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Updated write_trajectory() to not clobber existing file
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- write_trajectory() now appends data to an existing file. This
  is a pre-requisite to being able to write trajectories mid-run
  and thereby reduce the extreme i/o buffer sizes and i/o PE memory
  requirements when writing trajectories only at the end of the run.
- Relevant to issue #1.
- No answer changes.
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@adcroft
adcroft committed Jul 16, 2015
1 parent b01c65b commit 19107e7
Showing 1 changed file with 143 additions and 82 deletions.
225 changes: 143 additions & 82 deletions icebergs_io.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -833,6 +833,7 @@ subroutine write_trajectory(trajectory)
integer :: ntrajs_sent_io,ntrajs_rcvd_io
integer :: from_pe,np
type(buffer), pointer :: obuffer_io=>null(), ibuffer_io=>null()
logical :: io_is_in_append_mode

! Get the stderr unit number
stderrunit=stderr()
Expand Down Expand Up @@ -909,93 +910,132 @@ subroutine write_trajectory(trajectory)
endif
if (verbose) write(*,'(2a)') 'diamonds, write_trajectory: creating ',filename

iret = nf_create(filename, NF_CLOBBER, ncid)
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_create failed'

! Dimensions
iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'

! Variables
lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
yearid = def_var(ncid, 'year', NF_INT, i_dim)
dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)

! Attributes
iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
call put_att(ncid, lonid, 'long_name', 'longitude')
call put_att(ncid, lonid, 'units', 'degrees_E')
call put_att(ncid, latid, 'long_name', 'latitude')
call put_att(ncid, latid, 'units', 'degrees_N')
call put_att(ncid, yearid, 'long_name', 'year')
call put_att(ncid, yearid, 'units', 'years')
call put_att(ncid, dayid, 'long_name', 'year day')
call put_att(ncid, dayid, 'units', 'days')
call put_att(ncid, uvelid, 'long_name', 'zonal spped')
call put_att(ncid, uvelid, 'units', 'm/s')
call put_att(ncid, vvelid, 'long_name', 'meridional spped')
call put_att(ncid, vvelid, 'units', 'm/s')
call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
call put_att(ncid, uoid, 'units', 'm/s')
call put_att(ncid, void, 'long_name', 'ocean meridional spped')
call put_att(ncid, void, 'units', 'm/s')
call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
call put_att(ncid, uiid, 'units', 'm/s')
call put_att(ncid, viid, 'long_name', 'ice meridional spped')
call put_att(ncid, viid, 'units', 'm/s')
call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
call put_att(ncid, uaid, 'units', 'm/s')
call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
call put_att(ncid, vaid, 'units', 'm/s')
call put_att(ncid, mid, 'long_name', 'mass')
call put_att(ncid, mid, 'units', 'kg')
call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
call put_att(ncid, mbid, 'units', 'kg')
call put_att(ncid, hdid, 'long_name', 'heat_density')
call put_att(ncid, hdid, 'units', 'J/kg')
call put_att(ncid, did, 'long_name', 'thickness')
call put_att(ncid, did, 'units', 'm')
call put_att(ncid, wid, 'long_name', 'width')
call put_att(ncid, wid, 'units', 'm')
call put_att(ncid, lid, 'long_name', 'length')
call put_att(ncid, lid, 'units', 'm')
call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
call put_att(ncid, sshxid, 'units', 'non-dim')
call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
call put_att(ncid, sshyid, 'units', 'non-dim')
call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
call put_att(ncid, sstid, 'units', 'degrees_C')
call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
call put_att(ncid, cnid, 'units', 'none')
call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
call put_att(ncid, hiid, 'units', 'm')
io_is_in_append_mode = .false.
iret = nf_create(filename, NF_NOCLOBBER, ncid)
if (iret .ne. NF_NOERR) then
iret = nf_open(filename, NF_WRITE, ncid)
io_is_in_append_mode = .true.
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_open failed'
endif

