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WRF tc.exe lead to segmentation fault in wrf.exe

C

cyc10

New member
I can run my WRF v4.5.2 successfully if i don't use tc.exe.

Once I used tc.exe for tc bogus, although i can run real.exe successfully, WRF show segmentation fault.

That's means there is bug in tc.exe.

I tried to use this code to move all soil data from original .nc file to new .nc file that created by tc.exe but it doesn't help:

ncks -A -v SOILCTOP,SOILCBOT,SM000010,SM010040,SM040100,SM100200,ST000010,ST010040,ST040100,ST100200,SOILTEMP amet_em.d01.2024-09-03_06:00:00.nc met_em.d01.2024-09-03_06:00:00.nc

wrf.exe showed:

taskid: 0 hostname: chung-1-0
module_io_quilt_old.F 2931 F
Quilting with 1 groups of 0 I/O tasks.
Ntasks in X 2 , ntasks in Y 2
Domain # 1: dx = 5000.000 m
Domain # 2: dx = 2500.000 m
WRF V4.5.2 MODEL
No git found or not a git repository, git commit version not available.
*************************************
Parent domain
ids,ide,jds,jde 1 280 1 280
ims,ime,jms,jme -4 147 -4 147
ips,ipe,jps,jpe 1 140 1 140
*************************************
DYNAMICS OPTION: Eulerian Mass Coordinate
alloc_space_field: domain 1 , 603633940 bytes allocated
med_initialdata_input: calling input_input
Input data is acceptable to use: wrfinput_d01
CURRENT DATE = 2024-09-03_06:00:00
SIMULATION START DATE = 2024-09-03_06:00:00
Timing for processing wrfinput file (stream 0) for domain 1: 0.92872 elapsed seconds
Max map factor in domain 1 = 1.01. Scale the dt in the model accordingly.
D01: Time step = 30.0000000 (s)
D01: Grid Distance = 5.00000000 (km)
D01: Grid Distance Ratio dt/dx = 6.00000000 (s/km)
D01: Ratio Including Maximum Map Factor = 6.03674555 (s/km)
D01: NML defined reasonable_time_step_ratio = 6.00000000
Climate GHG input from file from year 1765 to 2499
CO2 range = 277.91300000000001 579.26400000000001 ppm
N2O range = 274.37200000000001 359.79800000000000 ppb
CH4 range = 738.98599999999999 997.31100000000004 ppb
CFC11 range = 0.0000000000000000 1.4000000000000000E-002 ppt
CFC12 range = 0.0000000000000000 2.8809999999999998 ppt
Normal ending of CAMtr_volume_mixing_ratio file
GHG annual values from CAM trace gas file
Year = 2024 , Julian day = 247
CO2 = 4.2672609755227365E-004 volume mixing ratio
N2O = 3.3536219325490553E-007 volume mixing ratio
CH4 = 1.9535003694072682E-006 volume mixing ratio
CFC11 = 2.0659128958591467E-010 volume mixing ratio
CFC12 = 4.7529886111525907E-010 volume mixing ratio
INPUT LandUse = "MODIFIED_IGBP_MODIS_NOAH"
LANDUSE TYPE = "MODIFIED_IGBP_MODIS_NOAH" FOUND 61 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_2024-09-03_06:00:00 for domain 1: 2.01145 elapsed seconds
Input data is acceptable to use: wrfbdy_d01
Timing for processing lateral boundary for domain 1: 0.09721 elapsed seconds
WRF NUMBER OF TILES FROM OMP_GET_MAX_THREADS = 5
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 140 JS 1 JE 28
WRF TILE 2 IS 1 IE 140 JS 29 JE 56
WRF TILE 3 IS 1 IE 140 JS 57 JE 84
WRF TILE 4 IS 1 IE 140 JS 85 JE 112
WRF TILE 5 IS 1 IE 140 JS 113 JE 140
WRF NUMBER OF TILES = 5
Timing for main: time 2024-09-03_06:00:30 on domain 1: 12.36007 elapsed seconds

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 0x77d62d423930 in ???
#1 0x77d62d422a95 in ???
#2 0x77d62ce4298f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x59d857bf9423 in ???
#4 0x59d857bfd8ac in ???
#5 0x59d857c01b9f in ???
#6 0x59d8572fc345 in ???
#7 0x77d62d0a66a5 in ???
#8 0x59d857301082 in ???
#9 0x59d8567b0cd8 in ???
#10 0x59d856030ed4 in ???
#11 0x59d855d9270a in ???
#12 0x59d854fb1ada in ???
#13 0x59d854f331d7 in ???
#14 0x59d854f32605 in ???
#15 0x77d62ce2814f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#16 0x77d62ce28208 in __libc_start_main_impl
at ../csu/libc-start.c:360
#17 0x59d854f32644 in ???
#18 0xffffffffffffffff in ???
 
I tried to use this code to move all soil data from original .nc file to new .nc file that created by tc.exe but it doesn't help:

ncks -A -v SOILCTOP,SOILCBOT,SM000010,SM010040,SM040100,SM100200,ST000010,ST010040,ST040100,ST100200,SOILTEMP amet_em.d01.2024-09-03_06:00:00.nc met_em.d01.2024-09-03_06:00:00.nc

attached nc file: (i put on google drive temporarily)

Help - Google Drive

drive.google.com drive.google.com
 
let me reupload the nc file in google drive on nextcloud


no matter i create 5km domain or another 15km domain, tc.exe still broke my wrf.exe and show segmentation fault.

I know that some said tc.exe lead to soil data problem so I move the soil data from orginal.nc file to new.nc file, but wrf.exe still show segmentation fault
 
Sorry that I don't have an immediate answer to your question.

Note that TC bogus is an old scheme developed years ago and it works fine with old versions of WRF (before v4.0). However, WRF vertical coordinate system has been changed since V4.0, while no changes have been made to the Bogus scheme. I am not sure whether this could be a concern.

We will look into this issue and get back to you if we find something.
 
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