[MITgcm-support] strange mnc behavior

[Martin Losch]

Hi Ruth,

on top of dumpFreq=0. you can also set dumpInitAndLast = .False., and 
that will get rid of any unwanted netcdf output.

Martin

On 12/05/2016 12:43 AM, Ruth Musgrave wrote:
> Hi Ryan,
>
> thanks for the fast reply.
>
> You are right - this was the problem, but for some reasonably
> non-obvious reasons (to me). The issue was that even though I was
> relying on the diagnostics package for my output, the simulation was
> still dumping state variables occasionally, and one of the state
> variables is a file named phiHyd*.nc. My data.diagnostics named my
> pressure output file PHIHYD*.nc. When the model went to dump state
> variables, it checked to see if phiHyd*.nc was present in the directory.
> I guess that something, somewhere is not case sensitive, and so it found
> my diagnostics output which has differently named dimensions
> (“Zmd000020" rather than “Z”), causing the fatal error and killing my
> run. The problem went away when I output all of my diagnostics into one
> file because it had a unique name (“outs_3D*”).
>
> Morals of the story:
> 1. calling your diagnostics output by the same name as one of the
> model’s state files is dangerous
> 2. don’t combine state and diagnostic output (this was just me being
> careless)
>
> I’ve now set "dumpFreq=0." in my data file, which allows me to continue
> to live dangerously (I still get a fatal error at the end of the
> simulation, but I can live with that).
>
> Thanks for your help,
>
> Ruth
>
>
>> On Dec 4, 2016, at 3:40 PM, Ryan Abernathey <ryan.abernathey at gmail.com
>> <mailto:ryan.abernathey at gmail.com>> wrote:
>>
>> Ruth,
>>
>> Often this types of errors occur when restarting a crashed/aborted
>> simulation when the target netcdf file is already present in the
>> output directory. One needs to be sure to erase any existing netcdf
>> files corresponding with the Iter0.
>>
>> Have you ruled out this possibility?
>>
>> Cheers,
>> Ryan
>>
>> On Sun, Dec 4, 2016 at 2:28 PM, Ruth Musgrave <rmusg at mit.edu
>> <mailto:rmusg at mit.edu>> wrote:
>>
>>     Hello,
>>
>>     when I configure my data.diagnostics to output each variable to a
>>     different file, I encounter the following error after 53 snapshots
>>     have already been written to the file phiHyd.0000052596.t001.nc
>>     <http://phihyd.0000052596.t001.nc/>:
>>
>>     (PID.TID 0000.0001) *** ERROR *** MNC ERROR: dimension 'Z' does
>>     not exist for file 'phiHyd.0000052596.t001.nc
>>     <http://phihyd.0000052596.t001.nc/>’
>>
>>     the error is in agreement with ncdump -h, which reports the
>>     dimensions present in the file phiHyd.0000052596.t001.nc
>>     <http://phihyd.0000052596.t001.nc/> are:
>>
>>     dimensions:
>>             T = UNLIMITED ; // (53 currently)
>>             Zmd000020 = 20 ;
>>             X = 240 ;
>>             Y = 46 ;
>>
>>     The vertical dimension is always recorded in my netcdf output as
>>     “Zmd000020” or “Zld000020”, depending on the variable - I only
>>     recall ever seeing a dimension “Z” in the “state*.nc” outputs. I
>>     am not sure why the code suddenly starts looking for that
>>     dimension half way through the run. The error occurs at the same
>>     timestep whether I start the simulation from a pickup or from t=0.
>>
>>     When I configure my data.diagnostics to output all of my variables
>>     to the same file, it completes my simulation without error.
>>
>>     This is not critically important as for the time being I’ve found
>>     a work around, but in case someone knows what’s going on it would
>>     be good to understand. I’m attaching two versions of my
>>     data.diagnostics: data.diagnosticsWORKS and data.diagnosticsFAILS.
>>     Hopefully the naming convention is self explanatory.
>>
>>     Thanks in advance for any clues.
>>
>>     Ruth
>>
>>
>>
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-- 
Martin Losch
Alfred Wegener Institute for Polar and Marine Research
Postfach 120161, 27515 Bremerhaven, Germany;
Tel./Fax: ++49(0471)4831-1872/1797