<div dir="ltr"><div>Thank you Jean-Michel for checking that my fix works,</div><div>and putting it in the git pipeline for a future release!</div><div>Gus<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 8, 2021 at 3:37 PM Jean-Michel Campin <<a href="mailto:jmc@mit.edu" target="_blank">jmc@mit.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Kunal,<br>
<br>
I put Gus' fix into my branch "fix_sibling_attempt", see:<br>
<a href="https://github.com/jm-c/MITgcm/blob/fix_sibling_attempt/pkg/bling/bling_main.F" rel="noreferrer" target="_blank">https://github.com/jm-c/MITgcm/blob/fix_sibling_attempt/pkg/bling/bling_main.F</a><br>
<br>
I also try to turn on useSIBLING (i.e., #define useSIBLING in BLING_OPTIONS.h)<br>
in verification/global_oce_biogeo_bling and was getting the same error as you ;<br>
After adding the fix in bling_main.F, I can run for 4 time-step but it was <br>
without any specific Silica forcing or initial conditions.<br>
<br>
Cheers,<br>
Jean-Michel<br>
<br>
On Wed, Sep 08, 2021 at 03:17:43PM -0400, Gus Correa wrote:<br>
> Hi Kunal<br>
> <br>
> Hmmm ... interesting ... I took a more careful look at what Michael pointed<br>
> out ...<br>
> <br>
> I also have missing G_SI in the call to BLING_BIO_NITROGEN in bling_main.F<br>
> in checkpoint_67w.<br>
> I enclose the code snippet below.<br>
> <br>
> On other hand, G_SI is present in the subroutine BLING_BIO_NITROGEN<br>
> definiition<br>
> in bling_bio_nitrogen.F. (See that other code snippet, which I sent<br>
> yesterday, down the email pile.)<br>
> <br>
> So, the two don't match.<br>
> But they should.<br>
> <br>
> However, since I am not using silica as a ptracer, the bug doesn't affect<br>
> anything in the code that is actually compiled in my case.<br>
> The preprocessor removes any reference to PTR_SI and to G_SI,<br>
> removing the mismatch.<br>
> But in your case it does matter.<br>
> <br>
> In any case, it's better to fix the bug.<br>
> This snippet:<br>
> <br>
> #ifdef USE_SIBLING<br>
> O G_SI,<br>
> #endif<br>
> <br>
> should be added right after the line<br>
> <br>
> U G_PO4, G_DOP, G_NO3, G_DON,<br>
> <br>
> in the code lines after<br>
> <br>
> call BLING_BIO_NITROGEN<br>
> <br>
> in bling_main.F,<br>
> to match the corresponding subroutine code in bling_bio_nitrogen.F,=.<br>
> <br>
> Then recompile fresh.<br>
> <br>
> Regards,<br>
> Gus<br>
> <br>
> ****** code snippet: call to BLING_BIO_NITROGEN in bling_main.F ***<br>
> <br>
> C call either "BLING" or "BLING + nitrogen"<br>
> #ifndef USE_BLING_V1<br>
> CALL BLING_BIO_NITROGEN(<br>
> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,<br>
> I PTR_NO3, PTR_DON,<br>
> #ifdef USE_SIBLING<br>
> I PTR_SI,<br>
> #endif<br>
> #ifdef ADVECT_PHYTO<br>
> I PTR_PHY,<br>
> #endif<br>
> U G_DIC, G_ALK, G_O2, G_FE,<br>
> U G_PO4, G_DOP, G_NO3, G_DON,<br>
> I bi, bj, imin, imax, jmin, jmax,<br>
> I myTime, myIter, myThid)<br>
> #else<br>
> CALL BLING_BIO(<br>
> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,<br>
> U G_DIC, G_ALK, G_O2, G_FE,<br>
> U G_PO4, G_DOP,<br>
> I bi, bj, imin, imax, jmin, jmax,<br>
> I myTime, myIter, myThid)<br>
> #endif<br>
> *****<br>
> <br>
