[MITgcm-support] Error related to BLING
kunal madkaiker
kunal.madkaiker02 at gmail.com
Wed Sep 8 09:53:38 EDT 2021
Thanks a lot Gus and Michael. I'll try as per the suggestions and will
provide an update on this.
Regards,
Kunal
On Tue, Sep 7, 2021 at 8:13 PM Gus Correa <gus at ldeo.columbia.edu> wrote:
> 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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