我需要将我的HDF5数据集并行写入一个HDF5文件，我想用一个线程创建我的文件，为此我可以使用if语句：
if( currentThread == 0)
{
createHDF5File( );
}
但我不知道哪个线程会先出现。例如，当线程1首先出现时，它会尝试将数据集写入不存在的文件。有没有办法选择第一个线程？或者有更好的方法吗？
答案 0 :(得分：1)
听起来你真的应该在HDF5上使用并行IO。如果您使用并行支持构建它，HDF5能够使用MPI-IO（引擎盖下）。
这是一个示例程序（在Fortran中）。
! Program to use MPI_Cart and Parallel HDF5
!
program hdf_pwrite
use, intrinsic :: iso_c_binding, only: c_double
use mpi
use hdf5
use kinds, only : r_dp
implicit none
! external interface
interface
subroutine get_walltime(t) &
bind(c, name="get_walltime")
import :: c_double
real(kind=c_double), intent(out) :: t
end subroutine get_walltime
end interface
! Local 4000x4000 with a 1x1 halo
integer, parameter :: ndims = 2
integer, parameter :: N = 4000
integer, parameter :: halo = 1
integer :: argc ! Command line args
integer :: ierr ! Error status
integer :: id ! My rank/ID
integer :: np ! Number of processors
integer :: iunit ! File descriptor
integer :: i,j ! Loop indexers
integer :: total ! Total dimension size
integer :: lcount ! Luster count size
integer :: lsize ! Lustre stripe size
character(len=1024) :: clcount, clsize ! Strings of LFS
integer :: info ! MPI IO Info
integer :: m_dims(ndims) ! MPI cart dims
integer :: coords(ndims) ! Co-ords of procs in the grid
logical :: is_periodic(ndims) ! Periodic boundary conditions
logical :: reorder ! Reorder the MPI structure
integer :: MPI_COMM_2D ! New communicator
integer(KIND=MPI_OFFSET_KIND) :: offset
character(len=1024) :: filename
integer(kind=hid_t) :: p_id, f_id, x_id, d_id
integer(kind=hid_t) :: memspace, filespace
! Local hyper slab info
integer(kind=hsize_t) :: d_size(ndims), s_size(ndims), h_size(ndims),&
stride(ndims), block(ndims)
! Global hyper slab info
integer(kind=hsize_t) :: g_size(ndims), g_start(ndims)
real(kind=r_dp), allocatable :: ld(:,:)
! Timing vars
real(kind=r_dp) :: s, e, dt, mdt
argc = 0
ierr = 0
offset = 0
m_dims = (/ 0, 0/)
is_periodic = .false. ! Non-periodic
reorder = .false. ! Not allowed to reorder
call mpi_init(ierr)
! Set up the MPI cartesian topology
call mpi_comm_size(MPI_COMM_WORLD, np, ierr)
call mpi_dims_create(np, ndims, m_dims, ierr)
call mpi_cart_create(MPI_COMM_WORLD, ndims, m_dims, is_periodic, &
reorder, MPI_COMM_2D, ierr)
call mpi_comm_rank(MPI_COMM_2D, id, ierr)
call mpi_cart_coords(MPI_COMM_2D, id, ndims, coords, ierr)
if (id .eq. 0) then
if (mod(N,np) .ne. 0) then
write(0,*) 'Must use divisiable number of procs.'
