SIGSEGV: Segmentation fault - invalid memory reference.

Any issues with the actual running of the WRF.

SIGSEGV: Segmentation fault - invalid memory reference.

Postby mauretto78 » Tue May 26, 2015 10:36 am

Hi guys,

please help me!!!....

I have a problem running wrf.exe .

I paste the final lines of rsl.error.0000:

Code: Select all
d03 2015-05-18_06:21:36            2  points exceeded cfl=2 in domain d03 at time 2015-05-18_06:21:36 hours
d03 2015-05-18_06:21:36  MAX AT i,j,k:          145          40          26  vert_cfl,w,d(eta)=   2.02072406       2.35066104       1.49673410E-02
d03 2015-05-18_06:21:36          334  points exceeded cfl=2 in domain d03 at time 2015-05-18_06:21:36 hours
d03 2015-05-18_06:21:36  MAX AT i,j,k:           29           1          25  vert_cfl,w,d(eta)=   6.90812683       4.85791969       1.75897405E-02
d03 2015-05-18_06:21:36            4  points exceeded cfl=2 in domain d03 at time 2015-05-18_06:21:36 hours
d03 2015-05-18_06:21:36  MAX AT i,j,k:           15         110          20  vert_cfl,w,d(eta)=   2.10974669      0.502937138       3.59381437E-02
Timing for main: time 2015-05-18_06:22:12 on domain   3:    3.43887 elapsed seconds
d03 2015-05-18_06:22:12          198  points exceeded cfl=2 in domain d03 at time 2015-05-18_06:22:12 hours
d03 2015-05-18_06:22:12  MAX AT i,j,k:           27           3          25  vert_cfl,w,d(eta)=   17.0072193       179.645950       1.75897405E-02
d03 2015-05-18_06:22:12          317  points exceeded cfl=2 in domain d03 at time 2015-05-18_06:22:12 hours
d03 2015-05-18_06:22:12  MAX AT i,j,k:           27           2          24  vert_cfl,w,d(eta)=   71.1212082       620.884277       2.06716061E-02
Timing for main: time 2015-05-18_06:22:48 on domain   3:    3.37094 elapsed seconds

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7F0302F220F7
#1  0x7F0302F226D4
#2  0x7F030266D49F
#3  0x25AF54C in __module_cu_kfeta_MOD_kf_eta_para
#4  0x25CCE9C in __module_cu_kfeta_MOD_kf_eta_cps
#5  0x1E9D07F in __module_cumulus_driver_MOD_cumulus_driver
#6  0x16BB31F in __module_first_rk_step_part1_MOD_first_rk_step_part1
#7  0x10A1E9F in solve_em_
#8  0xF9D005 in solve_interface_
#9  0x467BEA in __module_integrate_MOD_integrate
#10  0x468021 in __module_integrate_MOD_integrate
#11  0x4060A3 in __module_wrf_top_MOD_wrf_run


This is my namelist.input:

Code: Select all
 &time_control
 run_days                            = 0,
 run_hours                           = 18,
 run_minutes                         = 0,
 run_seconds                         = 0,
 start_year                          = 2015,2015,2015,
 start_month                         = 05,05,05,
 start_day                           = 18,18,18,
 start_hour                          = 00,00,00,
 start_minute                        = 00,00,00,
 start_second                        = 00,00,00,
 end_year                            = 2015,2015,2015,
 end_month                           = 05,05,05,
 end_day                             = 20,20,20,
 end_hour                            = 00,00,00,
 end_minute                          = 00,00,00,
 end_second                          = 00,00,00,
 end_second                          = 00,00,00,
 input_from_file                     = .true., .true., .true.,
 history_interval                    = 60,60,60,
 frames_per_outfile                  = 1, 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
 history_outname                     = "./wrf_out/wrfout_d<domain>.<date>",
 auxinput1_inname                    = "../wps_work/metgrid_out/met_em.d<domain>.<date>"
 /