if (io_is_in_append_mode) then
iret = nf_inq_dimid(ncid, 'i', i_dim)
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimid i failed'
lonid = inq_varid(ncid, 'lon')
latid = inq_varid(ncid, 'lat')
yearid = inq_varid(ncid, 'year')
dayid = inq_varid(ncid, 'day')
uvelid = inq_varid(ncid, 'uvel')
vvelid = inq_varid(ncid, 'vvel')
uoid = inq_varid(ncid, 'uo')
void = inq_varid(ncid, 'vo')
uiid = inq_varid(ncid, 'ui')
viid = inq_varid(ncid, 'vi')
uaid = inq_varid(ncid, 'ua')
vaid = inq_varid(ncid, 'va')
mid = inq_varid(ncid, 'mass')
mbid = inq_varid(ncid, 'mass_of_bits')
hdid = inq_varid(ncid, 'heat_density')
did = inq_varid(ncid, 'thickness')
wid = inq_varid(ncid, 'width')
lid = inq_varid(ncid, 'length')
sshxid = inq_varid(ncid, 'ssh_x')
sshyid = inq_varid(ncid, 'ssh_y')
sstid = inq_varid(ncid, 'sst')
cnid = inq_varid(ncid, 'cn')
hiid = inq_varid(ncid, 'hi')
else
! Dimensions
iret = nf_def_dim(ncid, 'i', NF_UNLIMITED, i_dim)
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_def_dim i failed'

! Variables
lonid = def_var(ncid, 'lon', NF_DOUBLE, i_dim)
latid = def_var(ncid, 'lat', NF_DOUBLE, i_dim)
yearid = def_var(ncid, 'year', NF_INT, i_dim)
dayid = def_var(ncid, 'day', NF_DOUBLE, i_dim)
uvelid = def_var(ncid, 'uvel', NF_DOUBLE, i_dim)
vvelid = def_var(ncid, 'vvel', NF_DOUBLE, i_dim)
uoid = def_var(ncid, 'uo', NF_DOUBLE, i_dim)
void = def_var(ncid, 'vo', NF_DOUBLE, i_dim)
uiid = def_var(ncid, 'ui', NF_DOUBLE, i_dim)
viid = def_var(ncid, 'vi', NF_DOUBLE, i_dim)
uaid = def_var(ncid, 'ua', NF_DOUBLE, i_dim)
vaid = def_var(ncid, 'va', NF_DOUBLE, i_dim)
mid = def_var(ncid, 'mass', NF_DOUBLE, i_dim)
mbid = def_var(ncid, 'mass_of_bits', NF_DOUBLE, i_dim)
hdid = def_var(ncid, 'heat_density', NF_DOUBLE, i_dim)
did = def_var(ncid, 'thickness', NF_DOUBLE, i_dim)
wid = def_var(ncid, 'width', NF_DOUBLE, i_dim)
lid = def_var(ncid, 'length', NF_DOUBLE, i_dim)
sshxid = def_var(ncid, 'ssh_x', NF_DOUBLE, i_dim)
sshyid = def_var(ncid, 'ssh_y', NF_DOUBLE, i_dim)
sstid = def_var(ncid, 'sst', NF_DOUBLE, i_dim)
cnid = def_var(ncid, 'cn', NF_DOUBLE, i_dim)
hiid = def_var(ncid, 'hi', NF_DOUBLE, i_dim)

