[Flash-X-users] Getting Flash-X to work
Ryan Farber
rjfarber at umich.edu
Thu Aug 29 22:48:39 CDT 2024
Hi Peter,
Thanks for attaching the file. As you can see, the files are sorted
alphabetically. I don't see any wl* files in your object directory,
suggesting there is in fact an issue.
Anyway, I am also running into some trouble getting Flash-X up and running
on my virtual private server.
Specifically, I have an HDF5 error:
" ../..//Modules/Library/SubcellReconstructionModule.F90 -o
SubcellReconstructionModule.o
../..//Modules/InputOutput/InputOutputModuleHDF.F90:1577:78
1577 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
DATASIZE, HDFERR )
|
1
Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
../..//Modules/InputOutput/InputOutputModuleHDF.F90:1526:78
1526 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
DATASIZE, HDFERR )
|
1
Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
../..//Modules/InputOutput/InputOutputModuleHDF.F90:1444:78
1444 | CALL H5DREAD_F( DATASET_ID, H5T_NATIVE_DOUBLE, Dataset,
DATASIZE, HDFERR )
|
1
Error: There is no specific subroutine for the generic ‘h5dread_f’ at (1)
make: *** [Makefile.Flash:171: InputOutputModuleHDF.o] Error 1
make: *** Waiting for unfinished jobs....
A setup internal error has occured, if possible please email the following
debugging info to flash-x-users at lists.cels.anl.gov
Arguments: ['/home/betelgeuse/FlashX/Flash-X/bin/setup.py', 'Relaxation',
'-auto', '-3d', '+cartesian', '+cube16', '+thornado', 'nE=16', 'swE=1',
'nSpecies=6', 'nNodes=2', 'nMoments=4', 'momentClosure=MINERBO',
'thornadoOrder=ORDER_V', '+weaklib', '-parfile=flash.par']
Python Version: 3.8.10
Platform Details: linux
I tried re-building HDF5 with 2003 features of Fortran enabled, but still
no dice.
Kiya, I noticed the following in the Miakefile.h you shared
earlier: -DH5_USE_16_API
Which version of HDF5 do you have installed (I was trying 1.8.22 with
openmpi using gcc 9ish)?
Best wishes,
--------
Ryan
On Thu, Aug 29, 2024 at 5:53 AM 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!b-8HHcrbuGXwVp_fU3xXRk07GBAHXxDUhzCqQfmXhOGpPl8eNkCr_GfdBPH-LFDDYYTVlbVxtrTDyMj_Xi2tjaCB9YZnYlZCuA$
>>>>>>> <https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!cy5tKVb9Qwu2rLLCi1LNfkq2D5uVYlmB4FWF6x2Pvqvq1OrrRPvzAwx-yFHLivQcBbWQTRySdjTQzVXdJjzC_Qh1vl2zpGdoLrGAwyOT$>
>>>>>>>
>>>>>>> Kind regards,
>>>>>>> Kiya
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Peter Manzella
>>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>>> 309 Bennett Hall
>>>>>> University of Maine
>>>>>> peter.manzella at maine.edu
>>>>>>
>>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>>> Allan Poe
>>>>>> --
>>>>>> Flash-X-users mailing list
>>>>>> Flash-X-users at lists.cels.anl.gov
>>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!b-8HHcrbuGXwVp_fU3xXRk07GBAHXxDUhzCqQfmXhOGpPl8eNkCr_GfdBPH-LFDDYYTVlbVxtrTDyMj_Xi2tjaCB9YYIvEq9kA$
>>>>>> <https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!Z1_GXydE2pV62oyGpM2ZteP_zTQdp-c9MRnUEZgvDy2eM0cBnqD656HBLPAkAMqZu7096jmjWOZzHL2ARHhx_LB-ZMcFtJGRTFtRFBtj$>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Peter Manzella
>>>>> PhD Candidate, Department of Physics and Astronomy
>>>>> 309 Bennett Hall
>>>>> University of Maine
>>>>> peter.manzella at maine.edu
>>>>>
>>>>> “If you run out of ideas follow the road; you'll get there.” – Edgar
>>>>> Allan Poe
>>>>> --
>>>>> Flash-X-users mailing list
>>>>> Flash-X-users at lists.cels.anl.gov
>>>>> https://urldefense.us/v3/__https://lists.cels.anl.gov/mailman/listinfo/flash-x-users__;!!G_uCfscf7eWS!b-8HHcrbuGXwVp_fU3xXRk07GBAHXxDUhzCqQfmXhOGpPl8eNkCr_GfdBPH-LFDDYYTVlbVxtrTDyMj_Xi2tjaCB9YYIvEq9kA$
>>>>>
>>>>
>>>
>>> --
>>> 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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