lukeconibear
commented
4 years ago Thanks for submitting the issue here.
Is this using the CEMAC method or a manual installation? Which versions of WRFotron and WRFChem are you using?
Do you have real.exe in the run folder? If you run ldd real.exe do the list of linked libraries from compilation show up?
Do you have the default settings within pre.bash of calling ${mpiCommandPre} ./real.exe and within config.bash that mpiCommandPre=mpirun?
chmltf
The runs I have been submitting do not create the wrfinput_d01 and wrfbdy_d01 files made from real.exe. The executable is copied to the run folder but it still cannot "find" it.
The pre.bash.exxxxxx reads: Name of source model =>NCEP GFS Analysis GRID 4
mpirun was unable to find the specified executable file, and therefore did not launch the job. This error was first reported for process rank 0; it may have occurred for other processes as well.
NOTE: A common cause for this error is misspelling a mpirun command line parameter option (remember that mpirun interprets the first unrecognized command line token as the executable).
Node: d8s0b4 Executable: real.exe
From what I can tell real.exe mostly requires a namelist.input file which is: &time_control ! time start_year = 2014, 2014, ! start year start_month = 01, 01, ! start month start_day = 02, 02, ! start day start_hour = 12, 12, ! start hour start_minute = 00, 00, ! start minute start_second = 00, 00, ! start second end_year = 2014, 2014, ! end year end_month = 01, 01, ! end month end_day = 05, 05, ! end day end_hour = 00, 00, ! end hour end_minute = 00, 00, ! end minute end_second = 00, 00, ! end second interval_seconds = 21600, ! interval between meteorological data files input_from_file = .true., .true., ! whether the nested run will have input files for domains other than domain 1 history_interval = 60, 60, ! history output file interval in minutes (integer only) frames_per_outfile = 1, 1, ! number of output times bulked into each history file restart = .false., ! whether this run is a restart restart_interval = 1440, ! restart output file interval in minutes io_form_history = 2 ! NetCDF io_form_restart = 2 ! NetCDF io_form_input = 2 ! NetCDF io_form_boundary = 2 ! NetCDF debug_level = 400 ! debugging level iofields_filename = "iofields" ,"iofields" ! an option to request particular variables to appear in output io_form_auxinput7 = 2, ! biomass burning-emissions input (wrffirechemi_d01) data format is WRF netCDF' ! biomass burning filename
auxinput7_interval_m = 60, ! biomass burning time interval, minutes
frames_per_auxinput7 = 1, ! biomass burning files per time interval
io_form_auxinput12 = 0, ! restart file type
/
auxinput7_inname = 'wrffirechemid
&domains ! domains - dimensions, nesting, parameters time_step = 180, ! timestep, meteorology, seconds time_step_fract_num = 0, ! numerator for fractional time step time_step_fract_den = 1, ! denominator for fractional time step max_dom = 1, ! number of domains e_we = 140, 154, ! westeast dimension e_sn = 140, 154, ! southnorth dimension e_vert = 33, 33, ! vertical dimension num_metgrid_levels = 27, ! number of vertical levels in WPS output num_metgrid_soil_levels = 4, ! number of soil levels or layers in WPS output dx = 30000, 2777.778, ! westeast resolution, metres dy = 30000, 2777.778, ! southnorth resolution, metres grid_id = 1, 2, ! grid ID parent_id = 1, 1, ! parent ID i_parent_start = 1, 70, ! x coordinate of the lower-left corner j_parent_start = 1, 60, ! y coordinate of the lower-left corner parent_grid_ratio = 1, 9, ! nesting ratio relative to the domain’s parent parent_time_step_ratio = 1, 9, ! parent-to-nest time step ratio feedback = 1, ! feedback from nest to its parent domain /
&physics ! physics mp_physics = 10, 10, ! microphysics scheme, 10 = Morrison 2-moment scheme
