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real.exe error invalid parent id for domain 2

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C

carinavb

Member
Hello: I just finish the install of WRFV3.8, Everything went ok but I get an error when I execute real.exe.

sudo mpirun --allow-run-as-root -np 1 ./real.exe

I get this error:

tail rsl.error.0000
================
taskid: 0 hostname: MYHOSTNAME
module_io_quilt_old.F 2931 T
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: module_dm.b LINE: 1903
invalid parent id for domain 2
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

tail rsl.out.0000
==============
taskid: 0 hostname: carlosM
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: module_dm.b LINE: 1903
invalid parent id for domain 2
-------------------------------------------

namelist.wps
============
&geogrid
parent_id = 1,1,
parent_grid_ratio = 1,3,
i_parent_start = 1,14,
j_parent_start = 1,17,
e_we = 100,88,
e_sn = 78,112,
geog_data_res = '10m','30s',

namelist.input
=============
&domains
time_step = 23,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 2,
e_we = 100, 88,
e_sn = 78, 112,
e_vert = 35, 35,
p_top_requested = 5000,
num_metgrid_levels = 40, 40
num_metgrid_soil_levels = 4,
dx = 3800,3800,
dy = 3800, 3800,
grid_id = 1, 2,
parent_id = 1, 1,
i_parent_start = 1, 14,
j_parent_start = 1, 17,
parent_grid_ratio = 1, 3,
parent_time_step_ratio = 1, 3,
feedback = 1,
smooth_option = 0,
/

Hope someone can guide me to resolve this.
Best regards.
 
Hi,

Can you issue the following command:

ncdump - h met_em.d02_full_date_time.nc | grep parent_id >& log.parentid

where you would use your actual date/time (file name of your first met_em.d02 file), and then send me the log.parentid file?

Thanks!
 
Hi,

The namelist.wps file and the namelist.input file that you sent do not match for nest information. There are a few differences (e.g., the size of d02, the i/j start locations. The parameter interval_seconds is also different. Can you take a look and ensure that you send me the namelists that match for both the WPS run, and for the WRF run? Thanks!
 
I generate de namelists with WRF Portal, this are the files. I don't know why I get the files different.

namelist.input
=============
&time_control
run_days = 4,
run_hours = 0,
run_minutes = 0,
run_seconds = 0,
start_year = 2018, 2018,
start_month = 08, 08,
start_day = 13, 13,
start_hour = 00, 00,
start_minute = 00, 00,
start_second = 00, 00,
end_year = 2018, 2018,
end_month = 08, 08,
end_day = 17, 17,
end_hour = 00, 00,
end_minute = 00, 00,
end_second = 00, 00,
interval_seconds = 21600,
input_from_file = .true., .true.,
history_interval = 60, 60,
frames_per_outfile = 1, 1,
restart = .false.,
restart_interval = 5000,
io_form_history = 2,
io_form_restart = 2,
io_form_input = 2,
io_form_boundary = 2,
debug_level = 0,
/

&domains
time_step = 17,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 2,
e_we = 100, 251,
e_sn = 72, 161,
e_vert = 35, 35,
p_top_requested = 5000,
num_metgrid_levels = 40,
num_metgrid_soil_levels = 4,
dx = 2900, 580,
dy = 2900, 580,
grid_id = 1, 2,
parent_id = 1, 1,
i_parent_start = 1, 15,
j_parent_start = 1, 27,
parent_grid_ratio = 1, 5,
parent_time_step_ratio = 1, 5,
feedback = 1,
smooth_option = 0,
/

&physics
mp_physics = 6, 6,
ra_lw_physics = 1, 1,
ra_sw_physics = 1, 1,
radt = 10, 10,
sf_sfclay_physics = 1, 1,
sf_surface_physics = 2, 2,
bl_pbl_physics = 1, 1,
bldt = 0, 0,
cu_physics = 0, 0,
cudt = 5, 5,
isfflx = 1,
ifsnow = 0,
icloud = 1,
surface_input_source = 1,
num_soil_layers = 4,
sf_urban_physics = 0, 0,
maxiens = 1,
maxens = 3,
maxens2 = 3,
maxens3 = 16,
ensdim = 144,
/

