[MITgcm-support] Error while creating bathymery : ini_masks_etc

Camille Mazoyer mazoyer at univ-tln.fr
Tue Jan 31 11:28:09 EST 2017


Thanks all for your replies and all your ideas.

Le 31/01/2017 03:26, Gus Correa a écrit :
> On 01/30/2017 05:35 PM, Jody Klymak wrote:
>> Hi Camille,
>>
>> Its not really clear what you are doing.  Did you save a depth file and
>> are reading it in with bathyFile='topo.bin’, (or whatever you named
>> it?). 
Yes.

>> The most obvious error would be that you saved some NaNs in that
>> file.

Yeesssss!!!!!!! Thanks a lot.
It was the problem! I made a mistake in Matlab while creating my 
bathymetry file, and I had NaN values.
Thank you very much.



>
> ... or perhaps 32-bit vs. 64-bit floating point ...
> ... or also big-endian vs. little-endian floating point ...
> ... both of which can be a source of confusion and distress.
> Check how you created the file first.
> (Matlab has fine control of both.)
>
> In MITgcm, reading 32-bit vs. 64-bit can be controlled via
>
> readBinaryPrec=32 (or 64) in the "data" file, &PARM01 namelist.
>
> Big-endian vs. little-endian in compiler flags such as
> -fconvert=big-endian (gfortran), -convert big_endian (Intel ifort).
>

Thank you also for these ideas, even if in my case, it appears to be a 
NaN values problem.

Cheers,
Camille


>
> I hope this helps,
> Gus Correa
>
>
>> If you are masking out land or something, set those values to zero
>> instead of NaN, and I think things should work.
>>
>> Good luck,
>>
>> Jody
>>
>>
>>> On 28 Jan 2017, at  14:58 PM, Camille Mazoyer <mazoyer at univ-tln.fr
>>> <mailto:mazoyer at univ-tln.fr>> wrote:
>>>
>>> Dear all,
>>>
>>> I am creating a new bathymetry for a Bay (Toulon Bay, France). My grid
>>> is  a 200x100x130 points grid.
>>> I want to generate a netcdf bathymetry file for step one: for that, I
>>> have no OBC, no initial state files.
>>> I have a binary bathymetry file and binary levels file.
>>> I use debugging options.
>>>
>>> I have a floating invalid problem that I don't understand.
>>> It's in ini_masks_etc.f, so I decided to modify the code with some
>>> "write toto" lines:
>>>
>>>   65 C      o Non-dimensional distance between grid bound. and domain
>>> lower_R bound.
>>>   66            hFacCtmp = (rF(k)-R_low(i,j,bi,bj))*recip_drF(k)
>>>   67            ! cmzy
>>>   68            write(*,*) 'i,j,k',i,j,k
>>>   69            write(*,*) 'rF(k)',rF(k)
>>>   70            write(*,*) 'hFacCtmpR_low(i,j,bi,bj)',R_low(i,j,bi,bj)
>>>   71            write(*,*) 'recip_drF(k)',recip_drF(k)
>>>   72            write(*,*) 'hFacCtmp',hFacCtmp
>>>   73 C      o Select between, closed, open or partial (0,1,0-1)
>>>   74            hFacCtmp=min( max( hFacCtmp, 0. _d 0) , 1. _d 0)
>>>
>>> And here is the output:
>>>
>>> ** Warning ** CAL_READPARMS: ignores "data.cal" file since
>>> ** Warning ** CAL_READPARMS: useCAL= F (set from "data.pkg")
>>> i,j,k          -2          -2           1
>>> rF(k)  0.000000000000000E+000
>>> hFacCtmpR_low(i,j,bi,bj)                     NaN
>>> recip_drF(k)   1.00000000000000
>>> hFacCtmp                     NaN
>>> forrtl: error (65): floating invalid
>>> Image              PC                Routine            Line Source
>>> mitgcmuv           0000000001730315  Unknown Unknown Unknown
>>> mitgcmuv           000000000172DF37  Unknown Unknown Unknown
>>> mitgcmuv           00000000016E4382  Unknown Unknown Unknown
>>> mitgcmuv           00000000016E41D6  Unknown Unknown Unknown
>>> mitgcmuv           000000000167CE25  Unknown Unknown Unknown
>>> mitgcmuv           00000000016805B7  Unknown Unknown Unknown
>>> libpthread.so.0    0000003AC5C0F710  Unknown Unknown Unknown
>>> mitgcmuv           0000000000410D92  ini_masks_etc_ 3151
>>> ini_masks_etc.f
>>> mitgcmuv           00000000014EDC49  initialise_fixed_ 1857
>>> initialise_fixed.f
>>> mitgcmuv           00000000015F89EA  the_model_main_ 2382
>>> the_model_main.f
>>> mitgcmuv           000000000113CEAF  MAIN__ 3919 main.f
>>> mitgcmuv           000000000040F41E  Unknown Unknown Unknown
>>> libc.so.6          0000003AC541ED5D  Unknown Unknown Unknown
>>> mitgcmuv           000000000040F329  Unknown Unknown Unknown
>>>
>>> Do you have any idea to help me? any test?
>>> I don't really understand what's going on....
>>> I must admit that I don't know why there is a point i=-2, j=-2 , and
>>> why the rfk = 0 there.... I thought my Levels file was ok.
>>> If somebody has already encounter this error?
>>>
>>> Thanks for any advice,
>>> Camille
>>>
>>> -- 
>>> ------------------------------------------
>>> Camille Mazoyer
>>> Phd Student
>>> Mediterranean Institute of Oceanography (MIO)
>>> Institut de Mathématiques de Toulon (IMATH)
>>> Université de TOULON
>>> Bat X - CS 60584
>>> 83041 TOULON cedex 9
>>> France
>>> tel: +33.4.94.14.24.50
>>> Email: mazoyer at univ-tln.fr <mailto:mazoyer at univ-tln.fr>
>>> http://mio.pytheas.univ-amu.fr/
>>> http://imath.fr/
>>>
>>>
>>> _______________________________________________
>>> MITgcm-support mailing list
>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>> -- 
>> Jody Klymak
>> http://web.uvic.ca/~jklymak/
>>
>>
>>
>>
>>
>>
>>
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>>
>
>
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-- 
------------------------------------------
Camille Mazoyer
Phd Student
Mediterranean Institute of Oceanography (MIO)
Institut de Mathématiques de Toulon (IMATH)
Université de TOULON
Bat X - CS 60584
83041 TOULON cedex 9
France
tel: +33.4.94.14.24.50
Email: mazoyer at univ-tln.fr
http://mio.pytheas.univ-amu.fr/
http://imath.fr/




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