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Segmentation fault with real.exe --> Subroutine input_chem_profile

kruthika

New member
Hello,

I am trying to run WRF-Chem v4.5.2. When I use chem_opt=201, real.exe stops with a seg fault error. I have tried this with WRF-Chem v4.4.2 and I receive the exact same segmentation fault error. I have looked at the other posts and none of those solutions worked for me. I am still waiting on the solutions for Program received signal SIGSEGV: Segmentation fault - invalid memory reference, Segmentation fault with real.exe and MOZCART, and STARTING WITH BACKGROUND CHEMISTRY Subroutine input_chem_profile: Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

(attached namelist.input and rsl.error.0000).

Subroutine input_chem_profile:
[a3-23:135859:0:135859] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x14dd87905b20)
==== backtrace (tid: 135859) ====
0 0x000000000004eb50 killpg() ???:0
1 0x000000000275692d __module_input_chem_data_MOD_make_chem_profile() ???:0
2 0x000000000275c5a6 __module_input_chem_data_MOD_input_chem_profile() ???:0
3 0x000000000044e73e med_sidata_input_() ???:0
4 0x000000000044f2fc MAIN__() real_em.f90:0
5 0x0000000000407061 main() ???:0
6 0x000000000003ad85 __libc_start_main() ???:0
7 0x000000000040709e _start() ???:0
=================================

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

Backtrace for this error:
#0 0x14de53a5bb4f in ???
#1 0x275692d in ???
#2 0x275c5a5 in ???
#3 0x44e73d in ???
#4 0x44f2fb in ???
#5 0x407060 in ???
#6 0x14de53a47d84 in ???
#7 0x40709d in ???
#8 0xffffffffffffffff in ???
 

Attachments

  • namelist_input.txt
    7.3 KB · Views: 1
  • output.txt
    838 bytes · Views: 0
  • rsl_error.txt
    15.3 KB · Views: 2
Hello,

I am trying to run WRF-Chem v4.5.2. When I use chem_opt=201, real.exe stops with a seg fault error. I have tried this with WRF-Chem v4.4.2 and I receive the exact same segmentation fault error. I have looked at the other posts and none of those solutions worked for me. I am still waiting on the solutions for Program received signal SIGSEGV: Segmentation fault - invalid memory reference, Segmentation fault with real.exe and MOZCART, and STARTING WITH BACKGROUND CHEMISTRY Subroutine input_chem_profile: Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

(attached namelist.input and rsl.error.0000).

Subroutine input_chem_profile:
[a3-23:135859:0:135859] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x14dd87905b20)
==== backtrace (tid: 135859) ====
0 0x000000000004eb50 killpg() ???:0
1 0x000000000275692d __module_input_chem_data_MOD_make_chem_profile() ???:0
2 0x000000000275c5a6 __module_input_chem_data_MOD_input_chem_profile() ???:0
3 0x000000000044e73e med_sidata_input_() ???:0
4 0x000000000044f2fc MAIN__() real_em.f90:0
5 0x0000000000407061 main() ???:0
6 0x000000000003ad85 __libc_start_main() ???:0
7 0x000000000040709e _start() ???:0
=================================

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

Backtrace for this error:
#0 0x14de53a5bb4f in ???
#1 0x275692d in ???
#2 0x275c5a5 in ???
#3 0x44e73d in ???
#4 0x44f2fb in ???
#5 0x407060 in ???
#6 0x14de53a47d84 in ???
#7 0x40709d in ???
#8 0xffffffffffffffff in ???

Hii Kruthika,

Did you solve the problem?

Kindly share if you have solved it. I am stuck with a similar problem!
 
Hii Kruthika,

Did you solve the problem?

Kindly share if you have solved it. I am stuck with a similar problem!
Hi Sanatan,

I used a script to run the real.exe (sub.real.sh) shown below. It seems that increasing the mem-per-cpu did not address the issue but when I increased ntasks-per-node to 50, it fixed my segmentation fault issue. I increased my ntasks-per-node for distributed parallelism until it ran successfully. I hope this helps!

Code:
#!/bin/tcsh
#SBATCH --job-name=real
#SBATCH --partition=batch
#SBATCH --time=03:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=50
#SBATCH --ntasks-per-node=50
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=8G
#SBATCH --output=%x_%j.out
cd $SLURM_SUBMIT_DIR

ml WRF-Chem-KPP/4.5.2-foss-2022a-dmpar
time mpirun -n 50 ./real.exe
 
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