ERROR: Abnormal termination: NetCDF OUTPUT.

[osean]

Hello ROMS experts

I am moving back into office so now I have a Ubuntu linux workstation. I was running ROMS previously on my Macbook, which has been pretty smooth. Now switching to Ubuntu linux, I am running into some unexpected issues when I try to re-run some stuff.

I have set up ROMS from scratch again here, all went well, upwelling test case fine, output files good, all fine.

However now when I re-run the domain that I configured myself, I am running into a NetCDF OUTPUT error that I have not seen before:

Code: Select all

ROMS/TOMS - Output NetCDF summary for Grid 01:

 Analytical header files used:

     ROMS/Functionals/ana_btflux.h
     ROMS/Functionals/ana_grid.h
     ROMS/Functionals/ana_initial.h
     ROMS/Functionals/ana_smflux.h
     ROMS/Functionals/ana_stflux.h
     ROMS/Functionals/ana_vmix.h
 Found Error: 03   Line: 391      Source: ROMS/Utility/close_io.F, close_out

 ROMS/TOMS - Output error ............ exit_flag: 3


 ERROR: Abnormal termination: NetCDF OUTPUT.
 REASON: No error                                                                        
Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO
ERROR STOP 

Error termination. Backtrace:
#0  0x7f6731b3e820 in ???
#1  0x7f6731b3f379 in ???
#2  0x7f6731b40a97 in ???
#3  0x56067103590e in ???
#4  0x7f67317c2564 in ???
#5  0x56067103595d in ???
#6  0xffffffffffffffff in ???

Looking up some old post, this looks like a very obsolete error. Some earlier posts pointed to memory issue, so I looked further up again:

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 0.000000E+00 (Beckmann and Haidvogel)
rx1 = 0.000000E+00 (Haney)

Initial domain volumes: TotVolume = 1.0000000000E+16 m3
MinCellVol = 5.9919432728E+08 m3
MaxCellVol = 1.6185126730E+10 m3
Max/Min = 2.7011481907E+01


NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000105120)


TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0001-01-01 00:00:00.00 5.003588E-03 2.460429E+04 2.460429E+04 1.000000E+16
(001,050,50) 5.972398E-02 0.000000E+00 0.000000E+00 9.953997E-01
DEF_HIS - Illegal output type, io_type = 0
Found Error: 03 Line: 82 Source: ROMS/Utility/def_his.F
Found Error: 03 Line: 187 Source: ROMS/Nonlinear/output.F
Found Error: 03 Line: 518 Source: ROMS/Nonlinear/main3d.F
Found Error: 03 Line: 301 Source: ROMS/Drivers/nl_roms.h, ROMS_run

Elapsed wall CPU time for each process (seconds):

Thread # 0 CPU: 1.134
Total: 1.134

Nonlinear model elapsed CPU time profile, Grid: 01

Allocation and array initialization .............. 0.976 (86.0304 %)
Ocean state initialization ....................... 0.104 ( 9.2130 %)
Reading of input data ............................ 0.000 ( 0.0017 %)
Processing of input data ......................... 0.000 ( 0.0215 %)
Processing of output time averaged data .......... 0.000 ( 0.0046 %)
Computation of vertical boundary conditions ...... 0.000 ( 0.0217 %)
Computation of global information integrals ...... 0.010 ( 0.8427 %)
2D/3D coupling, vertical metrics ................. 0.037 ( 3.3020 %)
Omega vertical velocity .......................... 0.008 ( 0.7063 %)
Equation of state for seawater ................... 0.012 ( 1.0810 %)
Total: 1.148 101.2249 %

Unique kernel(s) regions profiled ................ 1.148 101.2249 %
Residual, non-profiled code ...................... -0.014 -1.2249 %


All percentages are with respect to total time = 1.134


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Dynamic and Automatic memory (MB) usage for Grid 01: 200x100x50 tiling: 1x1

tile Dynamic Automatic USAGE

0 1227.22 62.70 1289.92

TOTAL 1227.22 62.70 1289.92

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Found Error: 03 Line: 85 Source: ROMS/Utility/close_io.F, close_file_nf90
Found Error: 03 Line: 85 Source: ROMS/Utility/close_io.F, close_file_nf90
Found Error: 03 Line: 85 Source: ROMS/Utility/close_io.F, close_file_nf90
Found Error: 03 Line: 85 Source: ROMS/Utility/close_io.F, close_file_nf90
Found Error: 03 Line: 85 Source: ROMS/Utility/close_io.F, close_file_nf90

Essentially as soon as the model started to run at grid 01 it encountered this error. Bizarre, and not sure why. I never had such an issue on Macbook, but now on a Linux PC there is this... Any idea how the dynamic and automatic memory usage here tells me about? Not super well versed with computers so I am trying to learn what it is telling me here...

Thanks all

[arango]

I don't think that is an I/O error:

Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO
ERROR STOP

Something is wrong in your configuration in roms.in that you get a division by zero. I updated the code yesterday to remove those confusing I/O errors when you have a configuration error that is the primary thing that you need to take care of.

[osean]

I don't think that is an I/O error:

Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO
ERROR STOP

Something is wrong in your configuration in roms.in that you get a division by zero. I updated the code yesterday to remove those confusing I/O errors when you have a configuration error that is the primary thing that you need to take care of.

Interesting... configuration in roms.in - I did not change anything roms.in, as I simply copied and pasted from my Mac to the Linux. It was running perfectly fine on the Mac, with no such an error. Should I check if anything has gone wrong during the copy process in those analytical files? I suspect if there's a division by zero it must be in the initial set-ups? I don't see anything to do with division in roms.in
thanks

[arango]

If you are using the latest version of the code, which I recommend using, you need to be sure that your roms.in is up to date. Compile with debugging flags so you get more information about the division by zero. We can get such errors when the arguments to MOD are zero or uninitialized. There are lots of MOD statements in ROMS.

[osean]

If you are using the latest version of the code, which I recommend using, you need to be sure that your roms.in is up to date. Compile with debugging flags so you get more information about the division by zero. We can get such errors when the arguments to MOD are zero or uninitialized. There are lots of MOD statements in ROMS.

Oh thanks a lot for explaining this. Indeed it is the roms.in version discrepancy. I just copied the new roms_upwelling.in and replaced it with the domain set ups. Now it is running. Magic

[reba1]

Hi all,
I am facing same error and Iam using roms version 3.9.


Found Error: 01 Line: 361 Source: ROMS/Utility/close_io.F, close_out

ROMS/TOMS - Blows up ................ exit_flag: 1

Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO IEEE_UNDERFLOW_FLAG
ERROR STOP

can you share the updated roms.in file

[AMIRHOSSEIN]

Hello reba1,
I had the same problem and I suggest that instead of downloading the src of ROMS from different places,
download the latest version of ROMS through the following instructured link by having the username
and password of the myroms.org site.
https://www.myroms.org/wiki/ROMS_UNSW2008

-Good luck-