> On Wed, Sep 8, 2021 at 9:53 AM kunal madkaiker <<a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>><br>
> wrote:<br>
> <br>
> > Thanks a lot Gus and Michael. I'll try as per the suggestions and will<br>
> > provide an update on this.<br>
> ><br>
> > Regards,<br>
> > Kunal<br>
> ><br>
> > On Tue, Sep 7, 2021 at 8:13 PM Gus Correa <<a href="mailto:gus@ldeo.columbia.edu" target="_blank">gus@ldeo.columbia.edu</a>> wrote:<br>
> ><br>
> >> PS - Not using silica as a ptracer here, so I don't know if it works.<br>
> >> To fix the code you need to modify both the subroutine interface in<br>
> >> bling_bio_nitrogen.F<br>
> >> and the call in bling_main.F.<br>
> >> Or switch to a newer MITgcm checkpoint/version that may have fixed it.<br>
> >><br>
> >><br>
> >> On Tue, Sep 7, 2021 at 10:18 AM Gus Correa <<a href="mailto:gus@ldeo.columbia.edu" target="_blank">gus@ldeo.columbia.edu</a>> wrote:<br>
> >><br>
> >>> Hi Kunal<br>
> >>><br>
> >>> Michael is right.<br>
> >>><br>
> >>> However, as I guessed, it is a missing argument (not the tracer itself,<br>
> >>> but the tendency G_SI) in a subroutine interface.<br>
> >>> The code I have (checkpoint_67w) has the interface below for<br>
> >>> the BLING_BIO_NITROGEN subroutine interface,<br>
> >>> which includes G_SI (the SI tendency) *IF *you compile with<br>
> >>> USE_SIBLING defined in BLING_OPTIONS.h.<br>
> >>> (The default is #undef, I think.).<br>
> >>> Silica as a passive tracer seems to have been introduced recently,<br>
> >>> so it may not have been fully tested.<br>
> >>><br>
> >>> So, two possibilities that I can imagine:<br>
> >>> 1. You didn't compile with #define USE_SIBLING in BLING_OPTIONS.h<br>
> >>> 2. You are using an older code that is really missing G_SI<br>
> >>> But it can always be something else.<br>
> >>><br>
> >>> Also, take a look at the doc/tag-index file in your main MITgcm code to<br>
> >>> see<br>
> >>> if there is anything relevant about BLING and silica there.<br>
> >>><br>
> >>> I hope this helps,<br>
> >>> Gus<br>
> >>><br>
> >>> *******<br>
> >>> SUBROUTINE BLING_BIO_NITROGEN(<br>
> >>> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,<br>
> >>> I PTR_NO3, PTR_DON,<br>
> >>> #ifdef USE_SIBLING<br>
> >>> I PTR_SI,<br>
> >>> #endif<br>
> >>> #ifdef ADVECT_PHYTO<br>
> >>> I PTR_PHY,<br>
> >>> #endif<br>
> >>> O G_DIC, G_ALK, G_O2, G_FE,<br>
> >>> O G_PO4, G_DOP, G_NO3, G_DON,<br>
> >>> #ifdef USE_SIBLING<br>
> >>> O G_SI,<br>
> >>> #endif<br>
> >>> I bi, bj, imin, imax, jmin, jmax,<br>
> >>> I myTime, myIter, myThid)<br>
> >>> *****<br>
> >>><br>
> >>><br>
> >>> On Tue, Sep 7, 2021 at 9:00 AM Michael Schaferkotter <<br>
> >>> <a href="mailto:schaferk@bellsouth.net" target="_blank">schaferk@bellsouth.net</a>> wrote:<br>
> >>><br>
> >>>> without looking at source code,<br>
> >>>> it seems that G_SI is missing in the BLING_BIO_NITROGEN call sequence,<br>
> >>>> unless it is defined in an include file somewhere. Also check that G_SI is<br>
> >>>> declared as an argument in the BLING_BIO_NITROGEN subroutine.<br>
> >>>><br>
> >>>> Sent from Here3.<br>
> >>>><br>
> >>>> On Sep 7, 2021, at 06:23, kunal madkaiker <<a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>><br>
> >>>> wrote:<br>
