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

Tue Sep 3 11:50:43 CDT 2024

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
This Message Is From an External Sender
This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd
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!eahdNOc6EVbq1UDnw8FWJfV34i1vmhxrlMI6NdayF1lUiczJBRqj5UtcPI59Pe_XsoPndgdW6X3WrJAfVkFYLyjM3rcBJw$ <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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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:
[cid:ii_m0bu46cz0]
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<mailto: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<mailto: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<mailto: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!eahdNOc6EVbq1UDnw8FWJfV34i1vmhxrlMI6NdayF1lUiczJBRqj5UtcPI59Pe_XsoPndgdW6X3WrJAfVkFYLyhA3WTIqw$ <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<mailto: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<mailto:Flash-X-users at lists.cels.anl.gov>
https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!eahdNOc6EVbq1UDnw8FWJfV34i1vmhxrlMI6NdayF1lUiczJBRqj5UtcPI59Pe_XsoPndgdW6X3WrJAfVkFYLygbuxVJmg$ <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<mailto: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<mailto:Flash-X-users at lists.cels.anl.gov>
https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!eahdNOc6EVbq1UDnw8FWJfV34i1vmhxrlMI6NdayF1lUiczJBRqj5UtcPI59Pe_XsoPndgdW6X3WrJAfVkFYLygbuxVJmg$ <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<mailto: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<mailto: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<mailto:peter.manzella at maine.edu>

“If you run out of ideas follow the road; you'll get there.” – Edgar Allan Poe
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.cels.anl.gov/pipermail/flash-x-users/attachments/20240903/abe4ce88/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 58932 bytes
Desc: image.png
URL: <http://lists.cels.anl.gov/pipermail/flash-x-users/attachments/20240903/abe4ce88/attachment-0001.png>