Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka #324

psharda · 2023-06-22T15:15:08Z

@BenWibking , look at this test change I made to EOS.hpp: for tests other than primordial chem, now, I want to use microphysics EOS to ComputeTgasFromEint. I create a burn_t object, add the density, Eint and mean_molecular_weight to it, and then use the eos(eos_input_re, ...) call to find the temperature.

While compiling a test that actually uses ComputeTgasFromEint (e.g., HydroShocktubeCMA), I get these errors:

[ 38%] Linking CXX executable test_hydro_shocktube_cma
CMakeFiles/test_hydro_shocktube_cma.dir/test_hydro_shocktube_cma.cpp.o: In function `HydroSystem<ShocktubeProblem>::EnforceLimits(double, double, double, double, double, amrex::MultiFab&)::{lambda(int, int, int, int)#1}::operator()(int, int, int, int) const':
test_hydro_shocktube_cma.cpp:(.text._ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii[_ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii]+0x22f): undefined reference to `EOSData::initialized'
test_hydro_shocktube_cma.cpp:(.text._ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii[_ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii]+0x252): undefined reference to `eos_rp::eos_assume_neutral'
test_hydro_shocktube_cma.cpp:(.text._ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii[_ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii]+0x26a): undefined reference to `EOSData::mine'
test_hydro_shocktube_cma.cpp:(.text._ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii[_ZZN11HydroSystemI16ShocktubeProblemE13EnforceLimitsEdddddRN5amrex8MultiFabEENKUliiiiE_clEiiii]+0x278): undefined reference to `EOSData::maxe'

I think the reason behind these errors is that I haven't initialized the microphysics eos and extern_parameters. In primordial chem test, I do init_extern_parameters() and eos_init() to initialize them. My question is, where should I carry out this initialization for other tests? In their respective test.cpp files? Or, in EOS.hpp itself?

for more information, see https://pre-commit.ci

BenWibking · 2023-06-22T15:45:58Z

This is a linking issue. It looks like the necessary EOS .cpp files aren't being linked into the binary, so these functions don't exist when it tries to link it together.

BenWibking · 2023-06-22T15:57:56Z

Hopefully it's just a missing *.cpp file. However, it can be something more exotic, in which case it is unfortunately necessary to understanding how the linker works in some detail.

If you are in the latter situation, I would recommend reading this: https://www.lurklurk.org/linkers/linkers.html.

psharda · 2023-07-25T09:25:37Z

/azp run

for more information, see https://pre-commit.ci

psharda · 2023-07-25T10:39:36Z

/azp run

BenWibking · 2023-07-25T13:04:06Z

Can you add a new *.rst file in docs/ that explains what mass_code_units is?

Since the rest of us were confused about this on the call, I think new users will be very confused without some documentation.

psharda · 2023-07-25T13:11:20Z

We don't need mass_code_units anymore (I thought that was clear from the discussion?). Anyway I will push a commit soon.

psharda · 2023-07-25T13:20:35Z

/azp run

azure-pipelines · 2023-07-25T13:20:41Z

No commit pushedDate could be found for PR 324 in repo quokka-astro/quokka

psharda · 2023-07-25T13:22:51Z

/azp run

outdated

psharda · 2023-07-25T15:25:51Z

this is ready @BenWibking

BenWibking · 2023-07-25T16:00:33Z

I'll take a look this afternoon.

src/Cooling/test_cooling.cpp

BenWibking · 2023-07-25T22:37:02Z

Looks good, except for the last remaining mass_code_units that can be deleted.

Automerge enabled.

BenWibking · 2023-07-25T22:38:18Z

This does seem a bit slower than usual.

