! $Id$ ! ! I/O via MPI root rank by collecting data from all processors. ! (storing data into one file, e.g. data/allprocs/var.dat) ! ! The file written by output_snap() (and used e.g. for 'var.dat') ! consists of the followinig records (not using record markers): ! 1. data(mxgrid,mygrid,mzgrid,nvar) ! 2. t(1), x(mxgrid), y(mygrid), z(mzgrid), dx(1), dy(1), dz(1) ! Where nvar denotes the number of variables to be saved. ! In the case of MHD with entropy, nvar is 8 for a 'var.dat' file. ! Only outer ghost-layers are written, so mzlocal is between nz and mz, ! depending on the corresponding ipz-layer. ! ! To read these snapshots in IDL, the parameter allprocs needs to be set: ! IDL> pc_read_var, obj=vars, /allprocs ! or in a much more efficient way by reading into an array: ! IDL> pc_read_var_raw, obj=data, tags=tags, grid=grid, /allprocs ! ! 13-Jan-2012/PABourdin: adapted from io_dist.f90 ! module Io ! use Cdata use Cparam, only: intlen, fnlen, max_int use File_io, only: file_exists use Messages, only: fatal_error, svn_id, warning ! implicit none ! include 'io.h' include 'record_types.h' ! logical :: lread_add=.true., lwrite_add=.true. ! ! Indicates if IO is done distributed (each proc writes into a procdir) ! or collectively (eg. by specialized IO-nodes or by MPI-IO). ! logical :: lcollective_IO=.true. character (len=labellen) :: IO_strategy="collect" ! integer :: persist_last_id=-max_int ! contains !*********************************************************************** subroutine register_io ! ! dummy routine, generates separate directory for each processor. ! VAR#-files are written to the directory directory_snap which will ! be the same as directory, unless specified otherwise. ! ! 04-jul-2011/Boudin.KIS: coded ! ! identify version number ! if (lroot) call svn_id ("$Id$") if (ldistribute_persist .and. .not. lseparate_persist) & call fatal_error ('io_collect', "For distibuted persistent variables, this module needs lseparate_persist=T") if (lread_from_other_prec) & call warning('register_io','Reading from other precision not implemented') ! lmonolithic_io = .true. ! endsubroutine register_io !*********************************************************************** subroutine finalize_io ! endsubroutine finalize_io !*********************************************************************** subroutine directory_names ! ! Set up the directory names: ! set directory name for the output (one subdirectory for each processor) ! if datadir_snap (where var.dat, VAR# go) is empty, initialize to datadir ! ! 02-oct-2002/wolf: coded ! use General, only: directory_names_std ! ! check whether directory_snap contains `/allprocs' -- if so, revert to the ! default name. ! Rationale: if directory_snap was not explicitly set in start.in, it ! will be written to param.nml as 'data/allprocs'. ! if ((datadir_snap == '') .or. (index(datadir_snap,'allprocs')>0)) & datadir_snap = datadir ! call directory_names_std ! endsubroutine directory_names !*********************************************************************** subroutine distribute_grid(x, y, z, gx, gy, gz) ! ! This routine distributes the global grid to all processors. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_real, mpirecv_real ! real, dimension(mx), intent(out) :: x real, dimension(my), intent(out) :: y real, dimension(mz), intent(out) :: z real, dimension(nxgrid+2*nghost), intent(in), optional :: gx real, dimension(nygrid+2*nghost), intent(in), optional :: gy real, dimension(nzgrid+2*nghost), intent(in), optional :: gz ! integer :: px, py, pz, partner integer, parameter :: tag_gx=680, tag_gy=681, tag_gz=682 ! if (lroot) then ! send local x-data to all leading yz-processors along the x-direction x = gx(1:mx) do px = 0, nprocx-1 if (px == 0) cycle call mpisend_real (gx(px*nx+1:px*nx+mx), mx, px, tag_gx) enddo ! send local y-data to all leading xz-processors along the y-direction y = gy(1:my) do py = 0, nprocy-1 if (py == 0) cycle call mpisend_real (gy(py*ny+1:py*ny+my), my, py*nprocx, tag_gy) enddo ! send local z-data to all leading xy-processors along the z-direction z = gz(1:mz) do pz = 0, nprocz-1 if (pz == 0) cycle call mpisend_real (gz(pz*nz+1:pz*nz+mz), mz, pz*nprocxy, tag_gz) enddo endif if (lfirst_proc_yz) then ! receive local x-data from root processor if (.not. lroot) call mpirecv_real (x, mx, 0, tag_gx) ! send local x-data to all other processors in the same yz-plane do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = ipx + py*nprocx + pz*nprocxy if (partner == iproc) cycle call mpisend_real (x, mx, partner, tag_gx) enddo enddo else ! receive local x-data from leading yz-processor call mpirecv_real (x, mx, ipx, tag_gx) endif if (lfirst_proc_xz) then ! receive local y-data from root processor if (.not. lroot) call mpirecv_real (y, my, 0, tag_gy) ! send local y-data to all other processors in the same xz-plane do px = 0, nprocx-1 