[Flash-X-users] Getting Flash-X to work
kiyarash Taghiniyarami
kiyarash.niyarami at gmail.com
Wed Sep 4 23:30:25 CDT 2024
Hi Ryan,
This is the Thornado version I am using:
*INFO: thornado git hash:
Before-Applications-Removal-1646-g2c2f6ba4-dirtyINFO: thornado git date:
2023-10-23INFO: thornado git branch: HEADINFO: thornado git url:
https://urldefense.us/v3/__https://github.com/endeve/thornado.git__;!!G_uCfscf7eWS!ZlROdihwAyiuPIHauSVMcT_7W_CbE1KoGyxKnPZp8m9FIpFlb6-TVxmd0PBDXLECpUDiQ8vwxImEo9e2dMsUHzPbwDMO_QWv6zFmyTYz$
<https://urldefense.us/v3/__https://github.com/endeve/thornado.git__;!!G_uCfscf7eWS!ZlROdihwAyiuPIHauSVMcT_7W_CbE1KoGyxKnPZp8m9FIpFlb6-TVxmd0PBDXLECpUDiQ8vwxImEo9e2dMsUHzPbwDMO_QWv6zFmyTYz$ >*
Best,
Kiya
On Thu, Sep 5, 2024 at 1:49 AM Ryan Farber <rjfarber at umich.edu> wrote:
> 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!ZlROdihwAyiuPIHauSVMcT_7W_CbE1KoGyxKnPZp8m9FIpFlb6-TVxmd0PBDXLECpUDiQ8vwxImEo9e2dMsUHzPbwDMO_QWv65CcAw2S$
>>>>>>>>> <https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>>>>>>>>
>>>>>>>>> Kind regards,
>>>>>>>>> Kiya
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Peter Manzella
>>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>>> 309 Bennett Hall
>>>>>>>> University of Maine
>>>>>>>> peter.manzella at maine.edu
>>>>>>>>
>>>>>>>> “If you run out of ideas follow the road; you'll get there.” –
>>>>>>>> Edgar Allan Poe
>>>>>>>> --
>>>>>>>> Flash-X-users mailing list
>>>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!ZlROdihwAyiuPIHauSVMcT_7W_CbE1KoGyxKnPZp8m9FIpFlb6-TVxmd0PBDXLECpUDiQ8vwxImEo9e2dMsUHzPbwDMO_QWv64cR8Nnl$
>>>>>>>> <https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Peter Manzella
>>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>>> 309 Bennett Hall
>>>>>>> University of Maine
>>>>>>> peter.manzella at maine.edu
>>>>>>>
>>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>>> Allan Poe
>>>>>>> --
>>>>>>> Flash-X-users mailing list
>>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!ZlROdihwAyiuPIHauSVMcT_7W_CbE1KoGyxKnPZp8m9FIpFlb6-TVxmd0PBDXLECpUDiQ8vwxImEo9e2dMsUHzPbwDMO_QWv64cR8Nnl$
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> 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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