/usr/bin/cmake -E chdir . ctest -E MatterEnergyExchange* -T Test --output-on-failure
   Site: avatargpue.anu.edu.au
   Build name: Linux-g++
Create new tag: 20230725-1425 - Experimental
Test project /avatar/bwibking/azure-pipelines-agent/_work/4/s/build
      Start  1: HydroShocktubeCMA
 1/28 Test  #1: HydroShocktubeCMA ................   Passed  915.15 sec
      Start  2: PrimordialChem
 2/28 Test  #2: PrimordialChem ...................   Passed    2.53 sec
      Start  3: ScalarAdvection
 3/28 Test  #3: ScalarAdvection ..................   Passed    8.05 sec
      Start  4: Advection2D
 4/28 Test  #4: Advection2D ......................   Passed   46.84 sec
      Start  5: ScalarAdvectionSemiEllipse
 5/28 Test  #5: ScalarAdvectionSemiEllipse .......   Passed    7.94 sec
      Start  6: HydroBlast3D
 6/28 Test  #6: HydroBlast3D .....................   Passed  736.15 sec
      Start  7: HydroContact
 7/28 Test  #7: HydroContact .....................   Passed    2.99 sec
      Start  8: HydroLeblanc
 8/28 Test  #8: HydroLeblanc .....................   Passed   59.05 sec
      Start  9: HydroShocktube
 9/28 Test  #9: HydroShocktube ...................   Passed   86.79 sec
      Start 10: ShuOsher
10/28 Test #10: ShuOsher .........................   Passed   30.77 sec
      Start 11: HydroSlowMovingShock
11/28 Test #11: HydroSlowMovingShock .............   Passed    8.35 sec
      Start 12: HydroVacuum
12/28 Test #12: HydroVacuum ......................   Passed    2.52 sec
      Start 13: HydroWave
13/28 Test #13: HydroWave ........................   Passed    3.26 sec
      Start 14: HydroQuirk
14/28 Test #14: HydroQuirk .......................   Passed    3.49 sec
      Start 15: HydroHighMach
15/28 Test #15: HydroHighMach ....................   Passed    2.60 sec
      Start 16: RadForce
16/28 Test #16: RadForce .........................   Passed   57.97 sec
      Start 17: MarshakWave
17/28 Test #17: MarshakWave ......................   Passed    7.43 sec
      Start 18: MarshakWaveCGS
18/28 Test #18: MarshakWaveCGS ...................   Passed    3.74 sec
      Start 19: RadiationPulse
19/28 Test #19: RadiationPulse ...................   Passed   38.29 sec
      Start 20: RadiationStreaming
20/28 Test #20: RadiationStreaming ...............   Passed    4.80 sec
      Start 21: SuOlsonTest
21/28 Test #21: SuOlsonTest ......................   Passed   12.78 sec
      Start 22: RadiationPressureTube
22/28 Test #22: RadiationPressureTube ............   Passed   11.76 sec
      Start 23: RadhydroShock
23/28 Test #23: RadhydroShock ....................   Passed  119.09 sec
      Start 24: RadhydroShockCGS
24/28 Test #24: RadhydroShockCGS .................   Passed  128.29 sec
      Start 25: ODEIntegration
25/28 Test #25: ODEIntegration ...................   Passed    2.40 sec
      Start 26: PassiveScalar
26/28 Test #26: PassiveScalar ....................   Passed   47.20 sec
      Start 27: FCQuantities
27/28 Test #27: FCQuantities .....................   Passed    2.46 sec
      Start 28: SphericalCollapse
28/28 Test #28: SphericalCollapse ................   Passed  199.84 sec

100% tests passed, 0 tests failed out of 28

Total Test time (real) = 2553.28 sec

psharda · 2023-07-26T07:42:44Z

This does seem a bit slower than usual.

/usr/bin/cmake -E chdir . ctest -E MatterEnergyExchange* -T Test --output-on-failure
   Site: avatargpue.anu.edu.au
   Build name: Linux-g++
Create new tag: 20230725-1425 - Experimental
Test project /avatar/bwibking/azure-pipelines-agent/_work/4/s/build
      Start  1: HydroShocktubeCMA
 1/28 Test  #1: HydroShocktubeCMA ................   Passed  915.15 sec
      Start  2: PrimordialChem
 2/28 Test  #2: PrimordialChem ...................   Passed    2.53 sec
      Start  3: ScalarAdvection
 3/28 Test  #3: ScalarAdvection ..................   Passed    8.05 sec
      Start  4: Advection2D
 4/28 Test  #4: Advection2D ......................   Passed   46.84 sec
      Start  5: ScalarAdvectionSemiEllipse
 5/28 Test  #5: ScalarAdvectionSemiEllipse .......   Passed    7.94 sec
      Start  6: HydroBlast3D
 6/28 Test  #6: HydroBlast3D .....................   Passed  736.15 sec
      Start  7: HydroContact
 7/28 Test  #7: HydroContact .....................   Passed    2.99 sec
      Start  8: HydroLeblanc
 8/28 Test  #8: HydroLeblanc .....................   Passed   59.05 sec
      Start  9: HydroShocktube
 9/28 Test  #9: HydroShocktube ...................   Passed   86.79 sec
      Start 10: ShuOsher
10/28 Test #10: ShuOsher .........................   Passed   30.77 sec
      Start 11: HydroSlowMovingShock
11/28 Test #11: HydroSlowMovingShock .............   Passed    8.35 sec
      Start 12: HydroVacuum
12/28 Test #12: HydroVacuum ......................   Passed    2.52 sec
      Start 13: HydroWave
13/28 Test #13: HydroWave ........................   Passed    3.26 sec
      Start 14: HydroQuirk
14/28 Test #14: HydroQuirk .......................   Passed    3.49 sec
      Start 15: HydroHighMach
15/28 Test #15: HydroHighMach ....................   Passed    2.60 sec
      Start 16: RadForce
16/28 Test #16: RadForce .........................   Passed   57.97 sec
      Start 17: MarshakWave
17/28 Test #17: MarshakWave ......................   Passed    7.43 sec
      Start 18: MarshakWaveCGS
18/28 Test #18: MarshakWaveCGS ...................   Passed    3.74 sec
      Start 19: RadiationPulse
19/28 Test #19: RadiationPulse ...................   Passed   38.29 sec
      Start 20: RadiationStreaming
20/28 Test #20: RadiationStreaming ...............   Passed    4.80 sec
      Start 21: SuOlsonTest
21/28 Test #21: SuOlsonTest ......................   Passed   12.78 sec
      Start 22: RadiationPressureTube
22/28 Test #22: RadiationPressureTube ............   Passed   11.76 sec
      Start 23: RadhydroShock
23/28 Test #23: RadhydroShock ....................   Passed  119.09 sec
      Start 24: RadhydroShockCGS
24/28 Test #24: RadhydroShockCGS .................   Passed  128.29 sec
      Start 25: ODEIntegration
25/28 Test #25: ODEIntegration ...................   Passed    2.40 sec
      Start 26: PassiveScalar
26/28 Test #26: PassiveScalar ....................   Passed   47.20 sec
      Start 27: FCQuantities
27/28 Test #27: FCQuantities .....................   Passed    2.46 sec
      Start 28: SphericalCollapse
28/28 Test #28: SphericalCollapse ................   Passed  199.84 sec

