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Changed the way chunking is done for netcdf files attempting to get m…
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…emory growth under control
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@daminton
daminton committed Oct 14, 2021
1 parent ec1a2c8 commit dc3a9f9
Showing 1 changed file with 72 additions and 10 deletions.
82 changes: 72 additions & 10 deletions src/netcdf/netcdf.f90
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Original file line number Diff line number Diff line change
Expand Up @@ -99,11 +99,14 @@ module subroutine netcdf_initialize_output(self, param)
logical :: fileExists
character(len=STRMAX) :: errmsg
integer(I4B) :: storage, ndims, i
integer(I4B), parameter :: chunk = 2048
integer(I4B) :: time_chunk, id_chunk

dfill = ieee_value(dfill, IEEE_QUIET_NAN)
sfill = ieee_value(sfill, IEEE_QUIET_NAN)

time_chunk = param%istep_out / param%istep_dump
id_chunk = param%maxid

! Check if the file exists, and if it does, delete it
inquire(file=param%outfile, exist=fileExists)
if (fileExists) then
Expand All @@ -127,80 +130,146 @@ module subroutine netcdf_initialize_output(self, param)

!! Define the variables
call check( nf90_def_var(self%ncid, TIME_DIMNAME, self%out_type, self%time_dimid, self%time_varid) )
call check( nf90_def_var_chunking(self%ncid, self%time_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, ID_DIMNAME, NF90_INT, self%id_dimid, self%id_varid) )
call check( nf90_def_var_chunking(self%ncid, self%id_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, NPL_VARNAME, NF90_INT, self%time_dimid, self%npl_varid) )
call check( nf90_def_var_chunking(self%ncid, self%npl_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, NTP_VARNAME, NF90_INT, self%time_dimid, self%ntp_varid) )
call check( nf90_def_var_chunking(self%ncid, self%ntp_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, NAME_VARNAME, NF90_CHAR, [self%str_dimid, self%id_dimid], self%name_varid) )
call check( nf90_def_var_chunking(self%ncid, self%name_varid, NF90_CHUNKED, [NAMELEN, id_chunk]) )
call check( nf90_def_var(self%ncid, PTYPE_VARNAME, NF90_CHAR, [self%str_dimid, self%id_dimid], self%ptype_varid) )
call check( nf90_def_var_chunking(self%ncid, self%ptype_varid, NF90_CHUNKED, [NAMELEN, id_chunk]) )
if ((param%out_form == XV) .or. (param%out_form == XVEL)) then
call check( nf90_def_var(self%ncid, XHX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%xhx_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, XHY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%xhy_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, XHZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%xhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%xhz_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, VHX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%vhx_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, VHY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%vhy_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, VHZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%vhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%vhz_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if

if ((param%out_form == EL) .or. (param%out_form == XVEL)) then
call check( nf90_def_var(self%ncid, A_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%a_varid) )
call check( nf90_def_var_chunking(self%ncid, self%a_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, E_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%e_varid) )
call check( nf90_def_var_chunking(self%ncid, self%e_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, INC_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%inc_varid) )
call check( nf90_def_var_chunking(self%ncid, self%inc_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, CAPOM_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%capom_varid) )
call check( nf90_def_var_chunking(self%ncid, self%capom_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, OMEGA_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%omega_varid) )
call check( nf90_def_var_chunking(self%ncid, self%omega_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, CAPM_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%capm_varid) )
call check( nf90_def_var_chunking(self%ncid, self%capm_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if

