[MITgcm-support] Error related to BLING
Gus Correa
gus at ldeo.columbia.edu
Tue Sep 7 10:42:47 EDT 2021
PS - Not using silica as a ptracer here, so I don't know if it works.
To fix the code you need to modify both the subroutine interface in
bling_bio_nitrogen.F
and the call in bling_main.F.
Or switch to a newer MITgcm checkpoint/version that may have fixed it.
On Tue, Sep 7, 2021 at 10:18 AM Gus Correa <gus at ldeo.columbia.edu> wrote:
> Hi Kunal
>
> Michael is right.
>
> However, as I guessed, it is a missing argument (not the tracer itself,
> but the tendency G_SI) in a subroutine interface.
> The code I have (checkpoint_67w) has the interface below for
> the BLING_BIO_NITROGEN subroutine interface,
> which includes G_SI (the SI tendency) *IF *you compile with
> USE_SIBLING defined in BLING_OPTIONS.h.
> (The default is #undef, I think.).
> Silica as a passive tracer seems to have been introduced recently,
> so it may not have been fully tested.
>
> So, two possibilities that I can imagine:
> 1. You didn't compile with #define USE_SIBLING in BLING_OPTIONS.h
> 2. You are using an older code that is really missing G_SI
> But it can always be something else.
>
> Also, take a look at the doc/tag-index file in your main MITgcm code to
> see
> if there is anything relevant about BLING and silica there.
>
> I hope this helps,
> Gus
>
> *******
> SUBROUTINE BLING_BIO_NITROGEN(
> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,
> I PTR_NO3, PTR_DON,
> #ifdef USE_SIBLING
> I PTR_SI,
> #endif
> #ifdef ADVECT_PHYTO
> I PTR_PHY,
> #endif
> O G_DIC, G_ALK, G_O2, G_FE,
> O G_PO4, G_DOP, G_NO3, G_DON,
> #ifdef USE_SIBLING
> O G_SI,
> #endif
> I bi, bj, imin, imax, jmin, jmax,
> I myTime, myIter, myThid)
> *****
>
>
> On Tue, Sep 7, 2021 at 9:00 AM Michael Schaferkotter <
> schaferk at bellsouth.net> wrote:
>
>> 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
>>>>>> > MITgcm-support at mitgcm.org
>>>>>> >
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