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

Tue Sep 3 11:23:52 CDT 2024

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!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
>>>>>> ZjQcmQRYFpfptBannerStart
>>>>>> This Message Is From an External Sender
>>>>>> This message came from outside your organization.
>>>>>>
>>>>>> ZjQcmQRYFpfptBannerEnd
>>>>>> 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:
>>>>>> [image: image.png]
>>>>>> 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
>>>>>>> ZjQcmQRYFpfptBannerStart
>>>>>>> This Message Is From an External Sender
>>>>>>> This message came from outside your organization.
>>>>>>>
>>>>>>> ZjQcmQRYFpfptBannerEnd
>>>>>>> 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!bBZBV3a8yrv2pVog4R4uZuLcufNptkroqa7xjPAm232Kl2Wp8JCdKEjfjMWJFui04WlxbPgmTRFDD5EXZFsRIf07uLSupqSoCbCQ37W4$ 
>>>>>>>> <https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>>>>>>>
>>>>>>>> Kind regards,
>>>>>>>> Kiya
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Peter Manzella
>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>> 309 Bennett Hall
>>>>>>> University of Maine
>>>>>>> peter.manzella at maine.edu
>>>>>>>
>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>>> Allan Poe
>>>>>>> --
>>>>>>> Flash-X-users mailing list
>>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!bBZBV3a8yrv2pVog4R4uZuLcufNptkroqa7xjPAm232Kl2Wp8JCdKEjfjMWJFui04WlxbPgmTRFDD5EXZFsRIf07uLSupqSoCSDo5WHR$ 
>>>>>>> <https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Peter Manzella
>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>> 309 Bennett Hall
>>>>>> University of Maine
>>>>>> peter.manzella at maine.edu
>>>>>>
>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>> Allan Poe
>>>>>> --
>>>>>> Flash-X-users mailing list
>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!bBZBV3a8yrv2pVog4R4uZuLcufNptkroqa7xjPAm232Kl2Wp8JCdKEjfjMWJFui04WlxbPgmTRFDD5EXZFsRIf07uLSupqSoCSDo5WHR$ 
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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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