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Hi Kiya, Thanks for mentioning your hdf5 version! I downloaded 1. 14. 4-3, built, and now setup succeeded for me - although I had 15 files copied whereas you had 23 files copied. Compiling FlashX failed due to the units module issue Peter also</div>
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<div dir="ltr">Hi Kiya,<div><br></div><div>Thanks for mentioning your hdf5 version! I downloaded 1.14.4-3, built, and now setup succeeded for me - although I had 15 files copied whereas you had 23 files copied.</div><div><br></div><div>Compiling FlashX failed due to the units module issue Peter also experienced. I cloned thornado and it looks like "SqrtTiny", "Zero", etc. were purged from the UnitsModule (which makes sense, since those don't really sound like units...).<br><br>Could you mention the commit hash of the thornado version you have checked out with your FlashX?<br><br>Best wishes,<br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">--------<div>Ryan</div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Aug 29, 2024 at 11:50 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 Ryan & Peter,<br><br>I share my Relaxation setup, lists of files and the Config with you if you want to compare. Just to correct myself: wl files of weaklib do not need to be present in the lists of files, because the Thornado calls them privately when FlashX calls the Thornado.<br>In the Config make sure the lines 9to11 are set properly due to your own paths.<br>Best ,<br>Kiya</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Aug 29, 2024 at 4:23 PM 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 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"><br></div><div class="gmail_default" style="font-family:monospace;font-size:large">Depending on how this troubleshooting goes, will decide whether I decide to do a fresh (re)start, I want to give it a chance before I go that route. As for Kiya's suggestions, I have been working on them, I tried changing "thornadoOrder=ORDER_1" to "thornadoOrder=ORDER_V" and along with that I have looked in the object directory, and grabbed that output and placed it in the file as Kiya, and you have suggested, see attached.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Aug 29, 2024 at 12:08 AM 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="ltr">Hi Peter,<div><br></div><div>1. Less of a Flash-X suggestion as much as personal life philosophy: yes sometimes the best path forward is a fresh (re)start. Along that vein, I've started the process of typing up a list of steps I need(ed) to take to "Get Flash-X to work" on my ubuntu virtual private server (which is definitely more of a pain since no packages are provided for me, but on the plus side I have full control over everything). I'm currently building lapack. (Will finish after I go to sleep likely.)<br><br>2. I don't know that you have to start over. Kiya mentioned two potentially helpful suggestions</div><div><br>i. Try changing "
<span style="font-family:monospace;font-size:large">thornadoOrder=ORDER_1" </span><font face="arial, sans-serif">in your setup line to a different value<br></font>ii. In your object directory, type "ls -l *.F90 > Flash-X-files.txt" and share that file with us. Then we can see if you the setup line correctly placed the files you need in the object directory, or if some are missing.</div><div><br></div><div>Best wishes,<br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr">--------<div>Ryan</div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Aug 28, 2024 at 8:28 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 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" 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 & 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>
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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>
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