PISCES and Segmentation fault

biogeochemistry
1

Hi everyone!

I had a problem when PISCES ran. After the model started calculating, the following appeared:

MAIN: started time-stepping

STEP time[DAYS] DIC ALK OXY POC PHY ZOO DOC NO3 FER
trd
0 9010.00000 2.3117408E+03 2.4039118E+03 1.7336273E+02 1.0000000E-02 4.9334064E-04 1.4240749E-04 1.7470662E+00 1.6560506E+00 2.8741285E-05 0

Number of days per year in file year2daydta = 0.0000000000000000

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 0x7fadf68238a0 in ???
#1 0x7fadf6822a45 in ???
#2 0x7fadf643e72f in ???
#3 0x43c260 in ???
#4 0x472882 in ???
#5 0x52b3a3 in ???
#6 0x4d5ec4 in ???
#7 0x4d664f in ???
#8 0x4b47db in ???
#9 0x4b4ca4 in ???
#10 0x4b471f in ???
#11 0x4036ac in ???
#12 0x7fadf64295cf in ???
#13 0x7fadf642967f in ???
#14 0x4036d4 in ???
#15 0xffffffffffffffff in ???

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

Backtrace for this error:

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

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

Backtrace for this error:
#0 0x7fad5b0238a0 in ???
#1 0x7fad5b022a45 in ???
#2 0x7fad5ac3e72f in ???
#3 0x43c260 in ???
#4 0x472882 in ???
#5 0x52b3a3 in ???
#6 0x4d5ec4 in ???
#7 0x4d664f in ???
#8 0x4b47db in ???
#9 0x4b4ca4 in ???
#10 0x4b471f in ???
#11 0x4036ac in ???
#12 0x7fad5ac295cf in ???
#13 0x7fad5ac2967f in ???
#14 0x4036d4 in ???
#15 0xffffffffffffffff in ???
#0 0x7f45c48238a0 in ???
#1 0x7f45c4822a45 in ???
#2 0x7f45c443e72f in ???
#3 0x43c260 in ???
#4 0x472882 in ???
#5 0x52b3a3 in ???
#6 0x4d5ec4 in ???
#7 0x4d664f in ???
#8 0x4b47db in ???
#9 0x4b4ca4 in ???
#10 0x4b471f in ???
#11 0x4036ac in ???
#12 0x7f45c44295cf in ???
#13 0x7f45c442967f in ???
#14 0x4036d4 in ???
#15 0xffffffffffffffff in ???

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

Backtrace for this error:

= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 241581 RUNNING AT n5
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

For context, this error appeared after activating PISCES. I ran CROCO for a few months with only physics, and then added biogeochemical variables in bry file and ini/rst file, I added rivers and nutrients to the croco.in file too. Why am I seeing this error? Is it a computer error, or did I do something wrong when compiling? I havenā€™t seen this error before.

I attach the log
202409_F_BIOLOGIA.txt (160.2 KB)

thanks in advance!
Catalina.

2

IĀ“m having the same error you described but only on the physical model. I didnĀ“t found a solution yet.

3

Did you make any changes before this error appeared? For example, did you have a different configuration, a different ini, bry, blk, or frc file, or did you use the same configuration but on a different domain? I had a similar error using AGRIF with PISCES light, as if the calculation was too heavy for the computer, because it worked if I used AGRIF only with physics and it worked if I used PISCES light without AGRIF.

4

Actually, IĀ“m using the tutorial files provided on website to test CROCO, so i didnĀ“t change anything to run the scripts. The only difference is that iĀ“m using a single domain instead of the AGRIF.

5

Which croco version do you use ?
Maybe you can do a try without input from rivers first.

6

Hi Catalina,

when checking the error, the following message appears: ā€˜**Number of days per year in file year2daydta = 0.0000000000000000ā€™. This is related to the file p4zsbc.F90 (PISCES surface boundary conditions of external inputs of nutrients), so the issue might be in the croco_frcbio.nc file (the one you generate with make_dust), or possibly in the options and/or values used in the configuration file namelist_ref. Best regards,

7

Hi Osvaldo,

I checked the namelist_ref file, I saw the ā€œparameters for inputs depositionā€ and it was ln_river = true. I tried run the model with lin_river = false and it worked! The problem was in namelist_ref file.

Thank you very much!

Regards

1 Like
8

Iā€™m using the latest version of croco.
In the end, i had to change the modules in the config.bash