> >>>><br>
> >>>> ???<br>
> >>>> ???<br>
> >>>><br>
> >>>> 2) bling_main.f<br>
> >>>><br>
> >>>> C biological activity<br>
> >>>> C call either "BLING" or "BLING + nitrogen"<br>
> >>>> CALL BLING_BIO_NITROGEN(<br>
> >>>> I PTR_O2, PTR_FE, PTR_PO4, PTR_DOP,<br>
> >>>> I PTR_NO3, PTR_DON,<br>
> >>>> I PTR_SI,<br>
> >>>> U G_DIC, G_ALK, G_O2, G_FE,<br>
> >>>> U G_PO4, G_DOP, G_NO3, G_DON,<br>
> >>>> I bi, bj, imin, imax, jmin, jmax,<br>
> >>>> 4199 I myTime, myIter, myThid)<br>
> >>>><br>
> >>>><br>
> >>>><br>
> >>>> On Mon, Sep 6, 2021 at 9:21 PM Gus Correa <<a href="mailto:gus@ldeo.columbia.edu" target="_blank">gus@ldeo.columbia.edu</a>><br>
> >>>> wrote:<br>
> >>>><br>
> >>>>> Hi Kunal<br>
> >>>>><br>
> >>>>> Along the line mentioned by Michael.<br>
> >>>>><br>
> >>>>> You can compile fresh adding the -devel flag to genmake2 (do a make<br>
> >>>>> CLEAN or just delete your build directory beforehand to avoid any leftover).<br>
> >>>>> Your build options file *probably* already has debug flags that are<br>
> >>>>> activated if you use -devel in genmake2.<br>
> >>>>> I think they are flags like FOPT or similar. Check.<br>
> >>>>><br>
> >>>>> Then add a namelist flag (can't remember by the exact name, check) to<br>
> >>>>> use debug at runtime in the eesupp namelist file ...<br>
> >>>>> hmmm .. debugMode-.TRUE. ... I think.<br>
> >>>>><br>
> >>>>> Finally, raise the debug level in the "data" PARM01 namelist<br>
> >>>>> debugLevel=4 (or 5).<br>
> >>>>><br>
> >>>>> This will drop more error messages in STDERR.???? and traceback the<br>
> >>>>> call stack the point of failure,<br>
> >>>>> more verbose than it is now.<br>
> >>>>><br>
> >>>>> I would guess some subroutine interface may be missing one of the<br>
> >>>>> tracers, probably silica, but it can be another thing.<br>
> >>>>><br>
> >>>>> I hope this helps<br>
> >>>>> Gus<br>
> >>>>><br>
> >>>>> On Sat, Sep 4, 2021 at 9:38 AM Michael Schaferkotter <<br>
> >>>>> <a href="mailto:schaferk@bellsouth.net" target="_blank">schaferk@bellsouth.net</a>> wrote:<br>
> >>>>><br>
> >>>>>> 1. just to be sure, if parameter values in *.h are altered, you must<br>
> >>>>>> recompile.<br>
> >>>>>><br>
> >>>>>> 2. for ifort compiler, recompile with:<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> g -check all -fpe0 -warn -traceback -debug extended<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> gfortran<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> -g -Wall -Wextra -Warray-temporaries -Wconversion -fimplicit-none -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow -finit-real=nan<br>
> >>>>>><br>
> >>>>>><br>
> >>>>>> rerun.<br>
> >>>>>><br>
> >>>>>> the stack trace will be more meaningful.<br>
> >>>>>><br>
> >>>>>> michael<br>
> >>>>>><br>
> >>>>>> Sent from Here3.<br>
> >>>>>><br>
> >>>>>> On Sep 4, 2021, at 02:14, kunal madkaiker <<br>
> >>>>>> <a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>> wrote:<br>
> >>>>>><br>
> >>>>>> ???<br>
> >>>>>> Thank you Matthew and Gus for your valuable suggestions. I could<br>
> >>>>>> resolve the 2nd query as suggested by Matt by adding apco2file in<br>
> >>>>>> data.bling.<br>
> >>>>>><br>
