From peter.manzella at maine.edu  Thu Apr 11 17:23:41 2024
From: peter.manzella at maine.edu (Peter Manzella)
Date: Thu, 11 Apr 2024 18:23:41 -0400
Subject: [Flash-X-users] Getting started with the code
Message-ID: <CA+s928iiVkdvfc2ZH+sJY6ikK1=RfcJGBTK77C-6Vq2JmFS-vA@mail.gmail.com>

Hi,

I was directed to send a message here. I have been having problems getting
my 2-dimensional simulations to work with FLASH, so someone suggested I use
FLASH-X instead. I already have access to the FLASH-X github, I've looked
around, and I am having trouble telling what exactly I need to do to get
the code.
There are also some things I had trouble understanding what it meant,
between looking at the documentation here (
https://urldefense.us/v3/__https://flash-x.github.io/Flash-X-docs/*__;Iw!!G_uCfscf7eWS!c_9R3wkTKfZEeCYKzTc_1Fr_5XxmLXeSOvG6HvH6ZcUZYtHDNabrjCDQmV5DpGkopvzVB5F_OCkk59BOxBXmTyA0eoYl4NGSHWwVmoVk$ ) and looking at the code on
github, particularly looking at the "CCSN_" folders in the simulation
directory

-- 
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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From kiyarash.niyarami at gmail.com  Sun Apr 21 14:07:52 2024
From: kiyarash.niyarami at gmail.com (kiyarash Taghiniyarami)
Date: Sun, 21 Apr 2024 22:37:52 +0330
Subject: [Flash-X-users] Problem of running Relaxation (two moment benchmark)
Message-ID: <CAJbtpo3ME0GLDOi+iOULP9t+eyW9ve0y-n0803yCD=Vz-31HLw@mail.gmail.com>

Dear users,

I tried to run the relaxation  for Neutrino statinary state in 1D with 16
nxb test but after running it I face the following problem:
mpirun -np 8 ./flashx:
---------------------------------------------

Source terms initialized
 Using Thornado Relaxation setting to initial radiation field ...
 [rho, T, Ye]:   1.032E+12   8.805E+10   1.347E-01
  iteration, no. not moved =            0           0
 refined: total leaf blocks =           16
 refined: total blocks =           16
 [amr_morton_process]: Initializing surr_blks using standard orrery
implementation
 INFO: Grid_fillGuardCells is ignoring masking.
  Finished with Grid_initDomain, no restart
 Ready to call Hydro_init
 Hydro initialized
 Gravity initialized
 Initial dt verified
 arrays freed
 *** Wrote checkpoint file to relaxation_hdf5_chk_0000 ****
 *** Wrote plotfile to relaxation_hdf5_plt_cnt_0000 ****
 Initial plotfile written
 Driver init all done

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0  0x7fd0421afd11 in ???
#1  0x7fd0421aeee5 in ???
#2  0x7fd041e7408f in ???

can anyone help me what is the issue with that?

Best,
Kiya
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From adubey at anl.gov  Sun Apr 21 20:09:32 2024
From: adubey at anl.gov (Dubey, Anshu)
Date: Mon, 22 Apr 2024 01:09:32 +0000
Subject: [Flash-X-users] Problem of running Relaxation (two moment
 benchmark)
In-Reply-To: <CAJbtpo3ME0GLDOi+iOULP9t+eyW9ve0y-n0803yCD=Vz-31HLw@mail.gmail.com>
References: <CAJbtpo3ME0GLDOi+iOULP9t+eyW9ve0y-n0803yCD=Vz-31HLw@mail.gmail.com>
Message-ID: <MN2PR09MB5529189E1668E541F3009146C7122@MN2PR09MB5529.namprd09.prod.outlook.com>

Can you send us the log file and setup line for what you were trying to do? We need to be able to reproduce your problem.
Best,
Anshu