 &domains                 
 time_step                = 180,
 time_step_fract_num      = 0,
 time_step_fract_den      = 1,
 max_dom                  = 3,
 e_we                     = 40,    146,      146,
 e_sn                     = 62,    146,      111,
 e_vert                   = 30,     30,       30,
 p_top_requested          = 5000,
 num_metgrid_levels       = 27,
 num_metgrid_soil_levels  = 4,
 dx                       = 10000,  2000.,   2000.,
 dy                       = 10000,  2000.,   2000.,
 grid_id                  = 1,        2,       3,
 parent_id                = 0,        1,       1,
 i_parent_start           = 1,        6,       6,
 j_parent_start           = 1,        6,      35,
 parent_grid_ratio        = 1,        5,       5,
 parent_time_step_ratio   = 1,        5,       5,
 feedback                 = 1,
 smooth_option            = 0,
 numtiles                 = 12,
 /

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

 &fdda
 /

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

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

 &grib2
 /

 &namelist_quilt
 nio_tasks_per_group = 0,
 nio_groups = 1,
 /


I tried changing the value of timestep...I tried with 36, 60 and 180. The result is the same: after 1 hour and one-half the wrf crashes.

I tried to remove the nested domains and run wrf.exe with only the main domain: everything works fine.

Any ideas?...PLEASE HELP MEEE

Thank you in advance guys...
mauretto78
 
Posts: 5
Joined: Fri May 08, 2015 10:56 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby herbert12345 » Thu May 28, 2015 6:10 am

Hi,

it looks like you are running into an unstable situation. This may have many different reasons and can be notoriously tricky to figure out. At a first glance, your nesting setup is strange. As far as I can tell, you have two directly neighbouring fine domains. Why don't you just join them into one larger domain? Especially with feedback on, your setup may be causing problems. Also, having them so close to the boundary is not optimal.

Another thing that helps sometimes with instabilities is increasing the value of epssm in the dynamics namelist.

HTH
herbert12345
 
Posts: 16
Joined: Tue Jun 30, 2009 8:45 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby mpalmer » Thu May 28, 2015 9:51 am

It should also be pointed out that your timestep of 180 is 3 times greater than the maximum recommended timestep for a domain of 10km resolution. My first step would be to reduce your timestep from 180 down to 60 or 50 and see if that makes the run more stable.
Michael Palmer, M.Sc.
Predictive Analytics Researcher | Green Power Labs
www.greenpowerlabs.com
mpalmer
 
Posts: 55
Joined: Fri Aug 30, 2013 12:08 pm

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby mauretto78 » Thu May 28, 2015 10:06 am

Thank u guys for the reply!!!...

@herbert12345

1. Will the final result be the same with only one nested domain (instead of two nested domains)?
2. I don't have epssm parameter in dynamics section. What value should be fine for you?

@mpalmer

I have tried with timestep = 60 (and segmentation also occurs); more stability but very large elaborating time. I need a 48 hours forecast...with my machine I calculate 24 hours of elaboration for the whole data set..I think is too much!....I tried to increase timestep in order to recuce elaborating time.

What you think about this?

Thank you guys in advance!
mauretto78
 
Posts: 5
Joined: Fri May 08, 2015 10:56 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby herbert12345 » Thu May 28, 2015 10:54 am

mauretto78 wrote:1. Will the final result be the same with only one nested domain (instead of two nested domains)?

No. But then again, it is more likely to be more meaningful because information can flow freely across the no longer existing boundary.

mauretto78 wrote:2. I don't have epssm parameter in dynamics section. What value should be fine for you?

It is there but it has a default value so you don't need to set it. Check your README.namelist. It states a default value of 0.1 but sometimes values around 0.5 are more stable.

mauretto78 wrote:I have tried with timestep = 60 (and segmentation also occurs); more stability but very large elaborating time. I need a 48 hours forecast...with my machine I calculate 24 hours of elaboration for the whole data set..I think is too much!....I tried to increase timestep in order to recuce elaborating time.