do pz = 0, nprocz-1 partner = px + ipy*nprocx + pz*nprocxy if (partner == iproc) cycle call mpisend_real (y, my, partner, tag_gy) enddo enddo else ! receive local y-data from leading xz-processor call mpirecv_real (y, my, ipy*nprocx, tag_gy) endif if (lfirst_proc_xy) then ! receive local z-data from root processor if (.not. lroot) call mpirecv_real (z, mz, 0, tag_gz) ! send local z-data to all other processors in the same xy-plane do px = 0, nprocx-1 do py = 0, nprocy-1 partner = px + py*nprocx + ipz*nprocxy if (partner == iproc) cycle call mpisend_real (z, mz, partner, tag_gz) enddo enddo else ! receive local z-data from leading xy-processor call mpirecv_real (z, mz, ipz*nprocxy, tag_gz) endif ! endsubroutine distribute_grid !*********************************************************************** subroutine output_snap(a, nv1, nv2, file, mode) ! ! write snapshot file, always write mesh and time, could add other things. ! ! 10-Feb-2012/PABourdin: coded ! 13-feb-2014/MR: made file optional (prep for downsampled output) ! use Mpicomm, only: globalize_xy, collect_grid use General, only: ioptest ! integer, optional,intent(IN) :: nv1,nv2 real, dimension (:,:,:,:), intent(in) :: a character (len=*), optional, intent(in) :: file integer, optional, intent(in) :: mode ! real, dimension (:,:,:,:), allocatable :: ga real, dimension (:), allocatable :: gx, gy, gz integer, parameter :: tag_ga=676 integer :: pz, pa, io_len, alloc_err, z_start, z_end, io_size, na, ne, iz real :: t_sp ! t in single precision for backwards compatibility ! if (.not. present (file)) call fatal_error ('output_snap', 'downsampled output not implemented for IO_collect') ! lwrite_add = .true. if (present (mode)) lwrite_add = (mode == 1) ! na=ioptest(nv1,1) ne=ioptest(nv2,mvar_io) ! if (lroot) then allocate (ga(mxgrid,mygrid,mz,ne-na+1), stat=alloc_err) if (alloc_err > 0) call fatal_error ('output_snap', 'Could not allocate memory for ga', .true.) ! inquire (IOLENGTH=io_len) t_sp if (lwrite_2d) then io_size=mxgrid*io_len else io_size=mxgrid*mygrid*io_len endif open (lun_output, FILE=trim (directory_snap)//'/'//file, status='replace', access='direct', recl=io_size) ! ! iterate through xy-leading processors in the z-direction do pz = 0, nprocz-1 z_start = n1 z_end = n2 if (pz == 0) z_start = 1 if (pz == nprocz-1) z_end = mz ! receive data from the xy-plane of the pz-layer call globalize_xy (a(:,:,z_start:z_end,na:ne), ga(:,:,z_start:z_end,:), source_pz=pz) ! iterate through variables do pa = 1, ne-na+1 ! iterate through xy-planes and write each plane separately do iz = z_start, z_end if (lwrite_2d) then write (lun_output, rec=iz+pz*nz+(pa-1)*mzgrid) ga(:,m1,iz,pa) else write (lun_output, rec=iz+pz*nz+(pa-1)*mzgrid) ga(:,:,iz,pa) endif enddo enddo enddo ! else z_start = n1 z_end = n2 if (ipz == 0) z_start = 1 if (ipz == nprocz-1) z_end = mz ! send data to root processor call globalize_xy (a(:,:,z_start:z_end,na:ne), dest_proc=-ipz*nprocxy) endif ! ! write additional data: if (lwrite_add) then if (lroot) then allocate (gx(mxgrid), gy(mygrid), gz(mzgrid), stat=alloc_err) if (alloc_err > 0) call fatal_error ('output_snap', 'Could not allocate memory for gx,gy,gz', .true.) endif call collect_grid (x, y, z, gx, gy, gz) ! if (lroot) then close (lun_output) open (lun_output, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', position='append', status='old') t_sp = real (t) write (lun_output) t_sp, gx, gy, gz, dx, dy, dz deallocate (gx, gy, gz) endif endif ! endsubroutine output_snap !*********************************************************************** subroutine output_snap_finalize ! ! Close snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! if (persist_initialized) then if (lroot .and. (ip <= 9)) write (*,*) 'finish persistent block' if (ldistribute_persist .or. lroot) then write (lun_output) id_block_PERSISTENT close (lun_output) endif persist_initialized = .false. persist_last_id = -max_int elseif (lwrite_add .and. lroot) then close (lun_output) endif ! endsubroutine output_snap_finalize !*********************************************************************** subroutine output_slice_position() ! ! Record slice positions. ! ! 13-nov-20/ccyang: wrapper ! use HDF5_IO, only: hdf5_output_slice_position ! call hdf5_output_slice_position() ! endsubroutine output_slice_position !*********************************************************************** subroutine output_slice(lwrite, time, label, suffix, pos, grid_pos, data) ! ! Append to a slice file ! ! 13-nov-20/ccyang: wrapper ! use HDF5_IO, only: hdf5_output_slice ! logical, intent(in) :: lwrite real, intent(in) :: time character(len=*), intent(in) :: label, suffix real, intent(in) :: pos integer, intent(in) :: grid_pos real, dimension(:,:), pointer :: data ! call hdf5_output_slice(lwrite, time, label, suffix, pos, grid_pos, data) ! endsubroutine output_slice !