From: Flash-X-users <flash-x-users-bounces at lists.cels.anl.gov> on behalf of kiyarash Taghiniyarami <kiyarash.niyarami at gmail.com>
Date: Monday, April 22, 2024 at 4:08?AM
To: flash-x-users at lists.cels.anl.gov <flash-x-users at lists.cels.anl.gov>
Subject: [Flash-X-users] Problem of running Relaxation (two moment benchmark)
Dear users, I tried to run the relaxation  for Neutrino statinary state in 1D with 16 nxb test but after running it I face the following problem: mpirun -np 8 ./flashx: --------------------------------------------- Source terms initialized Using
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd
Dear users,

I tried to run the relaxation  for Neutrino statinary state in 1D with 16 nxb test but after running it I face the following problem:
mpirun -np 8 ./flashx:
---------------------------------------------

Source terms initialized
 Using Thornado Relaxation setting to initial radiation field ...
 [rho, T, Ye]:   1.032E+12   8.805E+10   1.347E-01
  iteration, no. not moved =            0           0
 refined: total leaf blocks =           16
 refined: total blocks =           16
 [amr_morton_process]: Initializing surr_blks using standard orrery implementation
 INFO: Grid_fillGuardCells is ignoring masking.
  Finished with Grid_initDomain, no restart
 Ready to call Hydro_init
 Hydro initialized
 Gravity initialized
 Initial dt verified
 arrays freed
 *** Wrote checkpoint file to relaxation_hdf5_chk_0000 ****
 *** Wrote plotfile to relaxation_hdf5_plt_cnt_0000 ****
 Initial plotfile written
 Driver init all done

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7fd0421afd11 in ???
#1  0x7fd0421aeee5 in ???
#2  0x7fd041e7408f in ???

can anyone help me what is the issue with that?

Best,
Kiya
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From kiyarash.niyarami at gmail.com  Sun Apr 21 23:28:00 2024
From: kiyarash.niyarami at gmail.com (kiyarash Taghiniyarami)
Date: Mon, 22 Apr 2024 07:58:00 +0330
Subject: [Flash-X-users] Problem of running Relaxation (two moment
 benchmark)
In-Reply-To: <MN2PR09MB5529189E1668E541F3009146C7122@MN2PR09MB5529.namprd09.prod.outlook.com>
References: <CAJbtpo3ME0GLDOi+iOULP9t+eyW9ve0y-n0803yCD=Vz-31HLw@mail.gmail.com>
	<MN2PR09MB5529189E1668E541F3009146C7122@MN2PR09MB5529.namprd09.prod.outlook.com>
Message-ID: <CAJbtpo1wQKoh0ZBR57ufn2j07Kt7T0TB++mOQ5H+1vdb3BSb6w@mail.gmail.com>

Dear Anshu,

After checking the logfile, I found it was due to the weaklib opacity
tables path in flash.par which needed to be corrected.

Thanks.

Kiya



On Mon, 22 Apr 2024, 04:39 Dubey, Anshu, <adubey at anl.gov> wrote:

