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Kiya & Ryan, I finally got the chance to take a look at this, and what I'm gathering is that my installation of thornado is not correct. I am not sure how to troubleshoot this beyond "uninstall and reinstall" which I can assume</div>
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<div dir="ltr"><div class="gmail_default" style="font-family:monospace;font-size:large">Kiya & Ryan,</div><div class="gmail_default" style="font-family:monospace;font-size:large"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">I finally got the chance to take a look at this, and what I'm gathering is that my installation of thornado is not correct. I am not sure how to troubleshoot this beyond "uninstall and reinstall" which I can assume is not the way to go about this. Ryan mentioned that it may not be in the proper system PATH, I'm assuming this could be corrected in the makefile that is in the "sites" directory? <br><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">I do hope that my struggles prove to be useful and helpful for those in the future, so I very much thank you all for your help.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 27, 2024 at 12:42 AM kiyarash Taghiniyarami <<a href="mailto:kiyarash.niyarami@gmail.com">kiyarash.niyarami@gmail.com</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">Dear Peter & Ryan,<br>No problem. I am just trying to help and hope it will be useful.<br><br>I see in your setup syntax Thornado order is set to 1. Order one is not working properly (some files are missing in thornado order1 directory) since I asked Austin so far, he mentioned they tried to use orderV and then in flash.par setting v = 0.0 gives the same result as order1. So I am afraid Peter your setup is not complete yet and because of that <span style="color:rgb(80,0,80)">wlEOSInversionModule.F90 </span><font color="#000000">is missing in the directory created by setup</font>, check that out again.<br><br>If you get ls of the obj directory (or whatever created by setup) you could see list of codes linked there and check if wlEOSInversion in present there or not.<br><br>Best,<br>Kiya<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 27, 2024 at 6:31 AM Peter Manzella <<a href="mailto:peter.manzella@maine.edu" target="_blank">peter.manzella@maine.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>
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Ryan, Of course, many many thanks to Kiya, been extremely helpful. And many thanks to you for lending a helping hand too! I didn't see your email till very much after I had left my office, but noticed it and had to come in to take care of</div>
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<div dir="ltr"><div class="gmail_default" style="font-family:monospace;font-size:large">Ryan,</div><div class="gmail_default" style="font-family:monospace;font-size:large">Of course, many many thanks to Kiya, been extremely helpful. And many thanks to you for lending a helping hand too! I didn't see your email till very much after I had left my office, but noticed it and had to come in to take care of some other things, so it is a bit late, sorry.<br></div><div class="gmail_default" style="font-family:monospace;font-size:large">As asked (let me know if I didn't grab the right thing)</div><div class="gmail_default" style="font-family:monospace;font-size:large">1) screenshot of 'ls' in the problem directory:<br><img src="cid:ii_m0bu46cz0" alt="image.png" width="471" height="27"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">2) my setup command: </div><div class="gmail_default" style="font-family:monospace;font-size:large"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">./setup Relaxation -auto -3d +cartesian +cube16 +thornado nE=16 swE=0 nSpecies=6 nNodes=2 nMoments=4 momentClosure=MINERBO thornadoOrder=ORDER_1 +weaklib -parfile=flash.par</div><div class="gmail_default" style="font-family:monospace;font-size:large"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">3)full output in a compile.txt</div><div class="gmail_default" style="font-family:monospace;font-size:large"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">I really appreciate any and all help I can get, I've spent a bit on trying to get through it, but quite often it felt like I was going in circles.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 26, 2024 at 4:42 PM Ryan Farber <<a href="mailto:rjfarber@umich.edu" target="_blank">rjfarber@umich.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="auto">Hi Peter,<div><br></div><div>If you share the following I can take a look tonight:</div><div>1) screenshot of “ls” in your problem directory</div><div>2) your setup command</div><div>3) the full output and error streams of your compilation command (e.g., <font face="American Typewriter">make 2>&1 compile.txt</font></div><div><br></div><div>As an aside, thanks to Kiya for your kind contributions to this thread! I’m sure what you've provided will be useful in the future too!</div><div><br></div><div>Best wishes,</div><div>Ryan</div><div><br><div dir="ltr">Sent from my iPhone</div><div dir="ltr"><br><blockquote type="cite">On Aug 26, 2024, at 1:53 PM, Peter Manzella <<a href="mailto:peter.manzella@maine.edu" target="_blank">peter.manzella@maine.edu</a>> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">