call check( nf90_def_var(self%ncid, GMASS_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Gmass_varid) )
if (param%lrhill_present) call check( nf90_def_var(self%ncid, RHILL_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rhill_varid) )
if (param%lclose) call check( nf90_def_var(self%ncid, RADIUS_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%radius_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Gmass_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
if (param%lrhill_present) then
call check( nf90_def_var(self%ncid, RHILL_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rhill_varid) )
call check( nf90_def_var_chunking(self%ncid, self%rhill_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if
if (param%lclose) then
call check( nf90_def_var(self%ncid, RADIUS_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%radius_varid) )
call check( nf90_def_var_chunking(self%ncid, self%radius_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if
if (param%lrotation) then
call check( nf90_def_var(self%ncid, IP1_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip1_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Ip1_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, IP2_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip2_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Ip2_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, IP3_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Ip3_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Ip3_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, ROTX_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rotx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%rotx_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, ROTY_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%roty_varid) )
call check( nf90_def_var_chunking(self%ncid, self%roty_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, ROTZ_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%rotz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%rotz_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if
if (param%ltides) then
call check( nf90_def_var(self%ncid, K2_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%k2_varid) )
call check( nf90_def_var_chunking(self%ncid, self%k2_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
call check( nf90_def_var(self%ncid, Q_VARNAME, self%out_type, [self%id_dimid, self%time_dimid], self%Q_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Q_varid, NF90_CHUNKED, [id_chunk, time_chunk]) )
end if
if (param%lenergy) then
call check( nf90_def_var(self%ncid, KE_ORB_VARNAME, self%out_type, self%time_dimid, self%KE_orb_varid) )
call check( nf90_def_var_chunking(self%ncid, self%KE_orb_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, KE_SPIN_VARNAME, self%out_type, self%time_dimid, self%KE_spin_varid) )
call check( nf90_def_var_chunking(self%ncid, self%KE_spin_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, PE_VARNAME, self%out_type, self%time_dimid, self%PE_varid) )
call check( nf90_def_var_chunking(self%ncid, self%PE_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ORBX_VARNAME, self%out_type, self%time_dimid, self%L_orbx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_orbx_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ORBY_VARNAME, self%out_type, self%time_dimid, self%L_orby_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_orby_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ORBZ_VARNAME, self%out_type, self%time_dimid, self%L_orbz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_orbz_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_SPINX_VARNAME, self%out_type, self%time_dimid, self%L_spinx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_spinx_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_SPINY_VARNAME, self%out_type, self%time_dimid, self%L_spiny_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_spiny_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_SPINZ_VARNAME, self%out_type, self%time_dimid, self%L_spinz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_spinz_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ESCAPEX_VARNAME, self%out_type, self%time_dimid, self%L_escapex_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_escapex_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ESCAPEY_VARNAME, self%out_type, self%time_dimid, self%L_escapey_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_escapey_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, L_ESCAPEZ_VARNAME, self%out_type, self%time_dimid, self%L_escapez_varid) )
call check( nf90_def_var_chunking(self%ncid, self%L_escapez_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, ECOLLISIONS_VARNAME, self%out_type, self%time_dimid, self%Ecollisions_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Ecollisions_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, EUNTRACKED_VARNAME, self%out_type, self%time_dimid, self%Euntracked_varid) )
call check( nf90_def_var_chunking(self%ncid, self%Euntracked_varid, NF90_CHUNKED, [time_chunk]) )
call check( nf90_def_var(self%ncid, GMESCAPE_VARNAME, self%out_type, self%time_dimid, self%GMescape_varid) )
call check( nf90_def_var_chunking(self%ncid, self%GMescape_varid, NF90_CHUNKED, [time_chunk]) )
end if

call check( nf90_def_var(self%ncid, STATUS_VARNAME, NF90_CHAR, [self%str_dimid, self%id_dimid], self%status_varid) )
call check( nf90_def_var_chunking(self%ncid, self%status_varid, NF90_CHUNKED, [NAMELEN, id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_TYPE_VARNAME, NF90_CHAR, [self%str_dimid, self%id_dimid], self%origin_type_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_type_varid, NF90_CHUNKED, [NAMELEN, id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_TIME_VARNAME, self%out_type, self%id_dimid, self%origin_time_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_time_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, COLLISION_ID_VARNAME, self%out_type, self%id_dimid, self%collision_id_varid) )
call check( nf90_def_var_chunking(self%ncid, self%collision_id_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_XHX_VARNAME, self%out_type, self%id_dimid, self%origin_xhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_xhx_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_XHY_VARNAME, self%out_type, self%id_dimid, self%origin_xhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_xhy_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_XHZ_VARNAME, self%out_type, self%id_dimid, self%origin_xhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_xhz_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_VHX_VARNAME, self%out_type, self%id_dimid, self%origin_vhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_vhx_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_VHY_VARNAME, self%out_type, self%id_dimid, self%origin_vhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_vhy_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, ORIGIN_VHZ_VARNAME, self%out_type, self%id_dimid, self%origin_vhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%origin_vhz_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_TIME_VARNAME, self%out_type, self%id_dimid, self%discard_time_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_time_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_XHX_VARNAME, self%out_type, self%id_dimid, self%discard_xhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_xhx_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_XHY_VARNAME, self%out_type, self%id_dimid, self%discard_xhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_xhy_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_XHZ_VARNAME, self%out_type, self%id_dimid, self%discard_xhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_xhz_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_VHX_VARNAME, self%out_type, self%id_dimid, self%discard_vhx_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_vhx_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_VHY_VARNAME, self%out_type, self%id_dimid, self%discard_vhy_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_vhy_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_VHZ_VARNAME, self%out_type, self%id_dimid, self%discard_vhz_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_vhz_varid, NF90_CHUNKED, [id_chunk]) )
call check( nf90_def_var(self%ncid, DISCARD_BODY_ID_VARNAME, NF90_INT, self%id_dimid, self%discard_body_id_varid) )
call check( nf90_def_var_chunking(self%ncid, self%discard_body_id_varid, NF90_CHUNKED, [id_chunk]) )

! Set fill mode to NaN for all variables
call check( nf90_inquire(self%ncid, nVariables=nvar) )
Expand All @@ -216,13 +285,6 @@ module subroutine netcdf_initialize_output(self, param)
case(NF90_CHAR)
call check( nf90_def_var_fill(self%ncid, varid, 0, 0) )
end select

select case(vartype)
case(NF90_CHAR)
call check( nf90_def_var_chunking(self%ncid, varid, NF90_CHUNKED, [NAMELEN, chunk]) )
case default
call check( nf90_def_var_chunking(self%ncid, varid, NF90_CHUNKED, [(chunk, i = 1, ndims)]) )
end select
end do

! Take the file out of define mode
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