*********************************************************************** subroutine output_part_snap(ipar, a, mv, nv, file, label, ltruncate) ! ! Write particle snapshot file, always write mesh and time. ! ! 23-Oct-2018/PABourdin: adapted from output_snap ! integer, intent(in) :: mv, nv integer, dimension (mv), intent(in) :: ipar real, dimension (mv,mparray), intent(in) :: a character (len=*), intent(in) :: file character (len=*), optional, intent(in) :: label logical, optional, intent(in) :: ltruncate ! call fatal_error ('output_part_snap', 'not implemented for "io_collect"', .true.) ! endsubroutine output_part_snap !*********************************************************************** subroutine output_stalker_init(num, nv, snap, ID) ! ! Open stalker particle snapshot file and initialize with snapshot time. ! ! 03-May-2019/PABourdin: coded ! integer, intent(in) :: num, nv, snap integer, dimension(nv), intent(in) :: ID ! call fatal_error ('output_stalker_init', 'not implemented for "io_collect"', .true.) ! endsubroutine output_stalker_init !*********************************************************************** subroutine output_stalker(label, mv, nv, data, nvar, lfinalize) ! ! Write stalker particle quantity to snapshot file. ! ! 03-May-2019/PABourdin: coded ! character (len=*), intent(in) :: label integer, intent(in) :: mv, nv real, dimension (mv), intent(in) :: data logical, intent(in), optional :: lfinalize integer, intent(in), optional :: nvar ! call fatal_error ('output_stalker', 'not implemented for "io_collect"', .true.) ! endsubroutine output_stalker !*********************************************************************** subroutine output_part_finalize ! ! Close particle snapshot file. ! ! 03-May-2019/PABourdin: coded ! call fatal_error ('output_part_finalize', 'not implemented for "io_collect"', .true.) ! endsubroutine output_part_finalize !*********************************************************************** subroutine output_pointmass(file, labels, fq, mv, nc) ! ! Write pointmass snapshot file with time. ! ! 26-Oct-2018/PABourdin: adapted from output_snap ! character (len=*), intent(in) :: file integer, intent(in) :: mv, nc character (len=*), dimension (mqarray), intent(in) :: labels real, dimension (mv,mparray), intent(in) :: fq ! call fatal_error ('output_pointmass', 'not implemented for "io_collect"', .true.) ! endsubroutine output_pointmass !*********************************************************************** subroutine input_snap(file, a, nv, mode) ! ! read snapshot file, possibly with mesh and time (if mode=1) ! 10-Feb-2012/PABourdin: coded ! 13-jan-2015/MR: avoid use of fseek; if necessary comment the calls to fseek in fseek_pos ! use File_io, only: backskip_to_time use Mpicomm, only: localize_xy, mpibcast_real, MPI_COMM_WORLD use Syscalls, only: sizeof_real ! character (len=*) :: file integer, intent(in) :: nv real, dimension (mx,my,mz,nv), intent(out) :: a integer, optional, intent(in) :: mode ! real, dimension (:,:,:,:), allocatable :: ga real, dimension (:), allocatable :: gx, gy, gz integer, parameter :: tag_ga=675 integer :: pz, pa, z_start, io_len, alloc_err, io_size, iz integer(kind=8) :: rec_len real :: t_sp ! t in single precision for backwards compatibility ! lread_add = .true. if (present (mode)) lread_add = (mode == 1) ! if (lroot) then allocate (ga(mxgrid,mygrid,mz,nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('input_snap', 'Could not allocate memory for ga', .true.) if (ip <= 8) print *, 'input_snap: open ', file inquire (IOLENGTH=io_len) t_sp if (lwrite_2d) then io_size=mxgrid*io_len else io_size=mxgrid*mygrid*io_len endif open (lun_input, FILE=trim (directory_snap)//'/'//file, access='direct', recl=io_size, status='old') ! if (ip <= 8) print *, 'input_snap: read dim=', mxgrid, mygrid, mzgrid, nv ! iterate through xy-leading processors in the z-direction do pz = 0, nprocz-1 if (pz == 0) then z_start = 1 else ! for efficiency, some data that was already read can be moved ga(:,:,mz-5:mz,:) = ga(:,:,1:6,:) z_start = 4 endif ! iterate through variables do pa = 1, nv ! iterate through xy-planes and read each plane separately do iz = z_start, mz if (lwrite_2d) then read (lun_input, rec=iz+pz*nz+(pa-1)*mzgrid) ga(:,m1,iz,pa) else read (lun_input, rec=iz+pz*nz+(pa-1)*mzgrid) ga(:,:,iz,pa) endif enddo enddo ! distribute data in the xy-plane of the pz-layer call localize_xy (a, ga, dest_pz=pz) enddo ! else ! receive data from root processor call localize_xy (a, source_proc=-ipz*nprocxy) endif ! ! read additional data if (lread_add) then if (lroot) then allocate (gx(mxgrid), gy(mygrid), gz(mzgrid), stat=alloc_err) if (alloc_err > 0) call fatal_error ('input_snap', 'Could not allocate memory for gx,gy,gz', .true.) ! close (lun_input) open (lun_input, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', status='old', position='append') call backskip_to_time(lun_input) ! read (lun_input) t_sp, gx, gy, gz, dx, dy, dz call distribute_grid (x, y, z, gx, gy, gz) deallocate (gx, gy, gz) else call distribute_grid (x, y, z) endif call mpibcast_real (t_sp,comm=MPI_COMM_WORLD) t = t_sp endif ! endsubroutine input_snap !