I had not noticed the timestep issue. It can't be helped though. There are restrictions to the numerical stability of the algorithms involved. This is called the Courant-Friedrich-Levy (CFL) condition. In case of strong winds you run into the danger of violating this condition leading to catastrophic failures of the schemes. Therefore you need to have the short time step. Or use coarser resolutions.

You may try experimenting with the adaptive time step options. In my experience, this is somewhat tricky so I suggest you first try to get the model running.
herbert12345
 
Posts: 16
Joined: Tue Jun 30, 2009 8:45 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby mauretto78 » Thu May 28, 2015 11:30 am

Thank you Herbert for the quick reply,

I have another issue for you: if I launch the wrf with only ONE nested domain (the first one if you are looking to my original namelist.input file), the process is stable and does't give error messages.

Possible to have some error in second nested domain?
mauretto78
 
Posts: 5
Joined: Fri May 08, 2015 10:56 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby mauretto78 » Fri May 29, 2015 4:33 am

Hi guys,

I have an update.

I posted the topic on wrf mail-list, and I got a feedback.

This segmentation fault seems to be a bug of the current version on WRF, that occurs with nested subdomains (edges of child domains too close to that of their parents).

Anyone can confirm this?

Thx in advance
mauretto78
 
Posts: 5
Joined: Fri May 08, 2015 10:56 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby herbert12345 » Fri May 29, 2015 4:50 am

mauretto78 wrote:I have another issue for you: if I launch the wrf with only ONE nested domain (the first one if you are looking to my original namelist.input file), the process is stable and does't give error messages.

Possible to have some error in second nested domain?

You could try running with only the other domain to test that. Anyway, I really suggest you join the nests.

mauretto78 wrote:This segmentation fault seems to be a bug of the current version on WRF, that occurs with nested subdomains (edges of child domains too close to that of their parents).

Bug or not, moving so close to the outer edge of the parent domain is not recommended anyway. Basically, in this way you are barely giving it any time to do anything with the lateral boundary data before feeding them into the fine domains.

If I remember correctly, the suggestion is to have at least 20 grid cells between the outer edge and the nested domains. Note that increasing the size of the outer domain is usually relatively inexpensive since it has a larger timestep than the fine domains.
herbert12345
 
Posts: 16
Joined: Tue Jun 30, 2009 8:45 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby nsdecicco » Sun May 31, 2015 11:53 am

mauretto78 wrote:This segmentation fault seems to be a bug of the current version on WRF, that occurs with nested subdomains (edges of child domains too close to that of their parents).

Anyone can confirm this?


It's not that it's a bug that you can't put nested domains too close to the edges of their parents (afaik just yet), and more so that things can just start to get really unstable. The bug in this case is that when things do get unstable, instead of that bit of cumulus physics code (kf_eta_cps) noticing NaN values in one of the fields, it tries to use these as an index in an array, which naturally segfaults.
nsdecicco
 
Posts: 2
Joined: Sun May 31, 2015 11:34 am

Re: SIGSEGV: Segmentation fault - invalid memory reference.

Postby abusk » Thu Dec 28, 2017 3:44 pm

Dear Forum Users,

I installed the WRF 3.8 on a Linux (Ubuntu Dist. 16.04 LTS) Machine (32 GB RAM and 24 cores). I aim to run WRF over Turkey with subdomains. For the installation I followed the link https://github.com/camposdelano/configuring-wrf-3.8-on-ubuntu-server-16.04.

