[MITgcm-support] Error related to BLING
Jean-Michel Campin
jmc at mit.edu
Wed Sep 8 15:36:56 EDT 2021
Hi Kunal,
I put Gus' fix into my branch "fix_sibling_attempt", see:
https://github.com/jm-c/MITgcm/blob/fix_sibling_attempt/pkg/bling/bling_main.F
I also try to turn on useSIBLING (i.e., #define useSIBLING in BLING_OPTIONS.h)
in verification/global_oce_biogeo_bling and was getting the same error as you ;
After adding the fix in bling_main.F, I can run for 4 time-step but it was
without any specific Silica forcing or initial conditions.
Cheers,
Jean-Michel
On Wed, Sep 08, 2021 at 03:17:43PM -0400, Gus Correa wrote:
> Hi Kunal
>
> Hmmm ... interesting ... I took a more careful look at what Michael pointed
> out ...
>
> I also have missing G_SI in the call to BLING_BIO_NITROGEN in bling_main.F
> in checkpoint_67w.
> I enclose the code snippet below.
>
> On other hand, G_SI is present in the subroutine BLING_BIO_NITROGEN
> definiition
> in bling_bio_nitrogen.F. (See that other code snippet, which I sent
> yesterday, down the email pile.)
>
> So, the two don't match.
> But they should.
>
> However, since I am not using silica as a ptracer, the bug doesn't affect
> anything in the code that is actually compiled in my case.
> The preprocessor removes any reference to PTR_SI and to G_SI,
> removing the mismatch.
> But in your case it does matter.
>
> In any case, it's better to fix the bug.
> This snippet:
>
> #ifdef USE_SIBLING
> O G_SI,
> #endif
>
> should be added right after the line
>
> U G_PO4, G_DOP, G_NO3, G_DON,
>
> in the code lines after
>
> call BLING_BIO_NITROGEN
>
> in bling_main.F,
> to match the corresponding subroutine code in bling_bio_nitrogen.F,=.
>
> Then recompile fresh.
>
> Regards,
> Gus
>
> ****** code snippet: call to BLING_BIO_NITROGEN in bling_main.F ***
>
> C call either "BLING" or "BLING + nitrogen"
> #ifndef USE_BLING_V1
> CALL 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
> 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,
> I myTime, myIter, myThid)
> #else
> CALL BLING_BIO(
> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,
> U G_DIC, G_ALK, G_O2, G_FE,
> U G_PO4, G_DOP,
> I bi, bj, imin, imax, jmin, jmax,
> I myTime, myIter, myThid)
> #endif
> *****
>
> On Wed, Sep 8, 2021 at 9:53 AM kunal madkaiker <kunal.madkaiker02 at gmail.com>
> wrote:
>
> > 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
> >>>>>>>> >
> >>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__mailman.mitgcm.org_mailman_listinfo_mitgcm-2Dsupport&d=DwICAg&c=-35OiAkTchMrZOngvJPOeA&r=HSHS34ROdfL7f2oVxuKB761hrMvWN1RWA5k3SHGts_s&m=iOrbnncxN5Y2dAD0gIwZZlqCaFyQZtz6j7wWPBxR3O8&s=oDRvUUxOSUqUl1gJNzk7caygbs0kdrURo0TiIV6QfqQ&e=
> >>>>>>>>
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