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!
! Copyright (C) 2012, Northwestern University and Argonne National Laboratory
! See COPYRIGHT notice in top-level directory.
!
! $Id$
! This example makes a number of nonblocking API calls, each writes a single
! row of a 2D integer array. Each process writes NY rows and any two
! consecutive rows are of nprocs-row distance apart from each other.
! In this case, the fileview of each process interleaves with all other processes.
! If simply concatenating fileviews of all the nonblocking calls will result
! in a fileview that violates the MPI-IO requirement on the fileview of which
! flattened file offsets must be monotonically non-decreasing. PnetCDF handles
! this case by breaking down each nonblocking call into a list of offset-length
! pairs, merging the pairs across multiple nonblocking calls, and sorting
! them into an increasing order. The sorted pairs are used to construct a
! fileview that meets the monotonically non-decreasing offset requirement,
! and thus the nonblocking requests can be serviced by a single MPI-IO call.
!
! The compile and run commands are given below, together with an ncmpidump of
! the output file. Note ncdump is in C order (row major).
!
! % mpif77 -O2 -o column_wise column_wise.f -lpnetcdf
! % mpiexec -n 4 ./column_wise /pvfs2/wkliao/testfile.nc
!
! % ncmpidump /pvfs2/wkliao/testfile.nc
! netcdf testfile {
! // file format: CDF-5 (big variables)
! dimensions:
! Y = 10 ;
! X = 16 ;
! variables:
! int var(Y, X) ;
! data:
!
! var =
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3,
! 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 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"
integer NY, NX
PARAMETER(NX=10, NY=4)
character*256 filename, cmd
integer i, j, rank, nprocs, err, ierr, num_reqs, get_args
integer ncid, cmode, varid, dimid(2)
integer buf(NX, NY)
integer reqs(NY), sts(NY)
integer*8 G_NY, myOff, block_start, block_len, global_nx
integer*8 start(2), count(2)
integer*8 malloc_size, sum_size
logical verbose
integer dummy, info
call MPI_Init(err)
call MPI_Comm_rank(MPI_COMM_WORLD, rank, err)
call MPI_Comm_size(MPI_COMM_WORLD, nprocs, err)
! 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 an MPI-IO hint to disable file offset alignment for
! fixed-size variables
call MPI_Info_create(info, err)
call MPI_Info_set(info, "nc_var_align_size", "1", err)
! 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: ')
call MPI_Info_free(info, err)
! the global array is NX * (NY * nprocs) */
G_NY = NY * nprocs
myOff = NY * rank
! define dimensions
global_nx = NX
err = nfmpi_def_dim(ncid, 'Y', global_nx, dimid(2))
call check(err, 'In nfmpi_def_dim Y')
err = nfmpi_def_dim(ncid, 'X', G_NY, dimid(1))
call check(err, 'In nfmpi_def_dim X')
err = nfmpi_def_var(ncid, 'var', NF_INT, 2, dimid, varid)
call check(err, 'In nfmpi_def_var var')
! do not forget to exit define mode
err = nfmpi_enddef(ncid)
call check(err, 'In nfmpi_enddef: ')
! First, fill the entire array with zeros, using a blocking I/O.
! Every process writes a subarray of size NX * NY
do i=1, NY
do j=1, NX
buf(j,i) = 0
enddo
enddo
start(1) = myOff+1
start(2) = 1
count(1) = NY
count(2) = NX
err = nfmpi_put_vara_int_all(ncid, varid, start, count, buf)
call check(err, 'In nfmpi_put_vara_int_all: ')
err = nfmpi_flush(ncid)
call check(err, 'In nfmpi_flush: ')
! initialize the buffer with rank ID
do i=1, NY
do j=1, NX
buf(j,i) = rank
enddo
enddo
! each proc writes NY columns of the 2D array, block_len controls the
! the number of contiguous columns at a time
block_start = 0
block_len = 2 ! can be 1, 2, 3, ..., NY
if (block_len .GT. NY) block_len = NY
start(1) = rank + 1
start(2) = 1
count(1) = 1
count(2) = NX
num_reqs = 0
do i=1, NY
num_reqs = num_reqs + 1
err = nfmpi_iput_vara_int(ncid, varid, start, count,
+ buf(1,i), reqs(num_reqs))
call check(err, 'In nfmpi_iput_vara_int: ')
start(1) = start(1) + nprocs
enddo
err = nfmpi_wait_all(ncid, num_reqs, reqs, sts)
call check(err, 'In nfmpi_wait_all: ')
! check status of all requests
do i=1, num_reqs
if (sts(i) .NE. NF_NOERR) then
print*, "Error: nonblocking write fails on request",
+ i, ' ', nfmpi_strerror(sts(i))
stop 2
endif
enddo
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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