Running interannual simulation

run / config issues
1

Hi,
I am trying to run the interannual Benguela simulation and I got some errors; with and without MPI. I need some help decoding where this is coming from. Here’s the run output

Getting croco from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_IN
Getting AGRIF_FixedGrids.in from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_IN
/bin/cp: cannot stat ‘/home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_IN/AGRIF_FixedGrids.in’: No such file or directory
Getting croco_grd.nc from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_FILES
Getting croco_inter.in from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_IN
Getting croco_ini_SODA_Y2005M01.nc from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_FILES
Computing YEAR 2005 MONTH 01
Getting croco_blk_ECMWF_Y2005M01.nc from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_FILES
Getting croco_bry_SODA_Y2005M01.nc from /home/joseph/Documents/University_of_Ghana/DeptOfMath/Research/MODELS/croco/CONFIGS/BENGUELA_LR/CROCO_FILES
YEAR = 2005 MONTH = 1 DAYS = 31 DT = 3600 NTIMES = 0
No exact restart
set NUMRECINI = 1

Writing in croco_inter.in
USING DT = 3600
USING NFAST = 60
USING NUMTIMES = 744
USING NUMAVG = 72
USING NUMHIS = 744
USING NUMRST = 744
USING NUMRECINI = 1

Computing for Y2005M01
Tue 25 Jan 08:20:23 GMT 2022
[joseph-OptiPlex-7020:29993] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[joseph-OptiPlex-7020:29993] Set MCA parameter “orte_base_help_aggregate” to 0 to see all help / error messages
Tue 25 Jan 08:20:24 GMT 2022
Test croco_Y2005M01.out

Warning: month not finished properly

Run start date: xx/xx/x

CANCEL_KW ERROR: Can not cancel keyword: run_end_date
Check SCRUM/ROMS input script for possible duplicated keyword.

Run end date: xx/xx/xxxx xx:xx:xx

WARNING: Unrecognized keyword: start_date → DISREGARDED.

WARNING: Unrecognized keyword: origin_date → DISREGARDED.

READ_INP ERROR while reading block with keyword ‘output_time_steps’.

READ_INP ERROR: A total of 3 configuration errors discovered.

Month Y2005M01 did not work

2

Please post the content of your croco_Y2005M01.out file. That file contains a better explanation of what failed.

Are you sure you have all the forcings in the CROCO_FILES directory?

3

Hi Andres, thanks for replying. I think I have all the files; this is the first time I’m trying the inter-annual case so I might be wrong. I’ll post the content of croco_Y200501.out in the answer space…

4

Content of croco_Y2005M01.out:

CANCEL_KW ERROR: Can not cancel keyword: run_start_date
Check SCRUM/ROMS input script for possible duplicated keyword.

CANCEL_KW ERROR: Can not cancel keyword: run_start_date
Check SCRUM/ROMS input script for possible duplicated keyword.

CANCEL_KW ERROR: Can not cancel keyword: run_start_date
Check SCRUM/ROMS input script for possible duplicated keyword.

CANCEL_KW ERROR: Can not cancel keyword: run_end_date
Check SCRUM/ROMS input script for possible duplicated keyword.

CANCEL_KW ERROR: Can not cancel keyword: run_end_date
Check SCRUM/ROMS input script for possible duplicated keyword.

CANCEL_KW ERROR: Can not cancel keyword: run_end_date
Check SCRUM/ROMS input script for possible duplicated keyword.

READ_INP ERROR while reading block with keyword ‘output_time_steps’.

READ_INP ERROR while reading block with keyword ‘output_time_steps’.

READ_INP ERROR: A total of 3 configuration errors discovered.

READ_INP ERROR: A total of 3 configuration errors discovered.

READ_INP ERROR while reading block with keyword ‘output_time_steps’.

READ_INP ERROR: A total of 3 configuration errors discovered.

Southern Benguela Interannual Run
744 ntimes Total number of timesteps for 3D equations.

MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 3.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

3600.00 dt Timestep [sec] for 3D equations
60 ndtfast Number of 2D timesteps within each 3D step.
1 ninfo Number of timesteps between runtime diagnostics.

7.000E+00 theta_s S-coordinate surface control parameter.
2.000E+00 theta_b S-coordinate bottom control parameter.
2.000E+02 Tcline S-coordinate surface/bottom layer width used in
vertical coordinate stretching, meters.

Run start date: XXXXXXX

Run end date: XXXXXXX

CANCEL_KW ERROR: Can not cancel keyword: run_start_date
Check SCRUM/ROMS input script for possible duplicated keyword.

Run start date: xx/xx/x

CANCEL_KW ERROR: Can not cancel keyword: run_end_date
Check SCRUM/ROMS input script for possible duplicated keyword.

Run end date: xx/xx/xxxx xx:xx:xx

WARNING: Unrecognized keyword: start_date → DISREGARDED.

