I am not able to attach the files. I get the following error:
"The upload failed because the temporary directory was missing. The site administrator will need to resolve this before any files can be uploaded."
Initially, I created the grid file (grid.nc) from the global file (x1.163842.grid.nc), using a .pts file with the information of my domain. I also generated the partitioned files (.graph.info.part.*). Next, I generated the static.nc file using the init_atmosphere_model, with grid.nc as input. After that, I generated the invariant.nc file using static.nc as input. I then ran ungrib on the data to generate the initial conditions and boundary conditions. Then, I prepared the data by converting them to IODA-HDF5 format. I ran the model (atmosphere_model) to generate the background data for assimilation (config_jedi_da is set to False in namelist.atmosphere). When I tried to run the assimilation, I got the error mentioned earlier.
------ streams.atmosphere
<streams>
<immutable_stream name="invariant"
type="input"
precision="single"
filename_template="SaoPaulo.invariant.nc"
input_interval="initial_only" />
<immutable_stream name="input"
type="input"
precision="single"
filename_template="mpasin.2026-03-15T00.00.00.nc"
input_interval="initial_only" />
<immutable_stream name="da_state"
type="output"
precision="single"
io_type="pnetcdf,cdf5"
filename_template="mpasout.$Y-$M-$D_$h.$m.$s.nc"
output_interval="none"
clobber_mode="overwrite" />
<stream name="background"
type="input;output"
precision="single"
io_type="pnetcdf,cdf5"
filename_template="background.nc"
input_interval="none"
output_interval="none"
clobber_mode="overwrite">
<file name="stream_list.atmosphere.background"/>
</stream>
<stream name="analysis"
type="output"
precision="single"
io_type="pnetcdf,cdf5"
filename_template="analysis.nc"
output_interval="none"
clobber_mode="overwrite">
<file name="stream_list.atmosphere.analysis"/>
</stream>
<stream name="ensemble"
type="input;output"
precision="single"
io_type="pnetcdf,cdf5"
filename_template="ensemble.nc"
input_interval="none"
output_interval="none"
clobber_mode="overwrite">
<file name="stream_list.atmosphere.ensemble"/>
</stream>
<stream name="control"
type="input;output"
precision="single"
io_type="pnetcdf,cdf5"
filename_template="control.nc"
input_interval="none"
output_interval="none"
clobber_mode="overwrite">
<file name="stream_list.atmosphere.control"/>
</stream>
<stream name="output"
type="none"
filename_template="output.nc"
output_interval="0_01:00:00" >
</stream>
<stream name="diagnostics"
type="none"
filename_template="diagnostics.nc"
output_interval="0_01:00:00" >
</stream>
<immutable_stream name="iau"
type="none"
filename_template="SaoPaulo.AmB.$Y-$M-$D_$h.$m.$s.nc"
filename_interval="none"
packages="iau"
input_interval="none" />
<immutable_stream name="lbc_in"
type="input"
io_type="pnetcdf,cdf5"
filename_template="lbc.$Y-$M-$D_$h.$m.$s.nc"
filename_interval="input_interval"
packages="limited_area"
input_interval="3:00:00" />
</streams>
------ namelist.atmosphere
&nhyd_model
config_dt = 360
config_start_time = '2026-03-15_00:00:00'
config_run_duration = '00_06:00:00'
config_split_dynamics_transport = .true. !default
config_number_of_sub_steps = 2 !default
config_dynamics_split_steps = 3 !default
config_h_mom_eddy_visc2 = 0.0 !default
config_h_mom_eddy_visc4 = 0.0 !default
config_v_mom_eddy_visc2 = 0.0 !default
config_h_theta_eddy_visc2 = 0.0 !default
config_h_theta_eddy_visc4 = 0.0 !default
config_v_theta_eddy_visc2 = 0.0 !default
config_horiz_mixing = '2d_smagorinsky' !default
config_len_disp = 60000
config_visc4_2dsmag = 0.05 !default
config_w_adv_order = 3 !default
config_theta_adv_order = 3 !default
config_scalar_adv_order = 3 !default
config_u_vadv_order = 3 !default
config_w_vadv_order = 3 !default
config_theta_vadv_order = 3 !default
config_scalar_vadv_order = 3 !default
config_scalar_advection = .true. !default
config_positive_definite = .false. !default
config_monotonic = .true. !default
config_coef_3rd_order = 0.25 !default
config_epssm = 0.1 !default
config_smdiv = 0.1 !default
config_apvm_upwinding = 0.0
/
&damping
config_zd = 22000.0
config_xnutr = 0.2
/
&io
config_pio_num_iotasks = 0
config_pio_stride = 1
/
&decomposition
config_block_decomp_file_prefix = 'SaoPaulo.graph.info.part.'
/
&restart
config_do_restart = false
config_do_DAcycling = false
/
&printout
config_print_global_minmax_vel = true
config_print_detailed_minmax_vel = true
config_print_global_minmax_sca = true
/
&IAU
config_IAU_option = 'off'
config_IAU_window_length_s = 21600.
/
&physics
config_sst_update = .false.
config_sstdiurn_update = .false.
config_deepsoiltemp_update = .false.
config_radtlw_interval = '00:15:00'
config_radtsw_interval = '00:15:00'
config_o3climatology = .true.
config_bucket_update = 'none' !'1_00:00:00'
config_microp_re = .true.
config_sfc_albedo = .true.
config_sfc_snowalbedo = .true.
config_frac_seaice = .true.
config_physics_suite = 'mesoscale_reference'
config_convection_scheme = 'cu_grell_freitas'
/
config_lightning_flash = true
config_microp_scheme = 'mp_thompson'
config_lsm_scheme = 'noah'
config_pbl_scheme = 'bl_mynn'
config_gwdo_scheme = 'ysu_gwdo'
config_radt_cld_scheme = 'cld_fraction'
config_radt_lw_scheme = 'rrtmg_lw'
config_radt_sw_scheme = 'rrtmg_sw'
config_sfclayer_scheme = 'sf_monin_obukhov'
num_soil_layers = 4
config_bucket_rainc = 100.0
config_bucket_rainnc = 100.0
config_bucket_radt = 1.0e9
config_conv_interval = 'none'
config_pbl_interval = 'bl_mynn'
config_n_microp = 1
/
&limited_area
config_apply_lbcs = true !regional = true, global = false
/
&soundings
config_sounding_interval = 'none'
/
&assimilation
config_jedi_da = true
/