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OK, that makes more sense, I'll need to make sure those are in the file, not command line. I went to setup after adding those, and have this error, its related to equation of state, and I haven't been able to find anything in documentation</div>
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<div dir="ltr"><div class="gmail_default" style="font-family:monospace;font-size:large">OK, that makes more sense, I'll need to make sure those are in the file, not command line. I went to setup after adding those, and have this error, its related to equation of state, and I haven't been able to find anything in documentation about it. </div><div class="gmail_default" style="font-family:monospace;font-size:large"><div><image.png></div><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">This is the sort of thing that is frustrating, not being able to find where I need to look to troubleshoot. I tried using grep to find it, I've looked in the documentation link you sent me (I already knew about that, but it wasn't helpful beyond the quick start), but couldn't find it. Is this more of a thornado issue? Cause like I said I'm not super acquainted with large codes that require so many moving pieces.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Aug 26, 2024 at 2:28 PM kiyarash Taghiniyarami <<a href="mailto:kiyarash.niyarami@gmail.com" target="_blank">kiyarash.niyarami@gmail.com</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">Dear Peter,<br>These are not for command line (If you mean "command line" as setup for configuring a new run).<br>Before setup you need to make a directory in the Simulation unit (/source/Simulation/SimulationMain). In that directory you need some codes such as Simulation_data.F90, Simulation_init.F90, Simulation_initBlock.F90, and etc.<br>Say you need the "Half" variable in the Simulation_initBlock.F90. you can call it by KindModule from Thornado if you write the following in that fortran code:<br>Use KindModule, only: Half<br>so you can use the "Half" anywhere in that Simulation_initBlock.F90. It has nothing to do with typing in the command line and hitting enter.<br>If I understand correctly what you mean, there are some setup variables you can type in the command line (such as nxb,nyb, swE,nE and etc.) which are different from modules. setup variables can be set up in Config files in any physics subdirectories.<br><br>There is documentation for Flashx as well: <a href="https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$" target="_blank">https://flash-x.github.io/Flash-X-docs/#</a><br><br>Kind regards,<br>Kiya<br><br></div>
</blockquote></div><br clear="all"><br><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Peter Manzella<br></div><div>PhD Candidate, Department of Physics and Astronomy</div><div>309 Bennett Hall</div><div>University of Maine</div><div><a href="mailto:peter.manzella@maine.edu" target="_blank">peter.manzella@maine.edu</a></div><div><br></div><div><font face="arial, sans-serif">“If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe</font><br></div></div></div>
<span>-- </span><br><span>Flash-X-users mailing list</span><br><span><a href="mailto:Flash-X-users@lists.cels.anl.gov" target="_blank">Flash-X-users@lists.cels.anl.gov</a></span><br><span><a href="https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$" target="_blank">https://lists.cels.anl.gov/mailman/listinfo/flash-x-users</a></span><br></div></blockquote></div></div></blockquote></div><br clear="all"><br><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Peter Manzella<br></div><div>PhD Candidate, Department of Physics and Astronomy</div><div>309 Bennett Hall</div><div>University of Maine</div><div><a href="mailto:peter.manzella@maine.edu" target="_blank">peter.manzella@maine.edu</a></div><div><br></div><div><font face="arial, sans-serif">“If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe</font><br></div></div></div>
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</blockquote></div><br clear="all"><br><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div>Peter Manzella<br></div><div>PhD Candidate, Department of Physics and Astronomy</div><div>309 Bennett Hall</div><div>University of Maine</div><div><a href="mailto:peter.manzella@maine.edu" target="_blank">peter.manzella@maine.edu</a></div><div><br></div><div><font face="arial, sans-serif">“If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe</font><br></div></div></div>