> Can you send us the log file and setup line for what you were trying to
> do? We need to be able to reproduce your problem.
>
> Best,
>
> Anshu
>
>
>
> *From: *Flash-X-users <flash-x-users-bounces at lists.cels.anl.gov> on
> behalf of kiyarash Taghiniyarami <kiyarash.niyarami at gmail.com>
> *Date: *Monday, April 22, 2024 at 4:08?AM
> *To: *flash-x-users at lists.cels.anl.gov <flash-x-users at lists.cels.anl.gov>
> *Subject: *[Flash-X-users] Problem of running Relaxation (two moment
> benchmark)
>
> Dear users, I tried to run the relaxation  for Neutrino statinary state in
> 1D with 16 nxb test but after running it I face the following problem:
> mpirun -np 8 ./flashx: --------------------------------------------- Source
> terms initialized Using
>
> ZjQcmQRYFpfptBannerStart
>
> *This Message Is From an External Sender *
>
> This message came from outside your organization.
>
>
>
> ZjQcmQRYFpfptBannerEnd
>
> Dear users,
>
> I tried to run the relaxation  for Neutrino statinary state in 1D with 16
> nxb test but after running it I face the following problem:
> mpirun -np 8 ./flashx:
>
> ---------------------------------------------
>
>
> Source terms initialized
>  Using Thornado Relaxation setting to initial radiation field ...
>  [rho, T, Ye]:   1.032E+12   8.805E+10   1.347E-01
>   iteration, no. not moved =            0           0
>  refined: total leaf blocks =           16
>  refined: total blocks =           16
>  [amr_morton_process]: Initializing surr_blks using standard orrery
> implementation
>  INFO: Grid_fillGuardCells is ignoring masking.
>   Finished with Grid_initDomain, no restart
>  Ready to call Hydro_init
>  Hydro initialized
>  Gravity initialized
>  Initial dt verified
>  arrays freed
>  *** Wrote checkpoint file to relaxation_hdf5_chk_0000 ****
>  *** Wrote plotfile to relaxation_hdf5_plt_cnt_0000 ****
>  Initial plotfile written
>  Driver init all done
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0  0x7fd0421afd11 in ???
> #1  0x7fd0421aeee5 in ???
> #2  0x7fd041e7408f in ???
>
> can anyone help me what is the issue with that?
>
> Best,
> Kiya
>
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From kiyarash.niyarami at gmail.com  Mon Apr 22 02:02:36 2024
From: kiyarash.niyarami at gmail.com (kiyarash Taghiniyarami)
Date: Mon, 22 Apr 2024 10:32:36 +0330
Subject: [Flash-X-users] Problem of running Relaxation (two moment
 benchmark)
In-Reply-To: <MN2PR09MB5529FA78571BB09CE64B4248C7122@MN2PR09MB5529.namprd09.prod.outlook.com>
References: <CAJbtpo3ME0GLDOi+iOULP9t+eyW9ve0y-n0803yCD=Vz-31HLw@mail.gmail.com>
	<MN2PR09MB5529189E1668E541F3009146C7122@MN2PR09MB5529.namprd09.prod.outlook.com>
	<CAJbtpo1wQKoh0ZBR57ufn2j07Kt7T0TB++mOQ5H+1vdb3BSb6w@mail.gmail.com>
	<MN2PR09MB5529FA78571BB09CE64B4248C7122@MN2PR09MB5529.namprd09.prod.outlook.com>
Message-ID: <CAJbtpo0ebmj16oVCjQj5tDkFXWDcCc8CRG7wpFybHfyGsB_oOg@mail.gmail.com>

Yup, thanks

On Mon, 22 Apr 2024, 10:25 Dubey, Anshu, <adubey at anl.gov> wrote:

