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pnetcdf_m.f90
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pnetcdf_m.f90
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!
! Copyright (C) 2013, Northwestern University
! See COPYRIGHT notice in top-level directory.
!
module pnetcdf_m
use mpi
use pnetcdf
use header
implicit none
integer ncid, dimid(5), varid
character(len=128) nc_filenm
integer(KIND=MPI_OFFSET_KIND) global_five_dbl, num_dumps
integer(KIND=MPI_OFFSET_KIND) put_size, get_size
integer, allocatable :: buftypes(:), reqs(:), sts(:)
logical doNonBlockingIO, doIndepIO, delayflush
double precision t_create, t_post_w, t_wait_w
double precision t_open, t_post_r, t_wait_r
private :: check
contains
!----< check() >-------------------------------------------------
subroutine check(err, message)
implicit none
integer err
character(len=*) message
! It is a good idea to check returned value for possible error
write(6,*) trim(message), trim(nfmpi_strerror(err))
call MPI_Abort(MPI_COMM_WORLD, -1, err)
end subroutine check
!----< create_buffer_type >--------------------------------------
subroutine create_buffer_type
implicit none
integer c, elemtype, err
integer sizes(3), gh_starts(3), subsizes(3)
! define MPI derived data type for local buffers
! Note dimensions of local cells, can differ slightly between cells
call MPI_Type_contiguous(5, MPI_DOUBLE_PRECISION, elemtype, err)
call MPI_Type_commit(elemtype, err)
! local array size
sizes(1) = IMAX+4
sizes(2) = JMAX+4
sizes(3) = KMAX+4
! (ghost length = 2 on both ends)
gh_starts(1) = 2
gh_starts(2) = 2
gh_starts(3) = 2
allocate(buftypes(ncells))
do c = 1, ncells
subsizes(1) = cell_size(1, c)
subsizes(2) = cell_size(2, c)
subsizes(3) = cell_size(3, c)
! Create buffer data type for a local cell
call MPI_Type_create_subarray(3, sizes, subsizes, gh_starts, &
MPI_ORDER_FORTRAN, elemtype, &
buftypes(c), err)
call MPI_Type_commit(buftypes(c), err)
enddo
call MPI_Type_free(elemtype, err)
end subroutine create_buffer_type
!----< pnetcdf_setup >-------------------------------------------
integer function pnetcdf_setup(io_mode, io_method)
implicit none
character io_mode ! 'w' for write and 'r' for read
integer io_method ! 2 for blocking I/O and 3 for nonblocking
! local variables
integer omode, info, err
double precision t
t_post_w = 0.0
t_wait_w = 0.0
t_post_r = 0.0
t_wait_r = 0.0
t = MPI_Wtime()
pnetcdf_setup = 1
if (io_method .GE. 10) then
io_method = io_method - 10
delayflush = .TRUE.
else
delayflush = .FALSE.
endif
if ((io_method .EQ. 2) .OR. (io_method .EQ. 4)) doNonBlockingIO = .FALSE.
if ((io_method .EQ. 3) .OR. (io_method .EQ. 5)) doNonBlockingIO = .TRUE.
if (io_method > 3) then
doIndepIO = .TRUE.
else
doIndepIO = .FALSE.
endif
call create_buffer_type
allocate(reqs(ncells))
allocate( sts(ncells))
nc_filenm = trim(dir_path)//'/btio.nc'
! disable data sieving for write operations
call MPI_Info_create(info, err)
call MPI_Info_set(info, 'romio_ds_write', 'disable', err)
call MPI_Info_set(info, 'romio_cb_write', 'enable', err)
call MPI_Info_set(info, "nc_var_align_size", "1", err);
call MPI_Info_set(info, "nc_in_place_swap", "enable", err);
if (io_mode .EQ. 'w') then
omode = IOR(NF_CLOBBER, NF_64BIT_DATA)
err = nfmpi_create(MPI_COMM_WORLD, nc_filenm, omode, &
info, ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_create:')
call pnetcdf_define
else
omode = NF_NOWRITE
err = nfmpi_open(MPI_COMM_WORLD, nc_filenm, omode, info, ncid)
if (err .ne. NF_NOERR) then
pnetcdf_setup = 0
if (err .EQ. NF_ENOENT) then
write(6,*)'Error: file does not exit'
else
write(6,*)'Error (file open): ',trim(nfmpi_strerror(err))
endif
return
endif
call pnetcdf_inquiry
endif
call MPI_Info_free(info, err)
! get the info object used by MPI-IO library
err = nfmpi_get_file_info(ncid, info_used)
t = MPI_Wtime() - t
if (io_mode .EQ. 'w') then
t_create = t
else
t_open = t
endif
end function pnetcdf_setup
!----< pnetcdf_define >-------------------------------------------
subroutine pnetcdf_define
implicit none
integer err
! define dimensions
global_five_dbl = 5
err = nfmpi_def_dim(ncid, 'FIVE_DBL', global_five_dbl, dimid(1))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_dim FIVE_DBL')
err = nfmpi_def_dim(ncid, 'X', grid_points(1), dimid(2))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_dim X')
err = nfmpi_def_dim(ncid, 'Y', grid_points(2), dimid(3))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_dim Y')
err = nfmpi_def_dim(ncid, 'Z', grid_points(3), dimid(4))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_dim Z')
err = nfmpi_def_dim(ncid, 'NUM_DUMPS', NFMPI_UNLIMITED, dimid(5))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_dim NUM_DUMPS')
err = nfmpi_def_var(ncid, 'var', NF_DOUBLE, 5, dimid, varid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_def_var var')
! exit define mode
err = nfmpi_enddef(ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_enddef:')
if (doIndepIO) then
err = nfmpi_begin_indep_data(ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_begin_indep_data:')
endif
end subroutine pnetcdf_define
!----< pnetcdf_inquiry >-------------------------------------------
subroutine pnetcdf_inquiry
implicit none
integer err