*********************************************************************** subroutine input_snap_finalize ! ! Close snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! if (persist_initialized) then persist_initialized = .false. persist_last_id = -max_int endif ! if (lroot) close (lun_input) ! endsubroutine input_snap_finalize !*********************************************************************** subroutine input_slice_real_arr(file, time, pos, data) ! ! Read a slice file. ! ! 13-nov-20/ccyang: wrapper ! use HDF5_IO, only: hdf5_input_slice ! character(len=*), intent(in) :: file real, intent(out):: time, pos real, dimension(:,:,:), intent(out):: data ! call hdf5_input_slice(file, time, pos, data) ! endsubroutine input_slice_real_arr !*********************************************************************** subroutine input_slice_scat_arr(file, pos, data, ivar, nt) ! ! Read a slice file. ! ! 13-nov-20/ccyang: wrapper ! use General, only: scattered_array use HDF5_IO, only: hdf5_input_slice ! character(len=*), intent(in) :: file real, intent(out):: pos type(scattered_array), pointer :: data !intent(inout) integer, intent(in) :: ivar integer, intent(out):: nt ! call hdf5_input_slice(file, pos, data, ivar, nt) ! endsubroutine input_slice_scat_arr !*********************************************************************** subroutine input_part_snap(ipar, ap, mv, nv, npar_total, file, label) ! ! Read particle snapshot file, mesh and time are read in 'input_snap'. ! ! 25-Oct-2018/PABourdin: apadpted and moved to IO module ! integer, intent(in) :: mv integer, dimension (mv), intent(out) :: ipar real, dimension (mv,mparray), intent(out) :: ap integer, intent(out) :: nv, npar_total character (len=*), intent(in) :: file character (len=*), optional, intent(in) :: label ! call fatal_error ('input_part_snap', 'not implemented for "io_collect"', .true.) ipar(1)=0; nv=0; npar_total=0; ap(1,1)=0. ! endsubroutine input_part_snap !*********************************************************************** subroutine input_pointmass(file, labels, fq, mv, nc) ! ! Read pointmass snapshot file. ! ! 26-Oct-2018/PABourdin: coded ! character (len=*), intent(in) :: file integer, intent(in) :: mv, nc character (len=*), dimension (nc), intent(in) :: labels real, dimension (mv,nc), intent(out) :: fq ! call fatal_error ('input_pointmass', 'not implemented for "io_collect"', .true.) fq(1,1)=0. ! endsubroutine input_pointmass !*********************************************************************** logical function init_write_persist(file) ! ! Initialize writing of persistent data to persistent file. ! ! 13-Dec-2011/PABourdin: coded ! character (len=*), intent(in), optional :: file ! character (len=fnlen), save :: filename="" ! persist_last_id = -max_int init_write_persist = .false. ! if (present (file)) then filename = file persist_initialized = .false. return endif ! if (ldistribute_persist .or. lroot) then if (filename /= "") then if (lroot .and. (ip <= 9)) write (*,*) 'begin write persistent block' if (lroot) close (lun_output) if (ldistribute_persist) then open (lun_output, FILE=trim (directory_dist)//'/'//filename, FORM='unformatted', status='replace') else open (lun_output, FILE=trim (directory_snap)//'/'//filename, FORM='unformatted', status='replace') endif filename = "" endif write (lun_output) id_block_PERSISTENT endif ! init_write_persist = .false. persist_initialized = .true. ! endfunction init_write_persist !*********************************************************************** logical function write_persist_id(label, id) ! ! Write persistent data to snapshot file. ! ! 13-Dec-2011/PABourdin: coded ! character (len=*), intent(in) :: label integer, intent(in) :: id ! write_persist_id = .true. if (.not. persist_initialized) write_persist_id = init_write_persist () if (.not. persist_initialized) return ! if (persist_last_id /= id) then if (ldistribute_persist .or. lroot) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent ID '//trim (label) write (lun_output) id endif persist_last_id = id endif ! write_persist_id = .false. ! endfunction write_persist_id !*********************************************************************** logical function write_persist_logical_0D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_logical, mpirecv_logical ! character (len=*), intent(in) :: label integer, intent(in) :: id logical, intent(in) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_log_0D = 700 logical, dimension (:,:,:), allocatable :: global logical :: buffer ! write_persist_logical_0D = .true. if (write_persist_id (label, id)) return ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_logical_0D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_logical (buffer, partner, tag_log_0D) global(px+1,py+1,pz+1) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global) else call mpisend_logical (value, 0, tag_log_0D) endif ! write_persist_logical_0D = .false. ! endfunction write_persist_logical_0D !