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Sudden WRF crash (WARN5: NaN temperature; I,J,L,P=) & SIGSEGV

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K

kagelos

New member
I have a computer running WRF 3.9.1.1 for about 5 months, doing 4 runs a day using GFS input. The past 3 runs have failed giving the following error:

Code: 
real_em: SUCCESS COMPLETE REAL_EM INIT
 WARN5: NaN temperature; I,J,L,P=           2          92           1              NaN

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

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

Backtrace for this error:

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

Backtrace for this error:

Backtrace for this error:

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

Backtrace for this error:

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

Backtrace for this error:
#0  0x7fcec19182da in ???
#0  0x7fcec19182da in ???
#0  0x7fcec19182da in ???
#1  0x7fcec1917503 in ???
#2  0x7fcec0b46f1f in ???
#3  0x563d2d5cbe58 in ???
#4  0x563d2d5cf609 in ???
#5  0x563d2d5d496c in ???
#6  0x563d2ceacd8a in ???
#1  0x7fcec1917503 in ???
#2  0x7fcec0b46f1f in ???
#7  0x7fcec134695d in ???
#1  0x7fcec1917503 in ???
#3  0x563d2d5cbe58 in ???
#8  0x7fcec0f006da in ???
#2  0x7fcec0b46f1f in ???
#4  0x563d2d5cf609 in ???
#3  0x563d2d5cbe58 in ???
#5  0x563d2d5d496c in ???
#9  0x7fcec0c2988e in ???
#10  0xffffffffffffffff in ???
#4  0x563d2d5cf609 in ???
#5  0x563d2d5d496c in ???
Segmentation fault (core dumped)

Anybody knows why? Has anything changed in GFS? I have literally not touched anything.
 
NCEP GFS is updated to 15.2 at November 7 12z with minor changes and no effect expected on downscaling GFS. However, I have a similar running error during wrf.exe after succussfully completed real.exe. It looks like model crushes during surface layer process as seen below. Does anybody have a solution to the issue?

Code: 
d01 2019-11-07_18:01:00  call phy_prep
d01 2019-11-07_18:01:00  DEBUG wrf_timetoa():  returning with str = [2019-11-07_18:01:00]
d01 2019-11-07_18:01:00  call radiation_driver
d01 2019-11-07_18:01:00 Top of Radiation Driver
d01 2019-11-07_18:01:00 calling inc/HALO_PWP_inline.inc
d01 2019-11-07_18:01:00  call surface_driver
d01 2019-11-07_18:01:00 in SFCLAY
d01 2019-11-07_18:01:00 in SFCLAY
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0xfffffffe0746ad00
 
