NF_FWRITE ERROR: nf_put_vara netCDF error code = -60 mynode = 5

biogeochemistry
1

Hi everyone!

I’ve benn working with biology lately. Using NPZD and now PISCES light. The same thing happened with both giving this error:
[…]
116000 8972.16667 2.2656067E+03 2.3696804E+00 1.7205821E+02 4.5360569E-03 4.9441040E-04 1.3789281E-04 1.7429429E+00 1.6539005E+00 2.8663648E-05 0

  WRT_HIS -- wrote history fields into time record = 581 / 581  mynode =  0

  NF_FWRITE ERROR: nf_put_vara netCDF error code =  -60  mynode =   5

  WRT_HIS ERROR while writing variable 'ubar' into history file.
       Time record:   581   netCDF error code -60    mynode =   5

I tried with PISCES light without rivers and it worked completing the month without errors. When I added rivers, It gave me that error. I thought it was probably the biological values in croco.in and ran the model changing values, but again it was the same error and the same time step.

Could the computer be the problem? Or is it purely the model or version?

2

@Catalina Is it rivers-TS or ln_river ? I hope Incompatibility with River input (pre-processing). check “ubar” correct or not in matlab code. I will recommend you run without PISCES with the river first (physical model simulation with TS input from rivers) then try Bio. :+1:

Best,

Subhadeep

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3

Hi @smaishal,

thanks for your recommendation. The model ran with rivers and without PISCES, and the simulation ends the month correctly. So, the problem could be run bio with rivers together.

Regards!

4

@Catalina
Perfect. can you just try PISCES+River TS. without Nutrients from rivers. you can off this nutrients input lines in your Matlab code (initially).
If it successful then we together check with nutrients from rivers. These issues are already well reported with others. I will recommend you try this testing with CROCO 2.0.1. we need to modify that . Help me to test this first. PISCES developers said this ln_rivers working with NEMO successfully. please confirm me PISCES+River-TS is working or not first.

Still I believe this problem is associated with sediment blocks. (coupling of biology and sediment in PISCES). this problem was first reported by Lawrence Patrick Bernardo from Tokyo, he faced this problem with version 1.3.1. I thought its updated. please let me know.
I will create a separate issue for that to fix. What grid resolutions are you used for simulation?
Best,
Subhadeep

5

@smaishal
The grid is 1 km approx. I will try without nutrients and with CROCO 2.0.1. Thanks for your help. I will be reporting back.

Regards!

7

@Catalina
BIO_NChlPZD its working. checking other options also.

8

Hi Catalina,

I’ve encountered that netCDF writing error a few times, typically when the hard drive is full (though I don’t think that’s the case here) or when there are compatibility issues between the type of netCDF used to create the files (classic or netCDF-4) and the netCDF libraries used to compile the model. Are you creating the files on the same machine where you’re running the model? I suggest checking the netCDF type of your input data using the command “ncdump -k file.nc”. If, for example, all files are in netCDF-4 format, ensure that your netCDF libraries have been compiled with netCDF-4 support enabled. If they are classic netCDF files, I recommend converting them to netCDF-4 using NCO commands (ncks -4 in.nc out.nc), for instance.

I hope this helps. Best regards.

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