! inquire dimension IDs and lengths
err = nfmpi_inq_dimid(ncid, 'FIVE_DBL', dimid(1))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimid FIVE_DBL')
err = nfmpi_inq_dimlen(ncid, dimid(1), global_five_dbl)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimlen X')
err = nfmpi_inq_dimid(ncid, 'X', dimid(2))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimid X')
err = nfmpi_inq_dimlen(ncid, dimid(2), grid_points(1))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimlen X')
err = nfmpi_inq_dimid(ncid, 'Y', dimid(3))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimid Y')
err = nfmpi_inq_dimlen(ncid, dimid(3), grid_points(2))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimlen Y')
err = nfmpi_inq_dimid(ncid, 'Z', dimid(4))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimid Z')
err = nfmpi_inq_dimlen(ncid, dimid(4), grid_points(3))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimlen Z')
err = nfmpi_inq_dimid(ncid, 'NUM_DUMPS', dimid(5))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimid NUM_DUMPS')
err = nfmpi_inq_dimlen(ncid, dimid(5), num_dumps)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_dimlen NUM_DUMPS')
! inquire variable ID
err = nfmpi_inq_varid(ncid, 'var', varid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_inq_varid')
end subroutine pnetcdf_inquiry
!---< pnetcdf_write >---------------------------------------------
subroutine pnetcdf_write
implicit none
integer c, err
integer(KIND=MPI_OFFSET_KIND) starts(6), counts(6), nReqs
double precision t_start, t_end
t_start = MPI_Wtime()
num_io = num_io + 1
nReqs = 1
do c = 1, ncells
starts(1) = 1
starts(2) = cell_low(1,c) + 1
starts(3) = cell_low(2,c) + 1
starts(4) = cell_low(3,c) + 1
starts(5) = num_io
counts(1) = 5
counts(2) = cell_size(1,c)
counts(3) = cell_size(2,c)
counts(4) = cell_size(3,c)
counts(5) = 1
if (doNonBlockingIO) then
if (delayflush) then
err = nfmpi_iput_vara(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c), %val(0))
else
err = nfmpi_iput_vara(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c), reqs(c))
endif
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_iput_vara:')
else
if (doIndepIO) then
err = nfmpi_put_vara(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_put_vara:')
else
err = nfmpi_put_vara_all(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_put_vara_all:')
endif
endif
enddo
t_end = MPI_Wtime()
t_post_w = t_post_w + t_end - t_start
t_start = t_end
if (.NOT. delayflush) then
if (doNonBlockingIO) then
if (doIndepIO) then
err = nfmpi_wait(ncid, ncells, reqs, sts)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_wait:')
else
err = nfmpi_wait_all(ncid, ncells, reqs, sts)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_wait_all:')
endif
else
err = nfmpi_flush(ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_flush:')
endif
endif
do c = 1, ncells
if (err .ne. NF_NOERR) &
call check(sts(c), 'In nfmpi_wait_all status error: ')
enddo
t_end = MPI_Wtime()
t_wait_w = t_wait_w + t_end - t_start
end subroutine pnetcdf_write
!---< pnetcdf_read >----------------------------------------------
subroutine pnetcdf_read
implicit none
integer c, err
integer(KIND=MPI_OFFSET_KIND) starts(6), counts(6), nReqs
double precision t_start, t_end
t_start = MPI_Wtime()
num_io = num_io + 1
nReqs = 1
do c = 1, ncells
starts(1) = 1
starts(2) = cell_low(1,c) + 1
starts(3) = cell_low(2,c) + 1
starts(4) = cell_low(3,c) + 1
starts(5) = num_io
counts(1) = 5
counts(2) = cell_size(1,c)
counts(3) = cell_size(2,c)
counts(4) = cell_size(3,c)
counts(5) = 1
if (doNonBlockingIO) then
err = nfmpi_iget_vara(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c), reqs(c))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_iget_vara:')
else
err = nfmpi_get_vara_all(ncid, varid, starts, counts, &
u(:,:,:,:,c), nReqs, buftypes(c))
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_get_vara_all:')
endif
enddo
t_end = MPI_Wtime()
t_post_r = t_post_r + t_end - t_start
t_start = t_end
if (doNonBlockingIO) then
err = nfmpi_wait_all(ncid, ncells, reqs, sts)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_wait_all:')
endif
do c = 1, ncells
if (err .ne. NF_NOERR) &
call check(sts(c), 'In nfmpi_wait_all status error: ')
enddo
t_end = MPI_Wtime()
t_wait_r = t_wait_r + t_end - t_start
end subroutine pnetcdf_read
!----< pnetcdf_cleanup >-----------------------------------------
subroutine pnetcdf_cleanup
implicit none
integer c, err
err = nfmpi_inq_put_size(ncid, put_size)
err = nfmpi_inq_get_size(ncid, get_size)
if (doIndepIO) then
err = nfmpi_end_indep_data(ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_begin_indep_data:')
endif
if (delayflush) then
if (doNonBlockingIO) then
if (doIndepIO) then
err = nfmpi_wait(ncid, NF_REQ_ALL, reqs, sts)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_wait:')
else
err = nfmpi_wait_all(ncid, NF_REQ_ALL, reqs, sts)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_wait_all:')
endif
endif
endif
err = nfmpi_close(ncid)
if (err .ne. NF_NOERR) call check(err, 'In nfmpi_close: ')
do c = 1, ncells
call MPI_Type_free(buftypes(c), err)
enddo
deallocate(buftypes)
deallocate(reqs)
deallocate(sts)
end subroutine pnetcdf_cleanup
end module pnetcdf_m