This is the complete output while running wrf.exe

Code: 
 Ntasks in X            1 , ntasks in Y            1
Setting blank km_opt entries to domain #1 values.
 --> The km_opt entry in the namelist.input is now max_domains.
Setting blank diff_opt entries to domain #1 values.
 --> The diff_opt entry in the namelist.input is now max_domains.
--- WARNING: traj_opt is zero, but num_traj is not zero; setting num_traj to zero.
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: sst_update is 0, setting io_form_auxinput4 = 0 and auxinput4_interval = 0 for all domains
--- NOTE: grid_fdda is 0 for domain      1, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain      1, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain      1, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain      2, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain      2, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain      2, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: grid_fdda is 0 for domain      3, setting gfdda interval and ending time to 0 for that domain.
--- NOTE: both grid_sfdda and pxlsm_soil_nudge are 0 for domain      3, setting sgfdda interval and ending time to 0 for that domain.
--- NOTE: obs_nudge_opt is 0 for domain      3, setting obs nudging interval and ending time to 0 for that domain.
--- NOTE: bl_pbl_physics /= 4, implies mfshconv must be 0, resetting
Need MYNN PBL for icloud_bl = 1, resetting to 0
--- NOTE: RRTMG radiation is not used, setting:  o3input=0 to avoid data pre-processing
*************************************
No physics suite selected.
Physics options will be used directly from the namelist.
*************************************
--- NOTE: num_soil_layers has been set to      4
WRF V3.9.1.1 MODEL
 *************************************
 Parent domain
 ids,ide,jds,jde            1         120           1         100
 ims,ime,jms,jme           -4         125          -4         105
 ips,ipe,jps,jpe            1         120           1         100
 *************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
 alloc_space_field: domain            1 ,             267215148  bytes allocated
med_initialdata_input: calling input_input
Timing for processing wrfinput file (stream 0) for domain        1:    0.03217 elapsed seconds
Max map factor in domain 1 =  1.01. Scale the dt in the model accordingly.
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
 Flerchinger USEd in NEW version. Iterations=          10
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 *************************************
 Nesting domain
 ids,ide,jds,jde            1         196           1         211
 ims,ime,jms,jme           -4         201          -4         216
 ips,ipe,jps,jpe            1         196           1         211
 INTERMEDIATE domain
 ids,ide,jds,jde           13          83          13          88
 ims,ime,jms,jme            8          88           8          93
 ips,ipe,jps,jpe           11          85          11          90
 *************************************
 alloc_space_field: domain            2 ,              35665920  bytes allocated
 alloc_space_field: domain            2 ,             839311924  bytes allocated
*** Initializing nest domain # 2 from an input file. ***
med_initialdata_input: calling input_input
Timing for processing wrfinput file (stream 0) for domain        2:    0.07934 elapsed seconds
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
 Flerchinger USEd in NEW version. Iterations=          10
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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
 Flerchinger USEd in NEW version. Iterations=          10
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Max map factor in domain 1 =  1.01. Scale the dt in the model accordingly.
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
 Flerchinger USEd in NEW version. Iterations=          10
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 *************************************
 Nesting domain
 ids,ide,jds,jde            1          73           1          43
 ims,ime,jms,jme           -4          78          -4          48
 ips,ipe,jps,jpe            1          73           1          43
 INTERMEDIATE domain
 ids,ide,jds,jde           87         116          11          30
 ims,ime,jms,jme           82         121           6          35
 ips,ipe,jps,jpe           85         118           9          32
 *************************************
 alloc_space_field: domain            3 ,               6144000  bytes allocated
 alloc_space_field: domain            3 ,              84434932  bytes allocated
*** Initializing nest domain # 3 from an input file. ***
med_initialdata_input: calling input_input
Timing for processing wrfinput file (stream 0) for domain        3:    0.00977 elapsed seconds
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
 Flerchinger USEd in NEW version. Iterations=          10
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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
 Flerchinger USEd in NEW version. Iterations=          10
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Max map factor in domain 1 =  1.01. Scale the dt in the model accordingly.
INPUT LandUse = "MODIFIED_IGBP_MODIS_NOAH"
 LANDUSE TYPE = "MODIFIED_IGBP_MODIS_NOAH" FOUND          33  CATEGORIES           2  SEASONS WATER CATEGORY =           17  SNOW CATEGORY =           15

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

Backtrace for this error:

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

Backtrace for this error:

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

Backtrace for this error:

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

Backtrace for this error:

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

Backtrace for this error:
#0  0x7f51489032da in ???
#0  0x7f51489032da in ???
#1  0x7f5148902503 in ???
#2  0x7f5147b31f1f in ???
#3  0x55e82833ce58 in ???
#4  0x55e828340609 in ???
#5  0x55e82834596c in ???
#6  0x55e827c1dd8a in ???
#0  0x7f51489032da in ???
#1  0x7f5148902503 in ???
#2  0x7f5147b31f1f in ???
#3  0x55e82833ce58 in ???
#4  0x55e828340609 in ???
#5  0x55e82834596c in ???
#6  0x55e827c1dd8a in ???
#7  0x7f514833195d in ???
#8  0x7f5147eeb6da in ???
#9  0x7f5147c1488e in ???
#10  0xffffffffffffffff in ???
 
I'm having also trouble with running wrf-GFS. I don't have a solution but the problem may be due to NCEP GFS update V15.2 from 11/7/2019 12z. Below are my error lines. Any help?
Code: 
d01 2019-11-07_18:01:00  call phy_prep
d01 2019-11-07_18:01:00  DEBUG wrf_timetoa():  returning with str = [2019-11-07_18:01:00]
d01 2019-11-07_18:01:00  call radiation_driver
d01 2019-11-07_18:01:00 Top of Radiation Driver
d01 2019-11-07_18:01:00 calling inc/HALO_PWP_inline.inc
d01 2019-11-07_18:01:00  call surface_driver
d01 2019-11-07_18:01:00 in SFCLAY
d01 2019-11-07_18:01:00 in SFCLAY
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0xfffffffe0746ad00
 
There was a scheduled update in GFS yesterday
https://www.weather.gov/media/notification/scn19-84gfs15_2.pdf

Is anyone else having issues currently?
 
The cause & solution is here https://forum.mmm.ucar.edu/phpBB3/viewtopic.php?f=40&t=8614&p=14965#p14965
 
I suppose you are using older version of WPS (older than WPSV4.0). Please let me know if I am wrong.
Please use WPSV4.0 and newer version to ungrid GFS data (update V15.2). Let me know if you still have the same problem.
 
WPS4.0 and newer version is able to correctly process GFS data (update V15.2). Please update WPS and reprocess this data. if you still have problems, please let us know. Thanks.
 
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