[Flash-X-users] Getting Flash-X to work

Tue Sep 3 12:23:16 CDT 2024

Yes, getting Thornado working is a good idea, my question was about that
link, I had just emailed the "ask for help" email listed at the bottom and
got my email returned saying my message was blocked, so I am unsure of how
to proceed with getting help on that front (or really Thornado in general).

On Tue, Sep 3, 2024 at 12:50 PM Dubey, Anshu <adubey at anl.gov> wrote:

> Dear Peter,
>
> Thornado is an imported module into Flash-X. It has its own developers and
> repository. So yes, making sure that you can get Thornado to work would be
> a good way to go.
>
> Best,
>
> Anshu
>
>
>
> *From: *Flash-X-users <flash-x-users-bounces at lists.cels.anl.gov> on
> behalf of Peter Manzella <peter.manzella at maine.edu>
> *Date: *Tuesday, September 3, 2024 at 11:24 AM
> *To: *kiyarash Taghiniyarami <kiyarash.niyarami at gmail.com>
> *Cc: *flash-x-users at lists.cels.anl.gov <flash-x-users at lists.cels.anl.gov>
> *Subject: *Re: [Flash-X-users] Getting Flash-X to work
>
> Hi, So, thornado has been my issue, I did some digging and found this link
> (https: //github. com/ranchu1/HowTo-FlashX-Thornado/tree/master) and just
> found this link and have started to follow the tests it lists, very helpful
> to take it a little
>
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> Hi,
>
> So, thornado has been my issue, I did some digging and found this link (
> https://urldefense.us/v3/__https://github.com/ranchu1/HowTo-FlashX-Thornado/tree/master__;!!G_uCfscf7eWS!fpkRd9Xa5iuvPRzgxKUoe9CvMHSb2v5dgMAoulCkDYpAhByaHvuyWUZMR-_BnolMSFdKjfPi5dCDPgA9OvoJARikTJVSbmZYf7ddfUbc$ 
> <https://urldefense.us/v3/__https:/github.com/ranchu1/HowTo-FlashX-Thornado/tree/master__;!!G_uCfscf7eWS!bBZBV3a8yrv2pVog4R4uZuLcufNptkroqa7xjPAm232Kl2Wp8JCdKEjfjMWJFui04WlxbPgmTRFDD5EXZFsRIf07uLSupqSoCX6ZRiRQ$>)
> and just found this link and have started to follow the tests it lists,
> very helpful to take it a little slower and retrace some steps. I've gotten
> through the setup successfully, but run into errors with 'make' I'm hoping
> that by taking it a little slower it will get me on track a little easier
> and faster. Does this seems like a good route to go?
>
>
>
> On Fri, Aug 30, 2024 at 2:50 AM kiyarash Taghiniyarami <
> kiyarash.niyarami at gmail.com> wrote:
>
> Dear Ryan & Peter,
>
> 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.
> In the Config make sure the lines 9to11 are set properly due to your own
> paths.
> Best ,
> Kiya
>
>
>
> On Thu, Aug 29, 2024 at 4:23 PM Peter Manzella <peter.manzella at maine.edu>
> wrote:
>
> Ryan,
>
>
>
> 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.
>
>
>
> On Thu, Aug 29, 2024 at 12:08 AM Ryan Farber <rjfarber at umich.edu> wrote:
>
> Hi Peter,
>
>
>
> 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.)
>
> 2. I don't know that you have to start over. Kiya mentioned two
> potentially helpful suggestions
>
>
> i. Try changing " thornadoOrder=ORDER_1" in your setup line to a
> different value
> 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.
>
>
>
> Best wishes,
>
> --------
>
> Ryan
>
>
>
>
>
> On Wed, Aug 28, 2024 at 8:28 AM Peter Manzella <peter.manzella at maine.edu>
> wrote:
>
> 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 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?
>
> 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.
>
>
>
> On Tue, Aug 27, 2024 at 12:42 AM kiyarash Taghiniyarami <
> kiyarash.niyarami at gmail.com> wrote:
>
> Dear Peter & Ryan,
> No problem. I am just trying to help and hope it will be useful.
>
> 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
> wlEOSInversionModule.F90 is missing in the directory created by setup,
> check that out again.
>
> 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.
>
> Best,
> Kiya
>
>
>