> So your problem is solved?
>
>
>
> *From: *kiyarash Taghiniyarami <kiyarash.niyarami at gmail.com>
> *Date: *Monday, April 22, 2024 at 1:28?PM
> *To: *Dubey, Anshu <adubey at anl.gov>, flash-x-users at lists.cels.anl.gov <
> flash-x-users at lists.cels.anl.gov>
> *Subject: *Re: [Flash-X-users] Problem of running Relaxation (two moment
> benchmark)
>
> Dear Anshu, After checking the logfile, I found it was due to the weaklib
> opacity tables path in flash. par which needed to be corrected. Thanks.
> Kiya On Mon, 22 Apr 2024, 04: 39 Dubey, Anshu, <adubey@ anl. gov> wrote:
> Can you send us the
>
> ZjQcmQRYFpfptBannerStart
>
> *This Message Is From an External Sender *
>
> This message came from outside your organization.
>
>
>
> ZjQcmQRYFpfptBannerEnd
>
> Dear Anshu,
>
>
>
> After checking the logfile, I found it was due to the weaklib opacity
> tables path in flash.par which needed to be corrected.
>
>
>
> Thanks.
>
>
>
> Kiya
>
>
>
>
>
> On Mon, 22 Apr 2024, 04:39 Dubey, Anshu, <adubey at anl.gov> wrote:
>
> Can you send us the log file and setup line for what you were trying to
> do? We need to be able to reproduce your problem.
>
> Best,
>
> Anshu
>
>
>
> *From: *Flash-X-users <flash-x-users-bounces at lists.cels.anl.gov> on
> behalf of kiyarash Taghiniyarami <kiyarash.niyarami at gmail.com>
> *Date: *Monday, April 22, 2024 at 4:08?AM
> *To: *flash-x-users at lists.cels.anl.gov <flash-x-users at lists.cels.anl.gov>
> *Subject: *[Flash-X-users] Problem of running Relaxation (two moment
> benchmark)
>
> Dear users, I tried to run the relaxation  for Neutrino statinary state in
> 1D with 16 nxb test but after running it I face the following problem:
> mpirun -np 8 ./flashx: --------------------------------------------- Source
> terms initialized Using
>
> ZjQcmQRYFpfptBannerStart
>
> *This Message Is From an External Sender *
>
> This message came from outside your organization.
>
>
>
> ZjQcmQRYFpfptBannerEnd
>
> Dear users,
>
> I tried to run the relaxation  for Neutrino statinary state in 1D with 16
> nxb test but after running it I face the following problem:
> mpirun -np 8 ./flashx:
>
> ---------------------------------------------
>
>
> Source terms initialized
>  Using Thornado Relaxation setting to initial radiation field ...
>  [rho, T, Ye]:   1.032E+12   8.805E+10   1.347E-01
>   iteration, no. not moved =            0           0
>  refined: total leaf blocks =           16
>  refined: total blocks =           16
>  [amr_morton_process]: Initializing surr_blks using standard orrery
> implementation
>  INFO: Grid_fillGuardCells is ignoring masking.
>   Finished with Grid_initDomain, no restart
>  Ready to call Hydro_init
>  Hydro initialized
>  Gravity initialized
>  Initial dt verified
>  arrays freed
>  *** Wrote checkpoint file to relaxation_hdf5_chk_0000 ****
>  *** Wrote plotfile to relaxation_hdf5_plt_cnt_0000 ****
>  Initial plotfile written
>  Driver init all done
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0  0x7fd0421afd11 in ???
> #1  0x7fd0421aeee5 in ???
> #2  0x7fd041e7408f in ???
>
> can anyone help me what is the issue with that?
>
> Best,
> Kiya
>
>
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From peter.manzella at maine.edu  Tue Apr 23 09:25:59 2024
From: peter.manzella at maine.edu (Peter Manzella)
Date: Tue, 23 Apr 2024 10:25:59 -0400
Subject: [Flash-X-users] Setup Internal Error
Message-ID: <CA+s928gTjBjegfDZb8A6-Kwh7GcG3ehYhcJrUWpiOYnW6nBwgA@mail.gmail.com>

Hi,

I've been trying to get a 2-dimensional CCSN simulation running, and I've
run into some problems, some that I could figure out how to fix, but I keep
hitting a wall on some, as I can't find documentation on how to
troubleshoot some of them, particularly this one, where it points to email
here,
[image: image.png]
Any help would be appreciated, I had tried for months to get 2d simulations
to work with FLASH, before someone suggested to try Flash-X.

-- 
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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From kiyarash.niyarami at gmail.com  Tue Apr 23 12:28:59 2024
From: kiyarash.niyarami at gmail.com (kiyarash Taghiniyarami)
Date: Tue, 23 Apr 2024 20:58:59 +0330
Subject: [Flash-X-users] Setup Internal Error
In-Reply-To: <CA+s928gTjBjegfDZb8A6-Kwh7GcG3ehYhcJrUWpiOYnW6nBwgA@mail.gmail.com>
References: <CA+s928gTjBjegfDZb8A6-Kwh7GcG3ehYhcJrUWpiOYnW6nBwgA@mail.gmail.com>
Message-ID: <CAJbtpo0K4yZQ4EUqOJBJyY1m5ws8hgipDpfu2tAfxrc_=CQ5Uw@mail.gmail.com>

Dear Peter,
Setup, compilation and running 2d CCSN at the first step needs too many
setups, libraries and details (thornad, Weaklib, Xnet and etc). I am not
sure if you setup everything correctly from the first as you have problem
in setup command so I share what I went through as follows:
 besides MPI, HDF5,Zlib, NCMPI you have installed in FLASH, for Flash-X you
may also need LAPACK, BLAS, MA28 and stdcxx to be installed and after that
in the directory of sites (Flash-X/sites) you have to make your own machine
directory (if is not set by default sites) then make the Makefile.h.
I will attach my own Makefile which is based on my laptop that may help you.