*********************************************************************** logical function write_persist_logical_1D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_logical, mpirecv_logical ! character (len=*), intent(in) :: label integer, intent(in) :: id logical, dimension(:), intent(in) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_log_1D = 701 logical, dimension (:,:,:,:), allocatable :: global logical, dimension (:), allocatable :: buffer ! write_persist_logical_1D = .true. if (write_persist_id (label, id)) return ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), buffer(nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_logical_1D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1,:) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_logical (buffer, nv, partner, tag_log_1D) global(px+1,py+1,pz+1,:) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global, buffer) else call mpisend_logical (value, nv, 0, tag_log_1D) endif ! write_persist_logical_1D = .false. ! endfunction write_persist_logical_1D !*********************************************************************** logical function write_persist_int_0D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_int, mpirecv_int ! character (len=*), intent(in) :: label integer, intent(in) :: id integer, intent(in) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_int_0D = 702 integer, dimension (:,:,:), allocatable :: global integer :: buffer ! write_persist_int_0D = .true. if (write_persist_id (label, id)) return ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_int_0D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_int (buffer, partner, tag_int_0D) global(px+1,py+1,pz+1) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global) else call mpisend_int (value, 0, tag_int_0D) endif ! write_persist_int_0D = .false. ! endfunction write_persist_int_0D !*********************************************************************** logical function write_persist_int_1D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_int, mpirecv_int ! character (len=*), intent(in) :: label integer, intent(in) :: id integer, dimension (:), intent(in) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_int_1D = 703 integer, dimension (:,:,:,:), allocatable :: global integer, dimension (:), allocatable :: buffer ! write_persist_int_1D = .true. if (write_persist_id (label, id)) return ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), buffer(nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_int_1D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1,:) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_int (buffer, nv, partner, tag_int_1D) global(px+1,py+1,pz+1,:) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global, buffer) else call mpisend_int (value, nv, 0, tag_int_1D) endif ! write_persist_int_1D = .false. ! endfunction write_persist_int_1D !*********************************************************************** logical function write_persist_real_0D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_real, mpirecv_real ! character (len=*), intent(in) :: label integer, intent(in) :: id real, intent(in) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_real_0D = 704 real, dimension (:,:,:), allocatable :: global real :: buffer ! write_persist_real_0D = .true. if (write_persist_id (label, id)) return ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_real_0D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_real (buffer, partner, tag_real_0D) global(px+1,py+1,pz+1) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global) else call mpisend_real (value, 0, tag_real_0D) endif ! write_persist_real_0D = .false. ! endfunction write_persist_real_0D !*********************************************************************** logical function write_persist_real_1D(label, id, value) ! ! Write persistent data to snapshot file. ! ! 12-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_real, mpirecv_real ! character (len=*), intent(in) :: label integer, intent(in) :: id real, dimension (:), intent(in) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_real_1D = 705 real, dimension (:,:,:,:), allocatable :: global real, dimension (:), allocatable :: buffer ! write_persist_real_1D = .true. if (write_persist_id (label, id)) return ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), buffer(nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('write_persist_real_1D', & 'Could not allocate memory for global buffer', .true.) ! global(ipx+1,ipy+1,ipz+1,:) = value do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpirecv_real (buffer, nv, partner, tag_real_1D) global(px+1,py+1,pz+1,:) = buffer enddo enddo enddo if (lroot .and. (ip <= 9)) write (*,*) 'write persistent '//trim (label) write (lun_output) global ! deallocate (global, buffer) else call mpisend_real (value, nv, 0, tag_real_1D) endif ! write_persist_real_1D = .false. ! endfunction write_persist_real_1D !