WARNING: Unrecognized keyword: origin_date → DISREGARDED.

READ_INP ERROR while reading block with keyword ‘output_time_steps’.

READ_INP ERROR: A total of 3 configuration errors discovered.

5

Hi Ansong,

Please post the content of your CROCO_FILES directory (ls -lh).

It seems there is a problem with the croco.in file. Could you post it here?

Here is a tutorial (in Spanish, sorry) that we used last year with the interannual case

http://mosa.dgeo.udec.cl/CROCO2021/CursoAvanzado/Tutorial_Interanual/Tutorial_CursoAvanzadoCROCO_SimulacionesInterannuales.pdf

The video from Gildas Cambon could be more helpful

https://www.youtube.com/watch?v=_lqVtvnfZIY

Regards,

Andrés

6

Content of CROCO_FILES directory:

-rw-rw-r-- 1 joseph joseph 24M Jan 22 19:52 croco_blk_ECMWF_Y2005M01.nc
-rw-rw-r-- 1 joseph joseph 22M Jan 22 19:53 croco_blk_ECMWF_Y2005M02.nc
-rw-rw-r-- 1 joseph joseph 24M Jan 22 19:53 croco_blk_ECMWF_Y2005M03.nc
-rw-rw-r-- 1 joseph joseph 1.9M Jan 20 19:46 croco_blk.nc
-rw-rw-r-- 1 joseph joseph 2.1M Jan 20 19:45 croco_bry.nc
-rw-rw-r-- 1 joseph joseph 543K Jan 21 09:03 croco_bry_SODA_Y2005M01.nc
-rw-rw-r-- 1 joseph joseph 543K Jan 21 09:03 croco_bry_SODA_Y2005M02.nc
-rw-rw-r-- 1 joseph joseph 543K Jan 21 09:04 croco_bry_SODA_Y2005M03.nc
-rw-rw-r-- 1 joseph joseph 981K Jan 20 19:44 croco_bry_Z.nc
-rw-rw-r-- 1 joseph joseph 23M Jan 20 19:45 croco_clm.nc
-rw-rw-r-- 1 joseph joseph 5.7M Jan 21 09:03 croco_clm_SODA_Y2005M01.nc
-rw-rw-r-- 1 joseph joseph 5.7M Jan 21 09:03 croco_clm_SODA_Y2005M02.nc
-rw-rw-r-- 1 joseph joseph 5.7M Jan 21 09:04 croco_clm_SODA_Y2005M03.nc
-rw-rw-r-- 1 joseph joseph 2.0M Jan 20 19:44 croco_frc.nc
-rw-rw-r-- 1 joseph joseph 427K Jan 20 19:43 croco_grd.nc
-rw-rw-r-- 1 joseph joseph 1.9M Jan 20 19:46 croco_ini.nc
-rw-rw-r-- 1 joseph joseph 1.9M Jan 21 09:02 croco_ini_SODA_Y2005M01.nc
-rw-rw-r-- 1 joseph joseph 22M Jan 20 19:45 croco_oa.nc

7

Here are the first couple of lines of croco_inter.in

title:
Southern Benguela Interannual Run
time_stepping: NTIMES dt[sec] NDTFAST NINFO
NUMTIMES TIMESTEP NFAST 1
S-coord: THETA_S, THETA_B, Hc (m)
7.0d0 2.0d0 200.0d0

run_start_date:
XXXXXXX
run_end_date:
XXXXXXX
run_start_date:
xx/xx/xx xx:xx:xx
run_end_date:
xx/xx/xxxx xx:xx:xx
start_date:
xx/xx/xxxx xx:xx:xx
origin_date:
xx/xx/xxxx xx:xx:xx
output_time_steps: DT_HIS(H), DT_AVG(H), DT_RST(H)
XX XX XX

grid: filename
croco_grd.nc
forcing: filename
croco_frc.nc
bulk_forcing: filename
croco_blk.nc
climatology: filename
croco_clm.nc
boundary: filename
croco_bry.nc
initial: NRREC / filename
NUMRECINI
croco_ini.nc
restart: NRST, NRPFRST / filename
NUMRST 0
croco_rst.nc
history: LDEFHIS, NWRT, NRPFHIS / filename
T NUMHIS 0
croco_his.nc
averages: NTSAVG, NAVG, NRPFAVG / filename
1 NUMAVG 0
croco_avg.nc

primary_history_fields: zeta UBAR VBAR U V wrtT(1:NT)
T T T T T 40*T
auxiliary_history_fields: rho Omega W Akv Akt Aks Bvf Visc3d Diff3d HBL HBBL Bostr
:

8

Thanks Andres, I’ve watched them before when you sent them to me, Joseph, after the workshop, and tried to follow as much as possible. Thanks again.