NF_NOFILL"
endif
endif
! set the fill mode back to NF_NOFILL for entire file
err = nfmpi_set_fill(ncid, NF_NOFILL, old_mode)
call check(err, 'In nfmpi_set_fill: ')
! set the variable's fill mode to NF_FILL with default fill value
err = nfmpi_def_var_fill(ncid, fix_varid, 0, NF_FILL_INT)
call check(err, 'In nfmpi_def_var_fill: ')
! set a customized fill value -1
fill_value = -1
err = nfmpi_put_att_int(ncid, rec_varid, "_FillValue", NF_INT,
+ one, fill_value)
call check(err, 'In nfmpi_put_att_int: ')
! do not forget to exit define mode
err = nfmpi_enddef(ncid)
call check(err, 'In nfmpi_enddef: ')
! now we are in data mode
! Note that in Fortran, array indices start with 1
starts(1) = nx * rank + 1
starts(2) = 1
counts(1) = nx
counts(2) = ny
! do not write the variable in full
counts(1) = counts(1) - 1
err = nfmpi_put_vara_int_all(ncid, fix_varid, starts, counts,
+ buf)
call check(err, 'In nfmpi_put_vara_int_all: ')
err = nfmpi_inq_var_fill(ncid, fix_varid, no_fill, fill_value)
if (no_fill .NE. 0) then
print*,"Error: expecting no_fill to be 0"
stop 2
endif
if (fill_value .NE. NF_FILL_INT) then
print*,"Error: expecting no_fill to be ",NF_FILL_INT,
+ " but got ", fill_value
stop 2
endif
! fill the 1st record of the record variable
starts(2) = 1
err = nfmpi_fill_var_rec(ncid, rec_varid, starts(2))
call check(err, 'In nfmpi_fill_var_rec: ')
! write to the 1st record
counts(2) = 1
err = nfmpi_put_vara_int_all(ncid, rec_varid, starts, counts,
+ buf)
call check(err, 'In nfmpi_put_vara_int_all: ')
! fill the 2nd record of the record variable
starts(2) = 2
err = nfmpi_fill_var_rec(ncid, rec_varid, starts(2))
call check(err, 'In nfmpi_fill_var_rec: ')
! write to the 2nd record
err = nfmpi_put_vara_int_all(ncid, rec_varid, starts, counts,
+ buf)
call check(err, 'In nfmpi_put_vara_int_all: ')
! close the file
err = nfmpi_close(ncid)
call check(err, 'In nfmpi_close: ')
! check if there is any PnetCDF internal malloc residue
998 format(A,I13,A)
err = nfmpi_inq_malloc_size(malloc_size)
if (err .EQ. NF_NOERR) then
call MPI_Reduce(malloc_size, sum_size, 1, MPI_INTEGER8,
+ MPI_SUM, 0, MPI_COMM_WORLD, err)
if (rank .EQ. 0 .AND. sum_size .GT. 0)
+ print 998,
+ 'heap memory allocated by PnetCDF internally has ',
+ sum_size/1048576, ' MiB yet to be freed'
endif
999 call MPI_Finalize(err)
! call EXIT(0) ! EXIT() is a GNU extension
end ! program main
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