> >>>>>> I wanted to add few points regarding my 1st query (about adding<br>
> >>>>>> silicate as 9th tracer) The PTRACERS_num ( in PTRACER_SIZE.h ),<br>
> >>>>>> PTRACERS_numInUse, PTRACERS_useGMRedi (in data.ptracers), etc are already<br>
> >>>>>> 9. So the error may not be due to this. Also the same model setup is<br>
> >>>>>> running fine for the MITgcm-checkpoint67j (2019/06/18 ) release. This is<br>
> >>>>>> the version where the USE_SIBLING option is added to the BLING package for<br>
> >>>>>> the first time. However, I want to use the latest (or recent year) release.<br>
> >>>>>> As Matthew asked I am also including the detailed message I get on screen<br>
> >>>>>> when the model crashes. My STDERR files don't contain any error messages.<br>
> >>>>>> So is this problem related to MITgcm release ?<br>
> >>>>>><br>
> >>>>>> Backtrace for this error:<br>
> >>>>>> #0 0x7f09681cc2ed in ???<br>
> >>>>>> #1 0x7f09681cb503 in ???<br>
> >>>>>> #2 0x7f0967a60fcf in ???<br>
> >>>>>> #3 0x5636cbe79533 in ???<br>
> >>>>>> #4 0x5636cbe8c909 in ???<br>
> >>>>>> #5 0x5636cbf36923 in ???<br>
> >>>>>> #6 0xffffffffffffffff in ???<br>
> >>>>>> Program received signal SIGSEGV: Segmentation fault - invalid memory<br>
> >>>>>> reference.<br>
> >>>>>><br>
> >>>>>> Backtrace for this error:<br>
> >>>>>><br>
> >>>>>> ============================================================<br>
> >>>>>> =======================<br>
> >>>>>> = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>
> >>>>>> = PID 63826 RUNNING AT ADRAO<br>
> >>>>>> = EXIT CODE: 139<br>
> >>>>>> = CLEANING UP REMAINING PROCESSES<br>
> >>>>>> = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
> >>>>>> ============================================================<br>
> >>>>>> =======================<br>
> >>>>>> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault<br>
> >>>>>> (signal 11)<br>
> >>>>>> This typically refers to a problem with your application.<br>
> >>>>>> Please see the FAQ page for debugging suggestions<br>
> >>>>>><br>
> >>>>>> Regards,<br>
> >>>>>> Kunal<br>
> >>>>>><br>
> >>>>>> On Sat, 4 Sep 2021, 01:14 Gus Correa, <<a href="mailto:gus@ldeo.columbia.edu" target="_blank">gus@ldeo.columbia.edu</a>> wrote:<br>
> >>>>>><br>
> >>>>>>><br>
> >>>>>>><br>
> >>>>>>> On Fri, Sep 3, 2021 at 1:48 PM Matthew Mazloff <<a href="mailto:mmazloff@ucsd.edu" target="_blank">mmazloff@ucsd.edu</a>><br>
> >>>>>>> wrote:<br>
> >>>>>>><br>
> >>>>>>>> Hello<br>
> >>>>>>>><br>
> >>>>>>>> 1) Do you have some more info on the error? Anything else given?<br>
> >>>>>>>> My first guess: did you set<br>
> >>>>>>>> PARAMETER(PTRACERS_num = 9 )<br>
> >>>>>>>> in PTRACERS_SIZE.h?<br>
> >>>>>>>><br>
> >>>>>>>> 2) You have to give the exf parameters in data.bling, not data.ext.<br>
> >>>>>>>><br>
> >>>>>>>> -Matt<br>
> >>>>>>>><br>
> >>>>>>><br>
> >>>>>>> Yes, as Matthew said, segfault is because<br>
> >>>>>>> PARAMETER(PTRACERS_num = )<br>
> >>>>>>> is probably less than 9.<br>
> >>>>>>> I had the same error before.<br>
> >>>>>>><br>
> >>>>>>> ... and add to data.ptracers:<br>
> >>>>>>><br>
> >>>>>>> PTRACERS_numInUse=9,<br>
> >>>>>>> PTRACERS_useGMRedi=9*.TRUE., (if using GMRedi)<br>
