Could not open new netcdf file structure

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Tuanph_1970
Posts: 1
Joined: Wed Aug 19, 2020 2:05 pm

Could not open new netcdf file structure

Post by Tuanph_1970 » Wed Aug 19, 2020 2:12 pm

Dear team,

I have downloaded a WRF Version 4.2.1 and build and tried to run it on Ubuntu system.
During running the program . I have encountered with problem wiith reading file 2019-05-09_11.nc file.
From the command window I saw the bug : The name list;s size í mismatch with input file.

I have attached the log file for this issue.

For more infomation of the issue:

If the size of nc file is about 16 Mb , it can read normally
From file 2019-05-09_11.nc file. the size of file is 24 Mb and the program could not open it

Here is the log content:

Timing for main: time 2019-05-09_11:21:00 on domain 1: 1.00036 elapsed seconds
d01 2019-05-09_11:21:00 2 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:21:00 hours
d01 2019-05-09_11:21:00 MAX AT i,j,k: 39 9 18 vert_cfl,w,d(eta)= 2.06013870 6.92384338 5.00418246E-02
Timing for main: time 2019-05-09_11:24:00 on domain 1: 1.04821 elapsed seconds
d01 2019-05-09_11:24:00 4 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:24:00 hours
d01 2019-05-09_11:24:00 MAX AT i,j,k: 39 9 19 vert_cfl,w,d(eta)= 2.13596010 6.65227842 4.97004390E-02
d01 2019-05-09_11:24:00 5 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:24:00 hours
d01 2019-05-09_11:24:00 MAX AT i,j,k: 39 9 20 vert_cfl,w,d(eta)= 2.22204113 9.77714252 4.88601625E-02
d01 2019-05-09_11:24:00 6 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:24:00 hours
d01 2019-05-09_11:24:00 MAX AT i,j,k: 39 9 19 vert_cfl,w,d(eta)= 2.23059511 6.66994476 4.97004390E-02
Timing for main: time 2019-05-09_11:27:00 on domain 1: 1.00049 elapsed seconds
d01 2019-05-09_11:27:00 6 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:27:00 hours
d01 2019-05-09_11:27:00 MAX AT i,j,k: 39 9 19 vert_cfl,w,d(eta)= 2.32532549 7.56556749 4.97004390E-02
d01 2019-05-09_11:27:00 7 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:27:00 hours
d01 2019-05-09_11:27:00 MAX AT i,j,k: 39 9 20 vert_cfl,w,d(eta)= 2.40695977 10.2986898 4.88601625E-02
d01 2019-05-09_11:27:00 8 points exceeded cfl=2 in domain d01 at time 2019-05-09_11:27:00 hours
d01 2019-05-09_11:27:00 MAX AT i,j,k: 39 9 19 vert_cfl,w,d(eta)= 2.39766121 6.96662617 4.97004390E-02
Timing for main: time 2019-05-09_11:30:00 on domain 1: 1.04442 elapsed seconds

Timing for main: time 2019-05-09_12:00:00 on domain 1: 0.98216 elapsed seconds
mediation_integrate.G 1944 DATASET=HISTORY
mediation_integrate.G 1945 grid%id 1 grid%oid 2
Timing for Writing wrfout_d01_2019-05-09_12:00:00 for domain 1: 0.62352 elapsed seconds
d01 2019-05-09_12:00:00 Input data is acceptable to use: wrfbdy_d01
Timing for processing lateral boundary for domain 1: 0.03864 elapsed seconds

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

Backtrace for this error:
#0 0x7F683AB5FE08
#1 0x7F683AB5EF90
#2 0x7F683A2904BF
#3 0x1BDBABC in taugb3.7253 at module_ra_rrtmg_lw.f90:?
#4 0x1BFE2BD in __rrtmg_lw_taumol_MOD_taumol
#5 0x1C222B8 in __rrtmg_lw_rad_MOD_rrtmg_lw
#6 0x1C33641 in __module_ra_rrtmg_lw_MOD_rrtmg_lwrad
#7 0x16799C5 in __module_radiation_driver_MOD_radiation_driver
#8 0x173F7FA in module_first_rk_step_part1_MOD_first_rk_step_part1
#9 0x127B29F in solve_em
#10 0x112BA90 in solve_interface
#11 0x475035 in __module_integrate_MOD_integrate
#12 0x407BF3 in __module_wrf_top_MOD_wrf_run

kwerner
Posts: 1926
Joined: Wed Feb 14, 2018 9:21 pm

Re: Could not open new netcdf file structure

Post by kwerner » Thu Aug 20, 2020 7:23 pm

Hi,
I don't see any problems with the netcdf file. You are getting a segmentation fault that is very likely due to the CFL errors you see listed in your error log. Take a look at this FAQ that discusses segmentation faults, specifically the part related to CFL error: viewtopic.php?f=73&t=133
NCAR/MMM

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