call mpi_abort(MPI_COMM_WORLD, 1, ierr)
endif
! get the filename
argc = iargc()
if (argc .lt. 1 ) then
write(0, *) 'Must supply a filename'
call exit(1)
endif
call get_command_argument(1, filename)
endif
! Broadcast the filename
call mpi_bcast(filename, len(filename), MPI_CHAR, 0, &
MPI_COMM_WORLD, ierr)
! Init the HDF5 library
call h5open_f(ierr)
! Set a stripe count of 4 and a stripe size of 4MB
lcount = 4
lsize = 4 * 1024 * 1024
write(clcount, '(I4)') lcount
write(clsize, '(I8)') lsize
call mpi_info_create(info, ierr)
call mpi_info_set(info, "striping_factor", trim(clcount), ierr)
call mpi_info_set(info, "striping_unit", trim(clsize), ierr)
! Set up the access properties
call h5pcreate_f(H5P_FILE_ACCESS_F, p_id, ierr)
call h5pset_fapl_mpio_f(p_id, MPI_COMM_2D, info, ierr)
! Open the file
call h5fcreate_f(filename, H5F_ACC_TRUNC_F, f_id, ierr, &
access_prp = p_id)
if (ierr .ne. 0) then
write(0,*) 'Unable to open: ', trim(filename), ': ', ierr
call mpi_abort(MPI_COMM_WORLD, 1, ierr)
endif
! Generate our 4000x4000 matrix with a 1x1 halo
total = N + 2 * halo
allocate(ld(0:total-1, 0:total-1))
ld = -99.99
! init the local data
do j = 1, N
do i = 1, N
ld(i,j) = (i - 1 + (j-1)*N)
enddo
enddo
! Create the local memory space and hyperslab
do i = 1, ndims
d_size(i) = total
s_size(i) = N
h_size(i) = halo
stride(i) = 1
block(i) = 1
enddo
call h5screate_simple_f(ndims, d_size, memspace, ierr)
call h5sselect_hyperslab_f(memspace, H5S_SELECT_SET_F, &
h_size, s_size, ierr, &
stride, block)
! Create the global file space and hyperslab
do i = 1, ndims
g_size(i) = N * m_dims(i)
g_start(i) = N * coords(i)
enddo
call h5screate_simple_f(ndims, g_size, filespace, ierr)
call h5sselect_hyperslab_f(filespace, H5S_SELECT_SET_F, &
g_start, s_size, ierr, &
stride, block)
! Create a data transfer property
call h5pcreate_f(H5P_DATASET_XFER_F, x_id, ierr)
call h5pset_dxpl_mpio_f(x_id, H5FD_MPIO_COLLECTIVE_F, ierr)
! Create the dataset id
call h5dcreate_f(f_id, "/data", H5T_IEEE_F64LE, filespace, d_id, &
ierr)
! Write the data
call get_walltime(s)
call h5dwrite_f(d_id, H5T_NATIVE_DOUBLE, ld, s_size, ierr, &
file_space_id=filespace, mem_space_id=memspace, &
xfer_prp=x_id)
call get_walltime(e)
dt = e - s
call mpi_reduce(dt, mdt, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_2D, ierr)
if (id .eq. 0) then
write(6,*) mdt / np
endif
if (allocated(ld)) then
deallocate(ld)
endif
! Close everything and exit
call h5dclose_f(d_id, ierr)
call h5sclose_f(filespace, ierr)
call h5sclose_f(memspace, ierr)
call h5pclose_f(x_id, ierr)
call h5pclose_f(p_id, ierr)
call h5fclose_f(f_id, ierr)
call h5close_f(ierr)
call mpi_finalize(ierr)
end program hdf_pwrite
请注意这是我的教学示例，我交互式地让课程玩。所以它有几个不同的东西。
iso_c_binding，因为我们在C（gettimeofday）包装器中有一个计时例程。希望这会有所帮助。
答案 1 :(得分：0)
您是否计算要并行写入的数据？如果是这样，您希望确保所有工作人员在您编写之前已完成处理，以便您的数据实际上已完成。
换句话说，
// Collect all the data using some form of MPI_Collect, MPI_Reduce
// or whatevs. I'll just put this here for proof-of-concept
MPI_Barrier();
// Now, all the threads have "joined", so you can write from 0 without worrying
// that some other thread got here way before
if (currentThread == 0) { createdHDF5File(); }
如果没有，我假设你想从每个线程写入数据。为什么不把它写到不同的文件？
// Calculate stuff on each thread
// Then write to different files depending on thread num
createHDF5File(currentThread); // Chooses file name that includes the thread num