After all these steps, my suggestion is to run the Relaxation and
DeleptonizationWave test. After successful runs, then you may go through a
complex run such as 2d CCSN. I am not sure how much time you do have but
fixing all setups mentioned above may take you at least two weeks (because
in every step you will face erros you need to resolve).

If you really want to understand what you are going through you need at
least a grasp on thornado lib (
https://urldefense.us/v3/__https://github.com/endeve/thornado/tree/883a6feefc2af3c14fafd7dd011f2cf6d4a66f07__;!!G_uCfscf7eWS!e0jSlyGJUmNjk0uM7BtwDH05f29eYR23kHJZQRA-XTdaZIBJBi47ozUzW3tb4RFcV6vBMJVU3gxMSr3nAHoL7RjfoF0pbxGGYsWXlKha$ 
).
check the link and in docs you can find the details of Neutrino Two moment
scheme.

Best,
Kiya

On Tue, Apr 23, 2024 at 5:56?PM Peter Manzella <peter.manzella at maine.edu>
wrote:

> Hi, I've been trying to get a 2-dimensional CCSN simulation running, and
> I've run into some problems, some that I could figure out how to fix, but I
> keep hitting a wall on some, as I can't find documentation on how to
> troubleshoot
> ZjQcmQRYFpfptBannerStart
> This Message Is From an External Sender
> This message came from outside your organization.
>
> ZjQcmQRYFpfptBannerEnd
> Hi,
>
> I've been trying to get a 2-dimensional CCSN simulation running, and I've
> run into some problems, some that I could figure out how to fix, but I keep
> hitting a wall on some, as I can't find documentation on how to
> troubleshoot some of them, particularly this one, where it points to email
> here,
> [image: image.png]
> Any help would be appreciated, I had tried for months to get 2d
> simulations to work with FLASH, before someone suggested to try Flash-X.
>
> --
> 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!e0jSlyGJUmNjk0uM7BtwDH05f29eYR23kHJZQRA-XTdaZIBJBi47ozUzW3tb4RFcV6vBMJVU3gxMSr3nAHoL7RjfoF0pbxGGYtkxokRZ$ 
>
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From kiyarash.niyarami at gmail.com  Fri Apr 26 04:09:05 2024
From: kiyarash.niyarami at gmail.com (kiyarash Taghiniyarami)
Date: Fri, 26 Apr 2024 12:39:05 +0330
Subject: [Flash-X-users] How to access the radiation data which computed by
 THORNADO
Message-ID: <CAJbtpo3uvrJcrUJFGKZ5T7sbm631n=dDYSizk=rSL1cbte+riw@mail.gmail.com>

Dear users,
After successful run of Relaxation test by following setup:
---------------------
./setup Relaxation -auto -2d +cartesian -nxb=10 -nyb=10 +thornado nE=16
swE=1 nSpecies=6 nNodes=2 nMoments=4 momentClosure=MINERBO
thornadoOrder=ORDER_V +weaklib -parfile=flash.par
------------------
I am trying to plot the intensity (J) for different energy groups (say
5,16,90 MeV) versus the Radius (sqrt (x^2+y^2)) but I do not know how to
set flash.par before run to save them. For instance I set the following in
the flash.par
plot_var_7 = "T001"
plot_var_8 = "T002"

but I do not  know if T002 is the J at the second energy group or is it the
flux (H)?
or does the T001 have all the information of J at every energy group?
After all, I could not understand how Flash would save THORNADO radiation
moments in an hdf5 file (as variables of T001 to T864) even by taking a
look at code scratches which the Relaxation test is written by.

Any help would be appreciated.


Best,
Kiya
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