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

Wed Sep 4 17:31:30 CDT 2024

Hi Peter,

The github repository you linked to hasn't been updated in two years, so
the more general information may be useful but in detail I wouldn't think
it'd be super useful.

Anyway, regarding the "SqrtTiny", "Zero", etc. not found in UnitsModule
compilation issue, a workaround is to copy those from
https://urldefense.us/v3/__https://github.com/endeve/thornado/blob/master/SandBox/AMReX/Modules/TwoMoment/MF_KindModule_old.f90__;!!G_uCfscf7eWS!bRKT6r9CCEVlwktfW1a3VPJR_lRuT_WhS9Lwtx12ttpcNxVWmEzUdwgvj1fCzfTA7pMogv9PgAtvJvhIUIO8DdOwBLCjGJnrwQ$ 
to FlashX/Flash-X/lib/thornado/source/Modules/Units/UnitsModule.f90

In that case, compilation succeeds for me.

Best wishes,
--------
Ryan

On Tue, Sep 3, 2024 at 10:23 AM Peter Manzella <peter.manzella at maine.edu>
wrote:

> 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
> ZjQcmQRYFpfptBannerStart
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> 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
>>
>> ZjQcmQRYFpfptBannerStart
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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!bRKT6r9CCEVlwktfW1a3VPJR_lRuT_WhS9Lwtx12ttpcNxVWmEzUdwgvj1fCzfTA7pMogv9PgAtvJvhIUIO8DdOwBLAkgMrgHg$ 
>> <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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>> *This Message Is From an External Sender *
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>>
>>
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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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>>
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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!bRKT6r9CCEVlwktfW1a3VPJR_lRuT_WhS9Lwtx12ttpcNxVWmEzUdwgvj1fCzfTA7pMogv9PgAtvJvhIUIO8DdOwBLDN-gHZkQ$ 
>> <https://urldefense.us/v3/__https:/flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>
>> Kind regards,
>> Kiya
>>
>>
>>
>> --
>>
>> Peter Manzella
>>
>> PhD Candidate, Department of Physics and Astronomy
>>
>> 309 Bennett Hall
>>
>> University of Maine
>>
>> peter.manzella at maine.edu
>>
>>
>>
>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>> Allan Poe
>>
>> --
>> Flash-X-users mailing list
>> Flash-X-users at lists.cels.anl.gov
>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!bRKT6r9CCEVlwktfW1a3VPJR_lRuT_WhS9Lwtx12ttpcNxVWmEzUdwgvj1fCzfTA7pMogv9PgAtvJvhIUIO8DdOwBLBOCHtXrQ$ 
>> <https://urldefense.us/v3/__https:/lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>
>>
>>
>> --
>>
>> Peter Manzella
>>
>> PhD Candidate, Department of Physics and Astronomy
>>
>> 309 Bennett Hall
>>
>> University of Maine
>>
>> peter.manzella at maine.edu
>>
>>
>>
>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>> Allan Poe
>>
>> --
>> Flash-X-users mailing list
>> Flash-X-users at lists.cels.anl.gov
>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!bRKT6r9CCEVlwktfW1a3VPJR_lRuT_WhS9Lwtx12ttpcNxVWmEzUdwgvj1fCzfTA7pMogv9PgAtvJvhIUIO8DdOwBLBOCHtXrQ$ 
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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
> --
> Flash-X-users mailing list
> Flash-X-users at lists.cels.anl.gov
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>
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