Within several times trying, I got always the same problem during the wrf.exe run.
The problem is :

ids,ide,jds,jde 1 34 1 64
ims,ime,jms,jme -4 27 -4 24
...skipping...
Skipping over LUTYPE = USGS
LANDUSE TYPE = MODIFIED_IGBP_MODIS_NOAH FOUND 20 CATEGORIES
INPUT SOIL TEXTURE CLASSIFICATION = STAS
SOIL TEXTURE CLASSIFICATION = STAS FOUND 19 CATEGORIES
INPUT LandUse = "MODIFIED_IGBP_MODIS_NOAH"
LANDUSE TYPE = "MODIFIED_IGBP_MODIS_NOAH" FOUND 33 CATEGORIES 2 SEASONS WATER CATEGORY = 17 SNOW CATEGORY = 15
INITIALIZE THREE Noah LSM RELATED TABLES
Skipping over LUTYPE = USGS
LANDUSE TYPE = MODIFIED_IGBP_MODIS_NOAH FOUND 20 CATEGORIES
INPUT SOIL TEXTURE CLASSIFICATION = STAS
SOIL TEXTURE CLASSIFICATION = STAS FOUND 19 CATEGORIES
Timing for Writing wrfout_d01_2017-12-27_00:00:00 for domain 1: 0.25588 elapsed seconds
Timing for processing lateral boundary for domain 1: 0.04486 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 50 JS 1 JE 13
WRF NUMBER OF TILES = 1
d01 2017-12-27_00:00:00 78 points exceeded cfl=2 in domain d01 at time 2017-12-27_00:00:00 hours
d01 2017-12-27_00:00:00 MAX AT i,j,k: 49 12 23 vert_cfl,w,d(eta)= 43.2297325 60.3941460 2.82827336E-02
Timing for Writing wrfout_d02_2017-12-27_00:00:00 for domain 2: 0.17272 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 17 JS 1 JE 13
WRF NUMBER OF TILES = 1
Timing for main: time 2017-12-27_00:00:20 on domain 2: 0.30770 elapsed seconds
Timing for main: time 2017-12-27_00:00:40 on domain 2: 0.07253 elapsed seconds
Timing for main: time 2017-12-27_00:01:00 on domain 2: 0.06596 elapsed seconds
Timing for Writing wrfout_d03_2017-12-27_00:00:00 for domain 3: 0.15594 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 33 JS 1 JE 5
WRF NUMBER OF TILES = 1
Timing for main: time 2017-12-27_00:00:20 on domain 3: 0.23114 elapsed seconds

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.


My namelist.input file is:

Code: Select all
&time_control
run_days                 = 0,
run_hours                = 12,
run_minutes              = 0,
run_seconds              = 0,
start_year               = 2017,     2017,     2017,
start_month              = 12,       12,       12,
start_day                = 27,       27,       27,
start_hour               = 00,       00,       00,
start_minute             = 00,       00,       00,
start_second             = 00,       00,       00,
end_year                 = 2017,     2017,     2017,
end_month                = 12,       12,       12,
end_day                  = 27,       27,       27,
end_hour                 = 12,       12,       12,
end_minute               = 00,       00,       00,
end_second               = 00,       00,       00,
interval_seconds         = 3600,
input_from_file          = .true.,   .true.,   .true.,
history_interval         = 180,       60,       60,
frames_per_outfile       = 1000,     1000,     1000,
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                = 60,
time_step_fract_num      = 0,
time_step_fract_den      = 1,
max_dom                  = 3,
e_we                     = 100,       34,       67,
e_sn                     = 64,       64,       22,
e_vert                   = 42,       42,       42,
p_top_requested          = 5000,
num_metgrid_levels       = 32,
num_metgrid_soil_levels  = 4,
dx                       = 35385.789,11795.263,11795.263,
dy                       = 34884.267,11628.089,11628.089,
grid_id                  = 1,        2,        3,
parent_id                = 1,        1,        1,
i_parent_start           = 1,       22,       53,
j_parent_start           = 1,       23,       34,
parent_grid_ratio        = 1,        3,        3,
parent_time_step_ratio   = 1,        3,        3,
feedback                 = 1,
smooth_option            = 0,
/

