[Flash-X-users] Getting Flash-X to work
Ryan Farber
rjfarber at umich.edu
Wed Sep 4 17:18:26 CDT 2024
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
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...).
Could you mention the commit hash of the thornado version you have checked
out with your FlashX?
Best wishes,
--------
Ryan
On Thu, Aug 29, 2024 at 11:50 PM 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!eMjmyRmoVwZ0mQgZcQnIosmTg1WBNTPFfFB2fXAHZZ18fETwXiPXjuyK_RZg0j_Nv3xDubZqJYuzMMhq0IuTRVa7CX_xQedhfg$
>>>>>>>> <https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>>>>>>>
>>>>>>>> Kind regards,
>>>>>>>> Kiya
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Peter Manzella
>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>> 309 Bennett Hall
>>>>>>> University of Maine
>>>>>>> peter.manzella at maine.edu
>>>>>>>
>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>>> Allan Poe
>>>>>>> --
>>>>>>> Flash-X-users mailing list
>>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!eMjmyRmoVwZ0mQgZcQnIosmTg1WBNTPFfFB2fXAHZZ18fETwXiPXjuyK_RZg0j_Nv3xDubZqJYuzMMhq0IuTRVa7CX9fxcA02w$
>>>>>>> <https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Peter Manzella
>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>> 309 Bennett Hall
>>>>>> University of Maine
>>>>>> peter.manzella at maine.edu
>>>>>>
>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>> Allan Poe
>>>>>> --
>>>>>> Flash-X-users mailing list
>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!eMjmyRmoVwZ0mQgZcQnIosmTg1WBNTPFfFB2fXAHZZ18fETwXiPXjuyK_RZg0j_Nv3xDubZqJYuzMMhq0IuTRVa7CX9fxcA02w$
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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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