> On Tue, Aug 27, 2024 at 6:31 AM Peter Manzella <peter.manzella at maine.edu>
> wrote:
>
> 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
>
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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 some other things, so it is a bit late, sorry.
>
> As asked (let me know if I didn't grab the right thing)
>
> 1) screenshot of 'ls' in the problem directory:
>
> 2) my setup command:
>
>
>
> ./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
>
>
>
> 3)full output in a compile.txt
>
>
>
> 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.
>
>
>
> On Mon, Aug 26, 2024 at 4:42 PM Ryan Farber <rjfarber at umich.edu> wrote:
>
> Hi Peter,
>
>
>
> If you share the following I can take a look tonight:
>
> 1) screenshot of “ls” in your problem directory
>
> 2) your setup command
>
> 3) the full output and error streams of your compilation command (e.g., make
> 2>&1 compile.txt
>
>
>
> 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!
>
>
>
> Best wishes,
>
> Ryan
>
>
>
> Sent from my iPhone
>
>
>
> On Aug 26, 2024, at 1:53 PM, Peter Manzella <peter.manzella at maine.edu>
> wrote:
>
> 
>
> 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
>
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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 about it.
>
> <image.png>
>
>
>
> 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.
>
>
>
> On Mon, Aug 26, 2024 at 2:28 PM kiyarash Taghiniyarami <
> kiyarash.niyarami at gmail.com> wrote:
>
> Dear Peter,
> These are not for command line (If you mean "command line" as setup for
> configuring a new run).
> 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.
> 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:
> Use KindModule, only: Half
> 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.
> 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.
>
> There is documentation for Flashx as well:
> https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!fpkRd9Xa5iuvPRzgxKUoe9CvMHSb2v5dgMAoulCkDYpAhByaHvuyWUZMR-_BnolMSFdKjfPi5dCDPgA9OvoJARikTJVSbmZYfyI1uyqS$ 
> <https://urldefense.us/v3/__https:/flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>
> Kind regards,
> Kiya
>
>
>
> --
>
> Peter Manzella
>
> PhD Candidate, Department of Physics and Astronomy
>
> 309 Bennett Hall
>
> University of Maine
>
> peter.manzella at maine.edu
>
>
>
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan
> Poe
>
> --
> Flash-X-users mailing list
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>
>
>
> --
>
> Peter Manzella
>
> PhD Candidate, Department of Physics and Astronomy
>
> 309 Bennett Hall
>
> University of Maine
>
> peter.manzella at maine.edu
>
>
>
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan
> Poe
>
> --
> Flash-X-users mailing list
> Flash-X-users at lists.cels.anl.gov
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>
>
>
> --
>
> Peter Manzella
>
> PhD Candidate, Department of Physics and Astronomy
>
> 309 Bennett Hall
>
> University of Maine
>
> peter.manzella at maine.edu
>
>
>
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan
> Poe
>
>
>
> --
>
> Peter Manzella
>
> PhD Candidate, Department of Physics and Astronomy
>
> 309 Bennett Hall
>
> University of Maine
>
> peter.manzella at maine.edu
>
>
>
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan
> Poe
>
>
>
> --
>
> Peter Manzella
>
> PhD Candidate, Department of Physics and Astronomy
>
> 309 Bennett Hall
>
> University of Maine
>
> peter.manzella at maine.edu
>
>
>
> “If you run out of ideas follow the road; you'll get there.” – Edgar Allan
> Poe
>

-- 
Peter Manzella
PhD Candidate, Department of Physics and Astronomy
309 Bennett Hall
University of Maine
peter.manzella at maine.edu

“If you run out of ideas follow the road; you'll get there.” – Edgar Allan
Poe
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