progn = 1, 1, ! prognostic number density, switch to use mix-activate scheme ra_lw_physics = 4, 4, ! longwave radiation scheme, 4 = RRTMG ra_sw_physics = 4, 4, ! shortwave radiation scheme, 4 = RRTMG radt = 30, 30, ! minutes between radiation physics calls, recommended 1 minute per km of dx (e.g. 10 for 10 km grid); use the same value for all nests sf_sfclay_physics = 5, 5, ! surface layer physics option, 5 = MYNN (Ravan's suggestion) sf_surface_physics = 2, 2, ! land surface physics option, 2 = NOAH bl_pbl_physics = 5, 5, ! boundary layer physics option, 5 = MYNN 2.5 bldt = 0, 0, ! minutes between boundary-layer physics calls, 0 = call every timestep cu_physics = 5, 0, ! cumulus parameterization option, 5 = Grell 3D, 0 = off cudt = 0, ! minutes between cumulus physics calls; should be set to 0 when using all cu_physics except Kain-Fritsch cugd_avedx = 1, ! number of grid boxes over which subsidence is spread, set to 3 for 4km run, 1 for 36km isfflx = 1, ! heat and moisture fluxes from the surface for real-data cases and when a PBL is used ifsnow = 1, ! snow-cover effects icloud = 1, ! cloud effect to the optical depth in radiation surface_input_source = 1, ! where landuse and soil category data come from, 1 = WPS num_soil_layers = 4, ! number of soil levels or layers in WPS output sf_urban_physics = 1, ! activate urban canopy model, 1 = single layer, 2 = multi layer mp_zero_out = 2, ! this keeps moisture variables above a threshold value ≥0 mp_zero_out_thresh = 1.e-8, ! critical value for moisture variable threshold, below which moisture arrays (except for Qv) are set to zero cu_rad_feedback = .true., .false., ! sub-grid cloud effect to the optical depth in radiation cu_diag = 1, 0, ! Additional time-averaged diagnostics from cu_physics slope_rad = 0, 1, ! use slope-dependent radiation topo_shading = 0, 1, ! applies neighboring-point shadow effects num_land_cat = 20, ! number of land categories in input data /
&fdda ! FDDA - options for grid, obs and spectral nudging grid_fdda = 1, 0, ! grid nudging gfdda_inname = "wrffdda_d", ! fdda filenames produced
gfdda_end_h = 10000, 0, ! time (hr) to stop nudging after the start of the forecast
gfdda_interval_m = 360, 0, ! time interval (in mins) between analysis times
if_no_pbl_nudging_uv = 1, 0, ! nudging of u and v in the PBL, 0 = yes, 1 = no
if_no_pbl_nudging_t = 1, 0, ! nudging of t in the PBL, 0 = yes, 1 = no
if_no_pbl_nudging_q = 1, 0, ! nudging of q in the PBL, 0 = yes, 1 = no
if_zfac_uv = 0, 0, ! nudge u and v in all layers, 0 = yes, 1 = limit to k_zfac_uv layers
k_zfac_uv = 2, ! model level below which nudging is switched off for u and v
if_zfac_t = 0, 0, ! nudge t in all layers, 0 = yes, 1 = limit to k_zfac_t layers
k_zfac_t = 2, ! model level below which nudging is switched off for t
if_zfac_q = 0, 0, ! nudge q in all layers, 0 = yes, 1 = limit to k_zfac_q layers
k_zfac_q = 2, ! model level below which nudging is switched off for q
guv = 0.0006, 0.0006, ! nudging coefficient for u and v (s-1)
gt = 0.0006, 0.0006, ! nudging coefficient for t (s-1)
gq = 0.0006, 0.0006, ! nudging coefficient for q (s-1)
if_ramping = 0, ! 0 = nudging ends as a step function, 1 = ramping nudging down at the end of the period
dtramp_min = 360, ! time (min) for ramping function
io_form_gfdda = 2, ! 2 = NetCDF
/
&dynamics ! dynamics - diffusion, damping options, advection options rk_ord = 3, ! time-integration scheme option, 3 = Runge-Kutta 3rd order w_damping = 1, ! vertical velocity damping flag, 1 = with damping diff_opt = 1, 1, ! turbulence and mixing option, 1 = evaluates 2nd order diffusion term on coordinate surfaces km_opt = 4, 4, ! eddy coefficient option, 4 = horizontal Smagorinsky first order closure diff_6th_opt = 0, 0, ! 6th-order numerical diffusion, 0 = none diff_6th_factor = 0.12, ! 6th-order numerical diffusion nondimensional rate base_temp = 290. ! base state temperature (K) damp_opt = 3, ! upper-level damping flag, 3 = Rayleigh damping zdamp = 5000., 5000., ! damping depth (m) from model top dampcoef = 0.2, 0.2, ! damping coefficient khdif = 0, 0, ! horizontal diffusion constant (m2/s) kvdif = 0, 0, ! vertical diffusion constant (m2/s) non_hydrostatic = .true., ! running the model in nonhydrostatic mode moist_adv_opt = 2, 2, ! advection options for moisture, 2 = monotonic chem_adv_opt = 2, 2, ! advection options for chemistry, 2 = monotonic scalar_adv_opt = 2, 2, ! advection options for scalars, 2 = monotonic tke_adv_opt = 2, 2, ! advection options for TKE, 2 = monotonic do_avgflx_em = 1, 1, ! outputs time-averaged masscoupled advective velocities, 1 = on /