&fdda
/

&dynamics
w_damping = 0,
diff_opt = 1,
km_opt = 4,
diff_6th_opt = 0, 0,
diff_6th_factor = 0.12, 0.12,
base_temp = 290.,
damp_opt = 0,
zdamp = 5000., 5000.,
dampcoef = 0.2, 0.2,
khdif = 0, 0,
kvdif = 0, 0,
non_hydrostatic = .true., .true.,
moist_adv_opt = 1, 1,
scalar_adv_opt = 1, 1,
/

&bdy_control
spec_bdy_width = 5,
spec_zone = 1,
relax_zone = 4,
specified = .true., .false.,
nested = .false., .true.,
/

&grib2
/

&namelist_quilt
nio_tasks_per_group = 0,
nio_groups = 1,
/

namelist.wps
============
&share
wrf_core = 'ARW',
max_dom = 2,
start_date = '2018-08-13_00:00:00', '2018-08-13_00:00:00',
end_date = '2018-08-17_00:00:00', '2018-08-17_00:00:00',
interval_seconds = 21600,
io_form_geogrid = 2,
opt_output_from_geogrid_path = '/home/cmateos/WRF/domain/norte/',
debug_level = 0,
/

&geogrid
parent_id = 1,1,
parent_grid_ratio = 1,5,
i_parent_start = 1,15,
j_parent_start = 1,27,
e_we = 100,251,
e_sn = 72,161,
geog_data_res = '30s','30s',
dx = 2900,
dy = 2900,
map_proj = 'mercator',
ref_lat = -23.278,
ref_lon = -65.745,
truelat1 = -23.278,
truelat2 = 0,
stand_lon = -65.745,
geog_data_path = '/home/cmateos/WRF/geog',
opt_geogrid_tbl_path = '/home/cmateos/WRF/domain/norte/',
ref_x = 50.0,
ref_y = 36.0,
/

&ungrib
out_format = 'WPS',
prefix = 'FILE',
/

&metgrid
fg_name = 'FILE',
io_form_metgrid = 2,
opt_output_from_metgrid_path = '/home/cmateos/WRF/domain/norte/',
opt_metgrid_tbl_path = '/home/cmateos/WRF/domain/norte/',
/

&mod_levs
press_pa = 201300 , 200100 , 100000 ,
95000 , 90000 ,
85000 , 80000 ,
75000 , 70000 ,
65000 , 60000 ,
55000 , 50000 ,
45000 , 40000 ,
35000 , 30000 ,
25000 , 20000 ,
15000 , 10000 ,
5000 , 1000
/


&domain_wizard
grib_data_path = 'null',
grib_vtable = 'Vtable.GFS',
dwiz_name =norte1
dwiz_desc =
dwiz_user_rect_x1 =2539
dwiz_user_rect_y1 =2528
dwiz_user_rect_x2 =2603
dwiz_user_rect_y2 =2571
dwiz_show_political =true
dwiz_center_over_gmt =true
dwiz_latlon_space_in_deg =10
dwiz_latlon_linecolor =-8355712
dwiz_map_scale_pct =50.0
dwiz_map_vert_scrollbar_pos =2372
dwiz_map_horiz_scrollbar_pos =2200
dwiz_gridpt_dist_km =2.9
dwiz_mpi_command =null
dwiz_tcvitals =null
dwiz_bigmap =Y
/
 
Thanks for sending those new files. With your new files, I was able to run real.exe (V3.8) without any problems. Since these new namelist files are both so completely different than the original files you sent, did you try to run again, starting from WPS, through real.exe with these particular files? Are you still getting the same error regarding an invalid parent_id?
 