*********************************************************************** logical function write_persist_torus_rect(label, id, value) ! ! Write persistent data to snapshot file. ! ! 16-May-2020/MR: coded ! use Geometrical_types character (len=*), intent(in) :: label integer, intent(in) :: id type(torus_rect), intent(in) :: value ! write_persist_torus_rect = .true. if (write_persist_id (label, id)) return ! !write (lun_output) value write_persist_torus_rect = .false. ! endfunction write_persist_torus_rect !*********************************************************************** logical function init_read_persist(file) ! ! Initialize reading of persistent data from persistent file. ! ! 13-Dec-2011/PABourdin: coded ! use File_io, only: file_exists use Mpicomm, only: mpibcast_logical, MPI_COMM_WORLD ! character (len=*), intent(in), optional :: file ! init_read_persist = .true. ! if (present (file)) then if (lroot) init_read_persist = .not. file_exists (trim (directory_snap)//'/'//file) call mpibcast_logical (init_read_persist,comm=MPI_COMM_WORLD) if (init_read_persist) return endif ! if (ldistribute_persist .or. lroot) then if (lroot .and. (ip <= 9)) write (*,*) 'begin read persistent block' if (present (file)) then if (lroot) close (lun_input) if (ldistribute_persist) then open (lun_input, FILE=trim (directory_dist)//'/'//file, FORM='unformatted', status='old') else open (lun_input, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', status='old') endif endif endif ! init_read_persist = .false. ! endfunction init_read_persist !*********************************************************************** logical function persist_exists(label) ! ! Dummy routine ! ! 12-Oct-2019/PABourdin: coded ! character (len=*), intent(in) :: label ! persist_exists = .false. ! endfunction persist_exists !*********************************************************************** logical function read_persist_id(label, id, lerror_prone) ! ! Read persistent block ID from snapshot file. ! ! 17-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpibcast_int, MPI_COMM_WORLD ! character (len=*), intent(in) :: label integer, intent(out) :: id logical, intent(in), optional :: lerror_prone ! logical :: lcatch_error integer :: io_err ! lcatch_error = .false. if (present (lerror_prone)) lcatch_error = lerror_prone ! if (ldistribute_persist .or. lroot) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent ID '//trim (label) if (lcatch_error) then if (lroot) then read (lun_input, iostat=io_err) id if (io_err /= 0) id = -max_int endif else read (lun_input) id endif endif ! call mpibcast_int (id,comm=MPI_COMM_WORLD) ! read_persist_id = .false. if (id == -max_int) read_persist_id = .true. ! endfunction read_persist_id !*********************************************************************** logical function read_persist_logical_0D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_logical, mpirecv_logical ! character (len=*), intent(in) :: label logical, intent(out) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_log_0D = 706 logical, dimension (:,:,:), allocatable :: global ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_logical_0D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_logical (global(px+1,py+1,pz+1), partner, tag_log_0D) enddo enddo enddo ! deallocate (global) else call mpirecv_logical (value, 0, tag_log_0D) endif ! read_persist_logical_0D = .false. ! endfunction read_persist_logical_0D !*********************************************************************** logical function read_persist_logical_1D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_logical, mpirecv_logical ! character (len=*), intent(in) :: label logical, dimension(:), intent(out) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_log_1D = 707 logical, dimension (:,:,:,:), allocatable :: global ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_logical_1D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1,:) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_logical (global(px+1,py+1,pz+1,:), nv, partner, tag_log_1D) enddo enddo enddo ! deallocate (global) else call mpirecv_logical (value, nv, 0, tag_log_1D) endif ! read_persist_logical_1D = .false. ! endfunction read_persist_logical_1D !