Segmentation fault while running wrf.exe using sf_urban_physics = 1

[mukeshkhadav00]

I am running the WRF model for an event using the urban physics scheme=1 and getting the below error.
WRF model version: 4.5.2
Simulation period: 22/05/2024_00 to 27/05/2024_18

Timing for Writing wrfout_d02_2024-05-22_00:00:00 for domain 2: 0.52564 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 208 JS 1 JE 205
WRF NUMBER OF TILES = 1
Timing for Writing wrfout_d03_2024-05-22_00:00:00 for domain 3: 1.76686 elapsed seconds
Tile Strategy is not specified. Assuming 1D-Y
WRF TILE 1 IS 1 IE 391 JS 1 JE 445
WRF NUMBER OF TILES = 1
Timing for main: time 2024-05-22_00:00:00 on domain 3: 24.30965 elapsed seconds

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

Backtrace for this error:
#0 0x1507077cfd11 in ???
#1 0x1507077ceee5 in ???
#2 0x15070746808f in ???
at /build/glibc-B3wQXB/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#3 0x559e89fd505f in ???
#4 0x559e89fda624 in ???
#5 0x559e89fde6a2 in ???
#6 0x559e897bd065 in ???
#7 0x559e88fe55c5 in ???
#8 0x559e88a2c538 in ???
#9 0x559e888c1953 in ???
#10 0x559e8790368e in ???
#11 0x559e87903cfb in ???
#12 0x559e87903cfb in ???
#13 0x559e8788a5a7 in ???
#14 0x559e87889fde in ???
#15 0x150707449082 in __libc_start_main
at ../csu/libc-start.c:308
#16 0x559e8788a01d in ???
#17 0xffffffffffffffff in ???

I am also attaching here the namelist.input, rsl.error and rsl.out files. Please give some solution if someone got this type of error.

 

[Ming Chen]

I looked at your namelist.input and have a few concerns:

(1) time_step =2 is too small for delx = 9km. Please change it to 45.
(2) please turn off cumulus scheme for D02 and D03, i.e., cu_physics = 1, 0, 0
(3) set radt = 9, 9, 9
(4) set sf_urban_physics = 1, 1, 1, this is because we require physics to be the same for all domains

In addition, this is a big case with large grid numbers in D03. Please run with more processors to avoid memory issues.

 

[mukeshkhadav00]

Thank you so much for replying.
I have done the correction which you mentioned, but still I am getting the same error.

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

Backtrace for this error:
#0 0x14634a37e692 in ???
#1 0x14634a37d825 in ???
#2 0x1463493b1acf in ???
#3 0x3009c15 in ???
#4 0x300dc09 in ???
#5 0x3012196 in ???
#6 0x272114c in ???
#7 0x1bda869 in ???
#8 0x1408648 in ???
#9 0x1218bcb in ???
#10 0x47b339 in ???
#11 0x47b999 in ???
#12 0x47b999 in ???
#13 0x406a71 in ???
#14 0x40605c in ???
#15 0x14634939dca2 in ???
#16 0x40609d in ???
#17 0xffffffffffffffff in ???

I am running this simulation in the institute HPC; I am attaching here the Slurm file.

Slurm file for submitting the job in HPC:

#!/bin/bash
#SBATCH --job-name=wrf_run # Job name
#SBATCH --partition=dgx # Partition to use
#SBATCH --ntasks=4 # Number of tasks
#SBATCH --cpus-per-task=1 # Number of CPU cores per task
#SBATCH --gres=gpu:1 # Include gpu for the task (only for gpu jobs)
#SBATCH --mem=16gb # Total memory limit
#SBATCH --time=48:00:00 # Time limit hrs:min:sec (optional)
#SBATCH --output=wrf_real_%j.log # Standard output and error log

echo "Job started on: $(date)"
echo "Running on node: $(hostname)"
echo "Working directory: $(pwd)"

# === Change to WRF run directory ===
cd /home/rs/sar/wrf/WRFV4.5/test/em_real/

# === Run WRF with mpirun ===
./wrf.exe

echo "Job ended on: $(date)"