I did, but I get this error..
rsl.error file
========
taskid: 0 hostname: carlosM
module_io_quilt_old.F 2931 T
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: module_dm.b LINE: 1903
invalid parent id for domain 2
-------------------------------------------
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0

rsl.out
======
taskid: 0 hostname: carlosM
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: module_dm.b LINE: 1903
invalid parent id for domain 2
-------------------------------------------
 
Can you try to modify your namelist files by hand instead of using the WRF portal to create them (we have seen problems with the portal before, and unfortunately we don't develop/support the portal here)? It may be that there are some strange characters being added to your files that your compiler isn't happy with, and it's causing real.exe to not be able to read a line correctly. I'll attach the default namelist.wps and namelist.input files for V3.8. You can modify them to match the settings you'd like to use, and then try to run again, beginning with the 3 WPS processes, and then real.exe.

Did you make any modifications to any of your code, or is it the default "out-of-the-box" code?
 

Attachments

  • namelist.wps
    1.4 KB · Views: 80
  • namelist.input
    4.3 KB · Views: 94
Dear all,

I do not see any further development of it, thus I re-open it....

I am experiencing an error message which I can not understand.

In my rsl.error.0000 appears:
Code: 
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE:  <stdin>  LINE:    5586
 invalid parent id for domain            2
-------------------------------------------

When I am looking to my namelist.input:
Code: 
(...)
 max_dom                             = 2,
 e_we                                = 393, 306,
 e_sn                                = 253, 306,
 e_vert                              = 60, 60
 hybrid_opt                          = 0,
 autolevels_opt                      = 1,
 p_top_requested                     = 1000,
 num_metgrid_levels                  = 38,
 num_metgrid_soil_levels             = 4,
 dx                                  = 8000, 1600,  3333.33,
 dy                                  = 8000, 1600,  3333.33,
 grid_id                             = 1,     2,
 parent_id                           = 1,     1,
 i_parent_start                      = 1,   212,
 j_parent_start                      = 1,   143,
 parent_grid_ratio                   = 1,     5,     3,
(...)

And my namelist.wps:
Code: 
(...)
 wrf_core = 'ARW'
 max_dom = 2,
(...)
 parent_id         =   1,    1,
 parent_grid_ratio =   1,    5,
 i_parent_start    =   1,  212,
 j_parent_start    =   1,  143,
 e_we              =  393, 306,
 e_sn              =  253, 306,
 geog_data_res     = '30s',  '30s',
 (...)

As far I understand it, it seems that it is messing with the domains id,... thus I looked into the code and I added a printing line to see what actually sees the code (WRF 4.0). In module 'frame/module_dm.F' at lines #1920 and #2135 I included the following code:

Code: 
PRINT *,'Lluis ', i, ' parent_id(i)', parent_id(i), 'max_domains', max_domains

Re-compiled and re-running I got:

Code: 
Lluis            2  parent_id(i)           0 max_domains          11
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE:  <stdin>  LINE:    5586
 invalid parent id for domain            2
-------------------------------------------

Which certainly is not what I have in my namelist. I tested with different options:
Code: 
 hybrid_opt                          = 0,
 autolevels_opt                      = 2,

and

Code: 
 hybrid_opt                          = 1,
 autolevels_opt                      = 2,

and always I get the same result.

Any help will be very appreciated!

Lluís
 
Update,

Using last version of WRF (directly from GIT), if i remove from namelist.input specification of vertical interpolation method and leave in namelist.input
Code: 
grid_id                             = 1,     2,
parent_id                           = 0,     1,

Although in namelist.wps I have:
Code: 
 parent_id         =   1,    1,

And from met_em.d02:
Code: 
$ ncdump -h met_em.d02.2018-11-11_00:00:00.nc | grep parent_id
        	:parent_id = 1 ;

real.exe runs!

Just to let you know that in namelist.output:
Code: 
HYBRID_OPT      =           2
 
Hi Lluís,
Can you attach your original namelist.input and namelist.wps files that were causing the problem, along with the updated files that allow the code to run properly (naming them accordingly)? It would help me to compare them more easily than to piece together the bits from each namelist listed here. To attach files, when you are in the reply text box, click on the tab below with 3 horizontal lines. That will allow you to attach files. Thank you!
 
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