&bdy_control ! Boundary condition control spec_bdy_width = 5, ! total number of rows for specified boundary value nudging spec_zone = 1, ! number of points in specified zone relax_zone = 4, ! number of points in relaxation zone specified = .true., ! specified boundary condition nested = .false., .true., ! nested boundary conditions /
&grib2 /
&namelist_quilt ! options for asynchronized I/O for MPI applications nio_tasks_per_group = 0, ! # of processors used for IO quilting per IO group nio_groups = 0 ! number of quilting groups /
&chem ! chemistry kemit = 1, ! number of vertical levels in the emissions input data file chem_opt = 202, 202, 202, ! chemistry option, 201 = MOZART-MOSAIC (4 bins + simplified SOA + no aqeuous chemistry), 202 = MOZART-MOSAIC (4 bins + VBS SOA + aqeuous chemistry). bioemdt = 3.0, 3.0, 3.0, ! timestep, biogenic, minutes photdt = 30., 10., 10., ! timestep, photolysis, minutes chemdt = 3.0, 3.0, 3.0, ! timestep, chemistry, minutes io_style_emissions = 2, ! anthropogenic emissions, files, two 12-h emissions data files used emiss_inpt_opt = 102, 102, 102, ! RADM2 emission speciation adapted after reading data file to follow the RADM2/SORGAM framework (including isoprene) emiss_opt = 10, 10, 10, ! anthropogenic emissions, setting, 10 = MOZART (MOZART + aerosols) emissions chem_in_opt = 1, 1, 1, ! initialize chemistry, 1 = uses previous simulation data phot_opt = 4, 4, 4, ! photolysis option, 1 = Full TUV, 3 = Madronich F-TUV, 4 = New full TUV scheme gas_drydep_opt = 1, 1, 1, ! dry deposition of gas species, 1 = on aer_drydep_opt = 1, 1, 1, ! dry deposition of aerosols, 1 = on bio_emiss_opt = 3, 3, 3, ! includes MEGAN biogenic emissions online based upon the weather, land use data gas_bc_opt = 1, 1, 1, ! gas boundary conditions, 1 = default gas_ic_opt = 1, 1, 1, ! gas initial conditions, 1 = default aer_bc_opt = 1, 1, 1, ! aerosol boundary conditions, 1 = default aer_ic_opt = 1, 1, 1, ! aerosol initial conditions, 1 = default gaschem_onoff = 1, 1, 1, ! gas phase chemistry, 1 = on aerchem_onoff = 1, 1, 1, ! aerosol chemistry, 1 = on wetscav_onoff = 1, 1, 1, ! wet scavenging in stratocumulus clouds, 1 = on cldchem_onoff = 0, 1, 1, ! aqueous chemistry in stratocumulus clouds, 1 = on vertmix_onoff = 1, 1, 1, ! vertical turbulent mixing, 1 = on chem_conv_tr = 1, 0, 0, ! subgrid convective transport, 1 = on conv_tr_wetscav = 1, 0, 0, ! wet scavenging in cumulus clouds, subgrid, 1 = on conv_tr_aqchem = 1, 0, 0, ! aqueous chemistry in cumulus clouds, subgrid, 1 = on seas_opt = 2, ! sea salt emissions, 2 = MOSAIC or MADE/SORGAM sea salt emissions dust_opt = 3, ! dust emissions, 3 = GOCART dust emissions with AFWA modifications dmsemis_opt = 1, ! include GOCART dms emissions from sea surface biomass_burn_opt = 2, 2, 2, ! biomass burning emissions, 2 = MOCART plumerisefire_frq = 30, 30, 30, ! time interval for calling the biomass burning plume rise subroutine scale_fire_emiss = .true., .true., .true., ! must be equal to .true. when running with FINN emissions aer_ra_feedback = 1, 1, 1, ! feedback from the aerosols to the radiation schemes, 1 = on ne_area = 500, ! total number of chemical species, in the chemical name list, best to set to a value larger than all chemical species opt_pars_out = 1, ! include optical properties in output have_bcs_chem = .true., .false., .false., ! gets lateral boundary data from wrfbdy (.true.) or idealized profile (.false.) have_bcs_upper = .false., .false., .false., ! upper boundary bounary condition for chemical species aer_op_opt = 2, 2, 2, ! aerosol optical properties, 1 = volume, 2 = approximate Maxwell-Garnet, 3 = complex volume-mixing, 4 = complex Maxwell-Garnet, 5 = complex core-shell bbinjectscheme = 1, 1, 1, ! 0 = plumerise (biomass_burn_opt), 1 = all ground level (recommended), 2 = flaming evenly in BL, 3 = flaming top BL, 4 = flaming injected at specific height /