*********************************************************************** logical function read_persist_int_0D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_int, mpirecv_int ! character (len=*), intent(in) :: label integer, intent(out) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_int_0D = 708 integer, dimension (:,:,:), allocatable :: global ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_int_0D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_int (global(px+1,py+1,pz+1), partner, tag_int_0D) enddo enddo enddo ! deallocate (global) else call mpirecv_int (value, 0, tag_int_0D) endif ! read_persist_int_0D = .false. ! endfunction read_persist_int_0D !*********************************************************************** logical function read_persist_int_1D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_int, mpirecv_int ! character (len=*), intent(in) :: label integer, dimension(:), intent(out) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_int_1D = 709 integer, dimension (:,:,:,:), allocatable :: global ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_int_1D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1,:) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_int (global(px+1,py+1,pz+1,:), nv, partner, tag_int_1D) enddo enddo enddo ! deallocate (global) else call mpirecv_int (value, nv, 0, tag_int_1D) endif ! read_persist_int_1D = .false. ! endfunction read_persist_int_1D !*********************************************************************** logical function read_persist_real_0D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_real, mpirecv_real ! character (len=*), intent(in) :: label real, intent(out) :: value ! integer :: px, py, pz, partner, alloc_err integer, parameter :: tag_real_0D = 710 real, dimension (:,:,:), allocatable :: global ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_real_0D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_real (global(px+1,py+1,pz+1), partner, tag_real_0D) enddo enddo enddo ! deallocate (global) else call mpirecv_real (value, 0, tag_real_0D) endif ! read_persist_real_0D = .false. ! endfunction read_persist_real_0D !*********************************************************************** logical function read_persist_real_1D(label, value) ! ! Read persistent data from snapshot file. ! ! 11-Feb-2012/PABourdin: coded ! use Mpicomm, only: mpisend_real, mpirecv_real ! character (len=*), intent(in) :: label real, dimension(:), intent(out) :: value ! integer :: px, py, pz, partner, nv, alloc_err integer, parameter :: tag_real_1D = 711 real, dimension (:,:,:,:), allocatable :: global ! nv = size (value) ! if (ldistribute_persist) then if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) value ! elseif (lroot) then allocate (global(nprocx,nprocy,nprocz,nv), stat=alloc_err) if (alloc_err > 0) call fatal_error ('read_persist_real_1D', & 'Could not allocate memory for global buffer', .true.) ! if (lroot .and. (ip <= 9)) write (*,*) 'read persistent '//trim (label) read (lun_input) global value = global(ipx+1,ipy+1,ipz+1,:) do px = 0, nprocx-1 do py = 0, nprocy-1 do pz = 0, nprocz-1 partner = px + py*nprocx + pz*nprocxy if (iproc == partner) cycle call mpisend_real (global(px+1,py+1,pz+1,:), nv, partner, tag_real_1D) enddo enddo enddo ! deallocate (global) else call mpirecv_real (value, nv, 0, tag_real_1D) endif ! read_persist_real_1D = .false. ! endfunction read_persist_real_1D !*********************************************************************** logical function read_persist_torus_rect(label,value) ! ! Read persistent data from snapshot file. ! ! 16-May-2020/MR: coded ! use Geometrical_types character (len=*), intent(in) :: label type(torus_rect), intent(out) :: value ! !read (lun_input) value read_persist_torus_rect = .false. ! endfunction read_persist_torus_rect !*********************************************************************** subroutine output_globals(file, a, nv, label) ! ! Write snapshot file of globals, ignore time and mesh. ! ! 10-Feb-2012/PABourdin: coded ! character (len=*) :: file integer :: nv real, dimension (mx,my,mz,nv) :: a character (len=*), intent(in), optional :: label ! call output_snap (a, nv2=nv, file=file, mode=0) call output_snap_finalize ! endsubroutine output_globals !*********************************************************************** subroutine input_globals(file, a, nv) ! ! Read globals snapshot file, ignore time and mesh. ! ! 10-Feb-2012/PABourdin: coded ! character (len=*) :: file integer :: nv real, dimension (mx,my,mz,nv) :: a ! call input_snap (file, a, nv, 0) call input_snap_finalize ! endsubroutine input_globals !*********************************************************************** subroutine log_filename_to_file(filename, flist) ! ! In the directory containing 'filename', append one line to file ! 