[MITgcm-support] Error related to BLING

Michael Schaferkotter schaferk at bellsouth.net
Tue Sep 7 09:00:29 EDT 2021


without looking at source code,
it seems that G_SI is missing in the BLING_BIO_NITROGEN call sequence, unless it is defined in an include file somewhere. Also check that G_SI is declared as an argument in the BLING_BIO_NITROGEN subroutine.

Sent from Here3.

> On Sep 7, 2021, at 06:23, kunal madkaiker <kunal.madkaiker02 at gmail.com> wrote:
> 
> 
>> 
> 2) bling_main.f
> 
> C  biological activity
> C  call either "BLING" or "BLING + nitrogen"
>        CALL BLING_BIO_NITROGEN(
>      I                 PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,
>      I                 PTR_NO3, PTR_DON,
>      I                 PTR_SI,
>      U                 G_DIC, G_ALK, G_O2, G_FE,
>      U                 G_PO4, G_DOP, G_NO3, G_DON,
>      I                 bi, bj, imin, imax, jmin, jmax,
> 4199   I                 myTime, myIter, myThid)
> 
> 
> 
>> On Mon, Sep 6, 2021 at 9:21 PM Gus Correa <gus at ldeo.columbia.edu> wrote:
>> Hi Kunal
>> 
>> Along the line mentioned by Michael.
>> 
>> You can compile fresh adding the -devel flag to genmake2 (do a make CLEAN or just delete your build directory beforehand to avoid any leftover).
>> Your build options file *probably* already has debug flags that are activated if you use -devel in genmake2. 
>> I think they are flags like FOPT or similar. Check.
>> 
>> Then add a namelist flag (can't remember by the exact name, check) to use debug at runtime in the eesupp namelist file ...  
>> hmmm ..  debugMode-.TRUE. ... I think. 
>> 
>> Finally, raise the debug level in the "data" PARM01 namelist debugLevel=4 (or 5).
>> 
>> This will drop more error messages in STDERR.???? and traceback the call stack the point of failure,
>> more verbose than it is now.
>> 
>> I would guess some subroutine interface may be missing one of the tracers, probably silica, but it can be another thing.
>> 
>> I hope this helps
>> Gus
>> 
>>> On Sat, Sep 4, 2021 at 9:38 AM Michael Schaferkotter <schaferk at bellsouth.net> wrote:
>>> 1. just to be sure, if parameter values in *.h are altered, you must recompile.
>>> 
>>> 2. for ifort compiler, recompile with:
>>> 
>>> g -check all -fpe0 -warn -traceback -debug extended
>>> 
>>> gfortran
>>> 
>>> -g -Wall -Wextra -Warray-temporaries -Wconversion -fimplicit-none -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow -finit-real=nan
>>> 
>>> rerun.
>>> 
>>> the stack trace will be more meaningful.
>>> 
>>> michael
>>> 
>>> Sent from Here3.
>>> 
>>>>> On Sep 4, 2021, at 02:14, kunal madkaiker <kunal.madkaiker02 at gmail.com> wrote:
>>>>> 
>>>> 
>>>> Thank you Matthew and Gus for your valuable suggestions. I could resolve the 2nd query as suggested by Matt by adding apco2file in data.bling.
>>>> 
>>>> I wanted to add few points regarding my 1st query (about adding silicate as 9th tracer) The PTRACERS_num ( in PTRACER_SIZE.h ), PTRACERS_numInUse, PTRACERS_useGMRedi (in data.ptracers), etc are already 9. So the error may not be due to this. Also the same model setup is running fine for the MITgcm-checkpoint67j (2019/06/18 ) release. This is the version where the USE_SIBLING option is added to the BLING package for the first time. However, I want to use the latest (or recent year) release. As Matthew asked I am also including the detailed message I get on screen when the model crashes. My STDERR files don't contain any error messages. So is this problem related to MITgcm release ?