100% tests passed, 0 tests failed out of 28

Total Test time (real) = 2553.28 sec

Yes, I found that too. I actually commented about it earlier but then edited my comment thinking it was probably a Gadi thingy, because on avatar it doesn't take any longer than before.

psharda · 2023-07-26T07:43:47Z

/azp run

azure-pipelines · 2023-07-26T07:43:54Z

No commit pushedDate could be found for PR 324 in repo quokka-astro/quokka

psharda · 2023-07-26T07:51:19Z

/azp run

psharda · 2023-07-26T12:50:25Z

Ready to be merged @BenWibking

psharda and others added 25 commits June 6, 2023 11:54

track branch from max

20f630e

Merge branch 'quokka-astro:development' into micro-max

360e567

enable two-EOS compilation

bfe6e05

use ifdefs for primordial chem

2040e58

include actual eos data header

9c3c5c2

[pre-commit.ci] auto fixes from pre-commit.com hooks

ba1dadb

for more information, see https://pre-commit.ci

updated microp

de5ef24

updated microp

4b8ba3c

update microp

ca15bbe

updated microphysics

d8f9120

use BEFORE keyword to set right priority of include dirs

6b1786c

updated microp: remove gammalaw eos params from primordial chem eos

ad854ab

Merge branch 'quokka-astro:development' into micro-max

8a33278

Merge branch 'quokka-astro:development' into micro-max

e855760

updated microp

c988c19

include QuokkaObjSources

da60ddc

updated microp

9b5169b

remove de-linking quokkaobj lib

8c50e09

only build some tests

8b18029

reattached microp

358e2cd

add QuokkaObjSources

2135136

build all tests

95e1744

Merge branch 'development' into micro-max

df02fdb

Merge branch 'quokka-astro:development' into micro-max

8d20b48

use microp EOS for all tests

03f4f6f

psharda requested a review from BenWibking June 22, 2023 15:15

[pre-commit.ci] auto fixes from pre-commit.com hooks

811a077

for more information, see https://pre-commit.ci

add gamma_law_sources to all tests

b03c827

fixed bug

9f60a17

psharda and others added 2 commits July 25, 2023 12:37

fixed bugs

99ec5f7

[pre-commit.ci] auto fixes from pre-commit.com hooks

9ce8fb7

for more information, see https://pre-commit.ci

remove mass_code_units

852ee12

BenWibking reviewed Jul 25, 2023

View reviewed changes

src/Cooling/test_cooling.cpp Outdated Show resolved Hide resolved

BenWibking enabled auto-merge July 25, 2023 22:36

remove mass_code_units

66d017c

psharda requested a review from BenWibking July 26, 2023 07:43

BenWibking approved these changes Jul 26, 2023

View reviewed changes

BenWibking added this pull request to the merge queue Jul 26, 2023

Merged via the queue into quokka-astro:development with commit aa288b5 Jul 26, 2023
8 checks passed

psharda deleted the micro-max branch July 31, 2023 08:24

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka #324

Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka #324

psharda commented Jun 22, 2023

BenWibking commented Jun 22, 2023

BenWibking commented Jun 22, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

BenWibking commented Jul 25, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

azure-pipelines bot commented Jul 25, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

BenWibking commented Jul 25, 2023

BenWibking commented Jul 25, 2023

BenWibking commented Jul 25, 2023 •

edited

Loading

psharda commented Jul 26, 2023

psharda commented Jul 26, 2023

azure-pipelines bot commented Jul 26, 2023

psharda commented Jul 26, 2023

psharda commented Jul 26, 2023

Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka #324

Use microphysics EOS in Quokka's EOS.hpp for all quokka tests + use amu instead of hydrogen mass throughout Quokka #324

Conversation

psharda commented Jun 22, 2023

BenWibking commented Jun 22, 2023

BenWibking commented Jun 22, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

BenWibking commented Jul 25, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

azure-pipelines bot commented Jul 25, 2023

psharda commented Jul 25, 2023

psharda commented Jul 25, 2023

BenWibking commented Jul 25, 2023

BenWibking commented Jul 25, 2023

BenWibking commented Jul 25, 2023 • edited Loading

psharda commented Jul 26, 2023

psharda commented Jul 26, 2023

azure-pipelines bot commented Jul 26, 2023

psharda commented Jul 26, 2023

psharda commented Jul 26, 2023

BenWibking commented Jul 25, 2023 •

edited

Loading