[MITgcm-support] Error related to BLING
Gus Correa
gus at ldeo.columbia.edu
Mon Sep 6 11:49:49 EDT 2021
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
>>> > MITgcm-support at mitgcm.org
>>> >
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