&physics
mp_physics               = 3,        3,        3,
ra_lw_physics            = 1,        1,        1,
ra_sw_physics            = 1,        1,        1,
radt                     = 30,       30,       30,
sf_sfclay_physics        = 1,        1,        1,
sf_surface_physics       = 2,        2,        2,
bl_pbl_physics           = 1,        1,        1,
bldt                     = 0,        0,        0,
cu_physics               = 1,        1,        0,
cudt                     = 5,        5,        5,
isfflx                   = 1,
ifsnow                   = 0,
icloud                   = 1,
surface_input_source     = 1,
num_soil_layers          = 4,
sf_urban_physics         = 0,        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,        0,
diff_6th_factor          = 0.12,     0.12,     0.12,
base_temp                = 290.,
damp_opt                 = 0,
zdamp                    = 5000.,    5000.,    5000.,
dampcoef                 = 0.2,      0.2,      0.2,
khdif                    = 0,        0,        0,
kvdif                    = 0,        0,        0,
non_hydrostatic          = .true.,   .true.,   .true.,
moist_adv_opt            = 1,        1,        1,
scalar_adv_opt           = 1,        1,        1,
/

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

&grib2
/

&namelist_quilt
nio_tasks_per_group      = 0,
nio_groups               = 1,
/



And the namelist.wps is:

Code: Select all
&share
 wrf_core = 'ARW',
 max_dom = 3,
 start_date = '2017-12-27_00:00:00', '2017-12-27_00:00:00', '2017-12-27_00:00:00',
 end_date   = '2017-12-27_12:00:00', '2017-12-27_12:00:00', '2017-12-27_12:00:00',
 interval_seconds = 3600,
 io_form_geogrid = 2,
 opt_output_from_geogrid_path = '/home/as2/Build_WRF/WPS/Turkey/',
 debug_level = 0,
/

&geogrid
 parent_id         = 1,1,1,
 parent_grid_ratio = 1,3,3,
 i_parent_start    = 1,22,53,
 j_parent_start    = 1,23,34,
 e_we          = 100,34,67,
 e_sn          = 64,64,22,
 geog_data_res = '30s','30s','30s',
 dx = 0.318282,
 dy = 0.313771,
 map_proj =  'lat-lon',
 ref_lat   = 39.161,
 ref_lon   = 35.09,
 truelat1  = 39.161,
 truelat2  = 39.161,
 stand_lon = 35.09,
 geog_data_path = '/home/as2/Build_WRF/WPS_GEOG',
 opt_geogrid_tbl_path = '/home/as2/Build_WRF/WPS/Turkey/',
 ref_x = 50.0,
 ref_y = 32.0,
/

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

&metgrid
 fg_name = 'FILE',
 io_form_metgrid = 2,
 opt_output_from_metgrid_path = '/home/as2/Build_WRF/WPS/Turkey/',
 opt_metgrid_tbl_path = '/home/as2/Build_WRF/WPS/Turkey/',
/
&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 = '/home/as2/Build_WRF/GribFiles/2017/12/27',
 grib_vtable = 'null',
 dwiz_name    =Turkey
 dwiz_desc    =
 dwiz_user_rect_x1 =1122
 dwiz_user_rect_y1 =229
 dwiz_user_rect_x2 =1299
 dwiz_user_rect_y2 =343
 dwiz_show_political =true
 dwiz_center_over_gmt =true
 dwiz_latlon_space_in_deg =10
 dwiz_latlon_linecolor =-8355712
 dwiz_map_scale_pct =12.5
 dwiz_map_vert_scrollbar_pos =0
 dwiz_map_horiz_scrollbar_pos =0
 dwiz_gridpt_dist_km =49.3
 dwiz_mpi_command =
 dwiz_tcvitals =null
 dwiz_bigmap =Y
/



Any help is very welcome.
abusk
 
Posts: 4
Joined: Thu Dec 28, 2017 3:33 pm

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