Ask Your Question
0

Running interannual simulation

asked 2022-01-26 13:41:38 +0200

this post is marked as community wiki

This post is a wiki. Anyone with karma >5 is welcome to improve it.

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

edit retag flag offensive close merge delete

5 answers

Sort by » oldest newest most voted
0

answered 2022-02-01 16:43:41 +0200

andres gravatar image

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

edit flag offensive delete link more

Comments

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 gravatar imageAnsong ( 2022-02-01 16:53:03 +0200 )edit
0

answered 2022-02-01 16:50:44 +0200

Ansong gravatar image

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 :

edit flag offensive delete link more
0

answered 2022-02-01 16:47:00 +0200

Ansong gravatar image

updated 2022-02-01 16:47:35 +0200

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

edit flag offensive delete link more
0

answered 2022-02-01 16:30:15 +0200

Ansong gravatar image

updated 2022-02-01 16:43:13 +0200

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.

edit flag offensive delete link more
0

answered 2022-02-01 16:21:01 +0200

andres gravatar image

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?

edit flag offensive delete link more

Comments

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 gravatar imageAnsong ( 2022-02-01 16:29:02 +0200 )edit
Login/Signup to Answer

Question Tools

2 followers

Stats

Asked: 2022-01-26 13:41:38 +0200

Seen: 2,626 times

Last updated: Feb 01 '22