! Attributes
iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_major_version', NF_INT, 1, 0)
iret = nf_put_att_int(ncid, NCGLOBAL, 'file_format_minor_version', NF_INT, 1, 1)
call put_att(ncid, lonid, 'long_name', 'longitude')
call put_att(ncid, lonid, 'units', 'degrees_E')
call put_att(ncid, latid, 'long_name', 'latitude')
call put_att(ncid, latid, 'units', 'degrees_N')
call put_att(ncid, yearid, 'long_name', 'year')
call put_att(ncid, yearid, 'units', 'years')
call put_att(ncid, dayid, 'long_name', 'year day')
call put_att(ncid, dayid, 'units', 'days')
call put_att(ncid, uvelid, 'long_name', 'zonal spped')
call put_att(ncid, uvelid, 'units', 'm/s')
call put_att(ncid, vvelid, 'long_name', 'meridional spped')
call put_att(ncid, vvelid, 'units', 'm/s')
call put_att(ncid, uoid, 'long_name', 'ocean zonal spped')
call put_att(ncid, uoid, 'units', 'm/s')
call put_att(ncid, void, 'long_name', 'ocean meridional spped')
call put_att(ncid, void, 'units', 'm/s')
call put_att(ncid, uiid, 'long_name', 'ice zonal spped')
call put_att(ncid, uiid, 'units', 'm/s')
call put_att(ncid, viid, 'long_name', 'ice meridional spped')
call put_att(ncid, viid, 'units', 'm/s')
call put_att(ncid, uaid, 'long_name', 'atmos zonal spped')
call put_att(ncid, uaid, 'units', 'm/s')
call put_att(ncid, vaid, 'long_name', 'atmos meridional spped')
call put_att(ncid, vaid, 'units', 'm/s')
call put_att(ncid, mid, 'long_name', 'mass')
call put_att(ncid, mid, 'units', 'kg')
call put_att(ncid, mbid, 'long_name', 'mass_of_bits')
call put_att(ncid, mbid, 'units', 'kg')
call put_att(ncid, hdid, 'long_name', 'heat_density')
call put_att(ncid, hdid, 'units', 'J/kg')
call put_att(ncid, did, 'long_name', 'thickness')
call put_att(ncid, did, 'units', 'm')
call put_att(ncid, wid, 'long_name', 'width')
call put_att(ncid, wid, 'units', 'm')
call put_att(ncid, lid, 'long_name', 'length')
call put_att(ncid, lid, 'units', 'm')
call put_att(ncid, sshxid, 'long_name', 'sea surface height gradient_x')
call put_att(ncid, sshxid, 'units', 'non-dim')
call put_att(ncid, sshyid, 'long_name', 'sea surface height gradient_y')
call put_att(ncid, sshyid, 'units', 'non-dim')
call put_att(ncid, sstid, 'long_name', 'sea surface temperature')
call put_att(ncid, sstid, 'units', 'degrees_C')
call put_att(ncid, cnid, 'long_name', 'sea ice concentration')
call put_att(ncid, cnid, 'units', 'none')
call put_att(ncid, hiid, 'long_name', 'sea ice thickness')
call put_att(ncid, hiid, 'units', 'm')
endif

! End define mode
iret = nf_enddef(ncid)

! Write variables
this=>traj4io; i=0
this=>traj4io
if (io_is_in_append_mode) then
iret = nf_inq_dimlen(ncid, i_dim, i)
if (iret .ne. NF_NOERR) write(stderrunit,*) 'diamonds, write_trajectory: nf_inq_dimlen i failed'
else
i = 0
endif
do while (associated(this))
i=i+1
call put_double(ncid, lonid, i, this%lon)
Expand Down Expand Up @@ -1086,6 +1126,27 @@ end function def_var

! ##############################################################################

integer function inq_varid(ncid, var)
! Arguments
integer, intent(in) :: ncid
character(len=*), intent(in) :: var
! Local variables
integer :: iret
integer :: stderrunit

! Get the stderr unit number
stderrunit=stderr()

iret = nf_inq_varid(ncid, var, inq_varid)
if (iret .ne. NF_NOERR) then
write(stderrunit,*) 'diamonds, inq_varid: nf_inq_varid failed for ',trim(var)
call error_mesg('diamonds, inq_varid', 'netcdf function returned a failure!', FATAL)
endif

end function inq_varid

! ##############################################################################

subroutine put_att(ncid, id, att, attval)
! Arguments
integer, intent(in) :: ncid, id
Expand Down

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