'flist' containing the file part of filename ! use General, only: parse_filename, safe_character_assign use Mpicomm, only: mpibarrier ! character (len=*) :: filename, flist ! character (len=fnlen) :: dir, fpart ! call parse_filename (filename, dir, fpart) if (dir == '.') call safe_character_assign (dir, directory_snap) ! if (lroot) then open (lun_output, FILE=trim (dir)//'/'//trim (flist), POSITION='append') write (lun_output, '(A,1x,e16.8)') trim (fpart),t close (lun_output) endif ! if (lcopysnapshots_exp) then call mpibarrier if (lroot) then open (lun_output,FILE=trim (datadir)//'/move-me.list', POSITION='append') write (lun_output,'(A)') trim (fpart) close (lun_output) endif endif ! endsubroutine log_filename_to_file !*********************************************************************** subroutine wgrid(file,mxout,myout,mzout,lwrite) ! ! Write grid coordinates. ! ! 10-Feb-2012/PABourdin: adapted for collective IO ! use Mpicomm, only: collect_grid use General, only: loptest ! character (len=*) :: file integer, optional :: mxout,myout,mzout logical, optional :: lwrite real, dimension (:), allocatable :: gx, gy, gz integer :: alloc_err real :: t_sp ! t in single precision for backwards compatibility ! if (lyang) return ! grid collection only needed on Yin grid, as grids are identical if (loptest(lwrite,.not.luse_oldgrid)) then if (lroot) then allocate (gx(nxgrid+2*nghost), gy(nygrid+2*nghost), gz(nzgrid+2*nghost), stat=alloc_err) if (alloc_err > 0) call fatal_error ('wgrid', 'Could not allocate memory for gx,gy,gz', .true.) ! open (lun_output, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', status='replace') t_sp = real (t) endif call collect_grid (x, y, z, gx, gy, gz) if (lroot) then write (lun_output) t_sp, gx, gy, gz, dx, dy, dz write (lun_output) dx, dy, dz write (lun_output) Lx, Ly, Lz endif call collect_grid (dx_1, dy_1, dz_1, gx, gy, gz) if (lroot) write (lun_output) gx, gy, gz call collect_grid (dx_tilde, dy_tilde, dz_tilde, gx, gy, gz) if (lroot) then write (lun_output) gx, gy, gz close (lun_output) endif endif ! endsubroutine wgrid !*********************************************************************** subroutine rgrid(file) ! ! Read grid coordinates. ! ! 21-jan-02/wolf: coded ! 15-jun-03/axel: Lx,Ly,Lz are now read in from file (Tony noticed the mistake) ! 10-Feb-2012/PABourdin: adapted for collective IO ! use Mpicomm, only: mpibcast_real, MPI_COMM_WORLD ! character (len=*) :: file ! real, dimension (:), allocatable :: gx, gy, gz integer :: alloc_err real :: t_sp ! t in single precision for backwards compatibility ! if (lroot) then allocate (gx(nxgrid+2*nghost), gy(nygrid+2*nghost), gz(nzgrid+2*nghost), stat=alloc_err) if (alloc_err > 0) call fatal_error ('rgrid', 'Could not allocate memory for gx,gy,gz', .true.) ! open (lun_input, FILE=trim (directory_snap)//'/'//file, FORM='unformatted', status='old') read (lun_input) t_sp, gx, gy, gz, dx, dy, dz call distribute_grid (x, y, z, gx, gy, gz) read (lun_input) dx, dy, dz read (lun_input) Lx, Ly, Lz read (lun_input) gx, gy, gz call distribute_grid (dx_1, dy_1, dz_1, gx, gy, gz) read (lun_input) gx, gy, gz call distribute_grid (dx_tilde, dy_tilde, dz_tilde, gx, gy, gz) close (lun_input) ! deallocate (gx, gy, gz) else call distribute_grid (x, y, z) call distribute_grid (dx_1, dy_1, dz_1) call distribute_grid (dx_tilde, dy_tilde, dz_tilde) endif ! call mpibcast_real (dx,comm=MPI_COMM_WORLD) call mpibcast_real (dy,comm=MPI_COMM_WORLD) call mpibcast_real (dz,comm=MPI_COMM_WORLD) call mpibcast_real (Lx,comm=MPI_COMM_WORLD) call mpibcast_real (Ly,comm=MPI_COMM_WORLD) call mpibcast_real (Lz,comm=MPI_COMM_WORLD) ! ! debug output ! if (lroot .and. ip <= 4) then print *, 'rgrid: Lx,Ly,Lz=', Lx, Ly, Lz print *, 'rgrid: dx,dy,dz=', dx, dy, dz endif ! endsubroutine rgrid !*********************************************************************** subroutine wproc_bounds(file) ! ! Export processor boundaries to file. ! ! 22-Feb-2012/PABourdin: adapted from io_dist ! 27-nov-2020/ccyang: make the file single ! character(len=*), intent(in) :: file ! integer :: ierr ! ! Only one process is needed. ! if (.not. lroot) return ! ! Write proc[xyz]_bounds. ! open (lun_output, FILE=file, FORM='unformatted', IOSTAT=ierr, status='replace') if (ierr /= 0) call fatal_error("wproc_bounds", "Cannot open " // trim(file)) write (lun_output) procx_bounds write (lun_output) procy_bounds write (lun_output) procz_bounds close (lun_output) ! endsubroutine wproc_bounds !*********************************************************************** subroutine rproc_bounds(file) ! ! Import processor boundaries from file. ! ! 22-Feb-2012/PABourdin: adapted from io_dist ! use Mpicomm, only: stop_it ! character (len=*) :: file ! integer :: ierr ! open (lun_input, FILE=file, FORM='unformatted', IOSTAT=ierr, status='old') if (ierr /= 0) call stop_it ( & "Cannot open " // trim(file) // " (or similar) for reading" // & " -- is data/ visible from all nodes?") read (lun_input) procx_bounds read (lun_input) procy_bounds read (lun_input) procz_bounds close (lun_input) ! endsubroutine rproc_bounds !*********************************************************************** endmodule Io