>>>> 
>>>> Backtrace for this error:
>>>> #0  0x7f09681cc2ed in ???
>>>> #1  0x7f09681cb503 in ???
>>>> #2  0x7f0967a60fcf in ???
>>>> #3  0x5636cbe79533 in ???
>>>> #4  0x5636cbe8c909 in ???
>>>> #5  0x5636cbf36923 in ???
>>>> #6  0xffffffffffffffff in ???
>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
>>>> 
>>>> Backtrace for this error:
>>>> 
>>>> ===================================================================================
>>>> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
>>>> =   PID 63826 RUNNING AT ADRAO
>>>> =   EXIT CODE: 139
>>>> =   CLEANING UP REMAINING PROCESSES
>>>> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
>>>> ===================================================================================
>>>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
>>>> This typically refers to a problem with your application.
>>>> Please see the FAQ page for debugging suggestions
>>>> 
>>>> Regards,
>>>> Kunal
>>>> 
>>>>> On Sat, 4 Sep 2021, 01:14 Gus Correa, <gus at ldeo.columbia.edu> wrote:
>>>>> 
>>>>> 
>>>>>> On Fri, Sep 3, 2021 at 1:48 PM Matthew Mazloff <mmazloff at ucsd.edu> wrote:
>>>>>> Hello
>>>>>> 
>>>>>> 1) Do you have some more info on the error? Anything else given?
>>>>>> My first guess: did you set
>>>>>>       PARAMETER(PTRACERS_num = 9 )
>>>>>> in PTRACERS_SIZE.h?
>>>>>> 
>>>>>> 2) You have to give the exf parameters in data.bling, not data.ext. 
>>>>>> 
>>>>>> -Matt
>>>>> 
>>>>> Yes, as Matthew said, segfault is because 
>>>>> PARAMETER(PTRACERS_num = )
>>>>> is probably less than 9.
>>>>> I had the same error before.
>>>>> 
>>>>> ... and add to data.ptracers:
>>>>> 
>>>>>  PTRACERS_numInUse=9,
>>>>>  PTRACERS_useGMRedi=9*.TRUE., (if using GMRedi)
>>>>>  PTRACERS_useKPP=9*.TRUE., (if using KPP)
>>>>> 
>>>>> and the ptracers name, long name, units, etc, for instance
>>>>> 
>>>>>  PTRACERS_names(1)='dic',
>>>>>  PTRACERS_long_names(1)='Dissolved Inorganic Carbon',
>>>>>  PTRACERS_units(1)='mol C/m^3',
>>>>>  PTRACERS_advScheme(1)=77,
>>>>>  PTRACERS_diffKh(1)=0.E3,
>>>>>  PTRACERS_diffKr(1)=3.E-5,
>>>>> 
>>>>> Gus
>>>>>> 
>>>>>> 
>>>>>> > On Sep 3, 2021, at 10:38 AM, kunal madkaiker <kunal.madkaiker02 at gmail.com> wrote:
>>>>>> > 
>>>>>> > Dear All,
>>>>>> > 
>>>>>> >        I have two queries regarding the BLING model.
>>>>>> > 
>>>>>> > 1) I am running the recent release of MITgcm coupled to the BLING module. The model is running fine if I use the default 8 tracer option. When I try to add silica as 9th tracer (#define USE_SIBLING in BLING_OPTIONS.h), the model crashes in the beginning giving the following error message "Program received signal SIGSEGV: Segmentation fault - invalid memory reference.".
>>>>>> > 
>>>>>> > 2) I want the model to read apco2 values from a file via the data.exf instead of giving a constant value in data.bling. I enabled it with #define USE_EXFCO2 in BLING_OPTIONS.h. However, the model crashes with the error "Fortran runtime error: Cannot match namelist object name apco2startdate1."
>>>>>> > 
>>>>>> > Please suggest some solutions to the above issues.
>>>>>> > 
>>>>>> > Regards
>>>>>> > Kunal
>>>>>> > _______________________________________________
>>>>>> > MITgcm-support mailing list
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>>>>>> 
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