<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>It looks like the mitgcmuv executable that you are using has not been compiled with “#define ALLOW_3D_DIFKR”. Does your STDOUT or output.txt file say that ALLOW_3D_DIFKR is defined?</div><div><br></div>Try deleting everything in your build directory then recompiling from scratch, genmake2, make depend, and make. After that, make sure that the CPP_OPTIONS.h file in your build directory contains the “#define ALLOW_3D_DIFKR”.<div><br></div><div>You should not get the error messages below if you compiled with “#define ALLOW_3D_DIFKR” and are using the correct executable.</div><div><br></div><div>The diffKrFile will be used for temperature and salinity. And by default, unless you request otherwise, also for ptracers.</div><div><div dir="ltr"><br><blockquote type="cite">On Feb 17, 2025, at 3:06 AM, Vanderborght, E.Y.P. (Elian) <e.y.p.vanderborght@uu.nl> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style>@font-face { font-family: "Cambria Math"; }
@font-face { font-family: Aptos; }
p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm; font-size: 11pt; font-family: Aptos, sans-serif; }
.MsoChpDefault { font-size: 11pt; }
@page WordSection1 { size: 612pt 792pt; margin: 70.85pt; }
div.WordSection1 { page: WordSection1; }</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear MITgcm Community,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I am encountering an issue related to specifying a space-dependent (longitude-latitude-depth) vertical diffusivity coefficient for temperature in MITgcm. Based on my understanding, this should be possible by enabling
the ALLOW_3D_DIFFKR flag in the CPP_OPTIONS.h file. After changing #undef ALLOW_3D_DIFFKR to #define ALLOW_3D_DIFFKR and copying the modified file to my code directory, I recompiled the code using the following command:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">$base_dir/tools/genmake2 -mods $base_dir/$code_dir -mpi -of=$OPTFILE_PATH<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This successfully generates the Makefile and the executable mitgcmuv. In my data script, I specify the variable diffusion coefficient with PARAMS05 as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">diffKrFile='diffKrFile.bin'<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">However, when I run the model, I encounter the following error message:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: diffKrFile is set but never used.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: Re-compile with: "#define ALLOW_3D_DIFFKR"<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** CONFIG_CHECK: detected 1 fatal error(s)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">(PID.TID 0000.0001) *** ERROR *** S/R ALL_PROC_DIE: ending the run<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">This suggests that the diffKrFile is not being loaded and the #define ALLOW_3D_DIFFKR flag is not being recognized. Despite verifying that the flag is correctly enabled (see attached), I still receive this error. Could
I be overlooking something? Is there any additional configuration or package that I need to include for this feature to work?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">For context, my PACKAGES section is as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">&PACKAGES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useDiagnostics = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useGMRedi = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> useRBCS = .TRUE.,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">&<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Finally, once the diffKrFile is loaded, will it only affect temperature as an active tracer, or could it also apply to other tracers if they are included in the model?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I look forward to any insights you may have.<o:p></o:p></span></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal">Elian<o:p></o:p></p>
</div>
<div><CPP_OPTIONS.h></div><span>_______________________________________________</span><br><span>MITgcm-support mailing list</span><br><span>MITgcm-support@mitgcm.org</span><br><span>http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</span><br></div></blockquote></div></body></html>