Running interannual simulation

asked 2022-01-26 13:41:38 +0100

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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

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answered 2022-02-01 16:43:41 +0100

andres

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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/Cu...

The video from Gildas Cambon could be more helpful

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

Regards,

Andrés

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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.

Ansong ( 2022-02-01 16:53:03 +0100 )edit

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answered 2022-02-01 16:50:44 +0100

Ansong
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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 :

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answered 2022-02-01 16:47:00 +0100

Ansong
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updated 2022-02-01 16:47:35 +0100

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

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answered 2022-02-01 16:30:15 +0100

Ansong
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updated 2022-02-01 16:43:13 +0100

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_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: 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.

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answered 2022-02-01 16:21:01 +0100

andres

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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?

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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...

Ansong ( 2022-02-01 16:29:02 +0100 )edit

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