<div dir="ltr"><div>Thanks a lot Gus and Michael. I'll try as per the suggestions and will provide an update on this.</div><div><br></div><div>Regards,</div><div>Kunal<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 7, 2021 at 8:13 PM Gus Correa <<a href="mailto:gus@ldeo.columbia.edu">gus@ldeo.columbia.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"><div dir="ltr"><div>PS - Not using silica as a ptracer here, so I don't know if it works.</div><div>To fix the code you need to modify both the subroutine interface in bling_bio_nitrogen.F</div><div>and the call in bling_main.F. <br></div><div>Or switch to a newer MITgcm checkpoint/version that may have fixed it.</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Hi Kunal</div><div><br></div><div>Michael is right.</div><div><br></div><div>However, as I guessed, it is a missing argument (not the tracer itself,</div><div>but the tendency G_SI) in a subroutine interface.<br></div><div>The code I have (checkpoint_67w) has the interface below for</div><div>the BLING_BIO_NITROGEN subroutine interface,</div><div>which includes G_SI (the SI tendency) <span style="color:rgb(0,0,255)"><b>IF </b></span>you compile with <br></div><div>USE_SIBLING defined in BLING_OPTIONS.h.</div><div>(The default is #undef, I think.).</div><div>Silica as a passive tracer seems to have been introduced recently,</div><div>so it may not have been fully tested.<br></div><div><br></div><div>So, two possibilities that I can imagine:</div><div>1. You didn't compile with #define USE_SIBLING in BLING_OPTIONS.h</div><div>2. You are using an older code that is really missing G_SI</div><div>But it can always be something else.</div><div><br></div><div>Also, take a look at the doc/tag-index file in your main MITgcm code to see <br></div><div>if there is anything relevant about BLING and silica there.<br></div><div><br></div><div>I hope this helps,</div><div>Gus<br></div><div><br></div><div>*******<br></div><div> 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></div><div>*****<br></div><div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 7, 2021 at 9:00 AM Michael Schaferkotter <<a href="mailto:schaferk@bellsouth.net" target="_blank">schaferk@bellsouth.net</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"><div dir="auto">without looking at source code,<div>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.<br><br><div dir="ltr">Sent from Here3.</div><div dir="ltr"><br><blockquote type="cite">On Sep 7, 2021, at 06:23, kunal madkaiker <<a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div>…</div><div><br></div><div>2) bling_main.f<br></div><div><br></div><div>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,</div><div>4199 I myTime, myIter, myThid)</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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>> 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"><div dir="ltr"><div dir="ltr"><div>Hi Kunal</div><div><br></div><div>Along the line mentioned by Michael.</div><div><br></div><div>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).</div><div>Your build options file *probably* already has debug flags that are activated if you use -devel in genmake2. <br></div><div>I think they are flags like FOPT or similar. Check.<br></div><div><br></div><div>Then add a namelist flag (can't remember by the exact name, check) to use debug at runtime in the eesupp namelist file ... <br></div><div>hmmm .. debugMode-.TRUE. ... I think. <br></div><div><br></div><div>Finally, raise the debug level in the "data" PARM01 namelist debugLevel=4 (or 5).</div><div><br></div><div>This will drop more error messages in STDERR.???? and traceback the call stack the point of failure,</div><div>more verbose than it is now.<br></div><div><br></div><div>I would guess some subroutine interface may be missing one of the tracers, probably silica, but it can be another thing.</div><div><br></div><div>I hope this helps<br></div><div>Gus<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Sep 4, 2021 at 9:38 AM Michael Schaferkotter <<a href="mailto:schaferk@bellsouth.net" target="_blank">schaferk@bellsouth.net</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"><div dir="auto">1. just to be sure, if parameter values in *.h are altered, you must recompile.<div><br></div><div>2. for ifort compiler, recompile with:</div><div><pre style="background-color:rgb(248,248,248);font-size:1em;overflow:auto;padding:0.5em;border:thin solid rgb(216,216,216);white-space:pre-wrap;color:rgb(34,34,34);text-align:justify"><code style="font-family:"Roboto Mono",monospace"><br></code></pre><pre style="background-color:rgb(248,248,248);font-size:1em;overflow:auto;padding:0.5em;border:thin solid rgb(216,216,216);white-space:pre-wrap;color:rgb(34,34,34);text-align:justify"><code style="font-family:"Roboto Mono",monospace">g -check all -fpe0 -warn -traceback -debug extended</code></pre><div><br></div>gfortran</div><div><pre style="background-color:rgb(248,248,248);font-size:1em;overflow:auto;padding:0.5em;border:thin solid rgb(216,216,216);white-space:pre-wrap;color:rgb(34,34,34);text-align:justify"><code style="font-family:"Roboto Mono",monospace"><br></code></pre><pre style="background-color:rgb(248,248,248);font-size:1em;overflow:auto;padding:0.5em;border:thin solid rgb(216,216,216);white-space:pre-wrap;color:rgb(34,34,34);text-align:justify"><code style="font-family:"Roboto Mono",monospace">-g -Wall -Wextra -Warray-temporaries -Wconversion -fimplicit-none -fbacktrace -ffree-line-length-0 -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow -finit-real=nan</code></pre><pre style="background-color:rgb(248,248,248);font-size:1em;overflow:auto;padding:5em;border:thin solid rgb(216,216,216);white-space:pre-wrap;color:rgb(34,34,34);text-align:justify"><code style="font-family:"Roboto Mono",monospace"><br></code></pre><div dir="ltr">rerun.