> >>>>>>> PTRACERS_useKPP=9*.TRUE., (if using KPP)<br>
> >>>>>>><br>
> >>>>>>> and the ptracers name, long name, units, etc, for instance<br>
> >>>>>>><br>
> >>>>>>> PTRACERS_names(1)='dic',<br>
> >>>>>>> PTRACERS_long_names(1)='Dissolved Inorganic Carbon',<br>
> >>>>>>> PTRACERS_units(1)='mol C/m^3',<br>
> >>>>>>> PTRACERS_advScheme(1)=77,<br>
> >>>>>>> PTRACERS_diffKh(1)=0.E3,<br>
> >>>>>>> PTRACERS_diffKr(1)=3.E-5,<br>
> >>>>>>><br>
> >>>>>>> Gus<br>
> >>>>>>><br>
> >>>>>>>><br>
> >>>>>>>><br>
> >>>>>>>> > On Sep 3, 2021, at 10:38 AM, kunal madkaiker <<br>
> >>>>>>>> <a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>> wrote:<br>
> >>>>>>>> ><br>
> >>>>>>>> > Dear All,<br>
> >>>>>>>> ><br>
> >>>>>>>> > I have two queries regarding the BLING model.<br>
> >>>>>>>> ><br>
> >>>>>>>> > 1) I am running the recent release of MITgcm coupled to the BLING<br>
> >>>>>>>> module. The model is running fine if I use the default 8 tracer option.<br>
> >>>>>>>> When I try to add silica as 9th tracer (#define USE_SIBLING in<br>
> >>>>>>>> BLING_OPTIONS.h), the model crashes in the beginning giving the following<br>
> >>>>>>>> error message "Program received signal SIGSEGV: Segmentation fault -<br>
> >>>>>>>> invalid memory reference.".<br>
> >>>>>>>> ><br>
> >>>>>>>> > 2) I want the model to read apco2 values from a file via the<br>
> >>>>>>>> data.exf instead of giving a constant value in data.bling. I enabled it<br>
> >>>>>>>> with #define USE_EXFCO2 in BLING_OPTIONS.h. However, the model crashes with<br>
> >>>>>>>> the error "Fortran runtime error: Cannot match namelist object name<br>
> >>>>>>>> apco2startdate1."<br>
> >>>>>>>> ><br>
> >>>>>>>> > Please suggest some solutions to the above issues.<br>
> >>>>>>>> ><br>
> >>>>>>>> > Regards<br>
> >>>>>>>> > Kunal<br>
> >>>>>>>> > _______________________________________________<br>
> >>>>>>>> > MITgcm-support mailing list<br>
> >>>>>>>> > <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a><br>
> >>>>>>>> ><br>
> >>>>>>>> <a href="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=" rel="noreferrer" target="_blank">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=</a><br>
> >>>>>>>><br>
> >>>>>>>> _______________________________________________<br>
> >>>>>>>> MITgcm-support mailing list<br>
> >>>>>>>> <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a><br>
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> >>>>>>>><br>
> >>>>>>> _______________________________________________<br>
> >>>>>>> MITgcm-support mailing list<br>
> >>>>>>> <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a><br>
> >>>>>>> <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" rel="noreferrer" target="_blank">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> >>>>>>><br>
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> >>>>>> MITgcm-support mailing list<br>
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> >>>>>><br>
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> >>>>>><br>
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> >>>><br>
> >>> _______________________________________________<br>
> >> MITgcm-support mailing list<br>
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