</div><div id="gmail-m_-2206409818549406604gmail-m_5783936597259361381gmail-m_-850534761960689714gmail-m_7176071164104963526gmail-m_-2839542332176928859AppleMailSignature" dir="ltr"><br></div><div id="gmail-m_-2206409818549406604gmail-m_5783936597259361381gmail-m_-850534761960689714gmail-m_7176071164104963526gmail-m_-2839542332176928859AppleMailSignature" dir="ltr">the stack trace will be more meaningful.</div><div id="gmail-m_-2206409818549406604gmail-m_5783936597259361381gmail-m_-850534761960689714gmail-m_7176071164104963526gmail-m_-2839542332176928859AppleMailSignature" dir="ltr"><br></div><div id="gmail-m_-2206409818549406604gmail-m_5783936597259361381gmail-m_-850534761960689714gmail-m_7176071164104963526gmail-m_-2839542332176928859AppleMailSignature" dir="ltr">michael</div><div id="gmail-m_-2206409818549406604gmail-m_5783936597259361381gmail-m_-850534761960689714gmail-m_7176071164104963526gmail-m_-2839542332176928859AppleMailSignature" dir="ltr"><br></div><div dir="ltr">Sent from Here3.</div><div dir="ltr"><br><blockquote type="cite">On Sep 4, 2021, at 02:14, kunal madkaiker <<a href="mailto:kunal.madkaiker02@gmail.com" target="_blank">kunal.madkaiker02@gmail.com</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="auto"><div style="font-family:sans-serif;font-size:12.8px" dir="auto">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.</div><div style="font-family:sans-serif;font-size:12.8px" dir="auto"><br></div><div style="font-family:sans-serif;font-size:12.8px" dir="auto">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 ?<br></div><div style="font-family:sans-serif;font-size:12.8px" dir="auto"><br></div><div style="font-family:sans-serif;font-size:12.8px" dir="auto">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 ???</div><div style="color:rgb(80,0,80);font-family:sans-serif;font-size:12.8px" dir="auto"><div>Program received signal SIGSEGV: Segmentation fault - invalid memory reference.</div><br></div><span style="font-family:sans-serif;font-size:12.8px">Backtrace for this error:</span><br style="font-family:sans-serif;font-size:12.8px"><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">==============================</span><span style="font-family:sans-serif;font-size:12.8px">==============================</span><span style="font-family:sans-serif;font-size:12.8px">=======================</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">= PID 63826 RUNNING AT ADRAO</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">= EXIT CODE: 139</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">= CLEANING UP REMAINING PROCESSES</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">==============================</span><span style="font-family:sans-serif;font-size:12.8px">==============================</span><span style="font-family:sans-serif;font-size:128px">=======================</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)</span><br style="font-family:sans-serif;font-size:12.8px"><span style="font-family:sans-serif;font-size:12.8px">This typically refers to a problem with your application.</span><br style="font-family:sans-serif;font-size:12.8px"><div style="font-family:sans-serif;font-size:12.8px" dir="auto">Please see the FAQ page for debugging suggestions</div><div style="font-family:sans-serif;font-size:12.8px" dir="auto"><br></div><div style="font-family:sans-serif;font-size:12.8px" dir="auto">Regards,</div><div style="font-family:sans-serif;font-size:12.8px" dir="auto">Kunal</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">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></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Sep 3, 2021 at 1:48 PM Matthew Mazloff <<a href="mailto:mmazloff@ucsd.edu" rel="noreferrer" target="_blank">mmazloff@ucsd.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">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></blockquote><div><br></div><div>Yes, as Matthew said, segfault is because </div><div>PARAMETER(PTRACERS_num = )</div><div>is probably less than 9.</div><div>I had the same error before.</div><div><br></div><div>... and add to data.ptracers:</div><div><br></div><div> PTRACERS_numInUse=9,<br> PTRACERS_useGMRedi=9*.TRUE., (if using GMRedi)<br> PTRACERS_useKPP=9*.TRUE., (if using KPP)</div><div><br></div><div>and the ptracers name, long name, units, etc, for instance<br></div><div><br></div><div> 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,</div><div><br></div><div>Gus<br> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
<br>
> On Sep 3, 2021, at 10:38 AM, kunal madkaiker <<a href="mailto:kunal.madkaiker02@gmail.com" rel="noreferrer" 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 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.".<br>
> <br>
> 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."<br>
> <br>
> Please suggest some solutions to the above issues.<br>
> <br>
> Regards<br>
> Kunal<br>
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