Code consolidation. Created function getPatchExtents() that returns patch hi and lo indicies.
38 lines of code changed in 1 file:
fixed Clang compiler warning
2 lines of code changed in 2 files:
Added dialog gui so the user can choose try server(s).
34 lines of code changed in 1 file:
HypreSolver: The user can modify the variables precond_tolerance and precond_maxiters. Previously they were hardcoded.
UPS_SPEC: Consolidate all solver:parameters specs into a new xml file (solver_spec).
ups_spec.xml: formatting, cleaning out unused specs.
Arches input files adjustmented so the regression tests pass.
21 lines of code changed in 2 files:
Splitting up the transport eqn eval so that sources may used the RHS
construction in cases of rate limiting.
Also cleaned up some warnings.
local_RT showed one test failing (CoalRadPropsPlank) with noise diffs.
282 lines of code changed in 11 files:
Fix VarLabel memory leak. (Note, the use of the VarLabel to synchronize the tasks is a hack and hopefully will be addressed at some point.)
11 lines of code changed in 2 files:
Compute Mass flow rate through inlet boundaries.
* for both, gas, and coal phase.
* Utility to be used along with boundary type specification.
* Boundary type="Inlet" to be specified for the in-flow boundary
faces to be included in the mass flow rate computation.
* Utility of type="mass_flow_rate" to be added to the .ups file.
Warning : Variable Reduction applied for mass flow rates per patch, at
every time-step. Hence, user is advised to exercise caution while using
this Utility.
Recommendation : Use this Utility for verification purposes only.
495 lines of code changed in 11 files:
to allow sole and per patch vars to read/write I added swapbytes functions and readNormal for specialized sole and per patch vars
146 lines of code changed in 18 files:
This commit brings the PIDX data I/O branch (named: pidx_xml) back into the trunk.
All PIDX data I/O is, by default, turned off. To use PIDX you have to configure
against the PIDX library (either installing manually and pointing at it, or using
the --with-pidx flag (not 100% certain that this works at the moment)), and you must
set <DataArchiver type="PIDX"> (as opposed to the default which is type="UDA") in
the .ups input file.
Other caveats:
- Particles are not (currently?) supported in PIDX so any simulation that has a
particle data type will fail (most will print an error that PIDX does not
support them, but it seems some just die).
- Simulations that have overlapping patches (this may just be AMR type
sims) (eg: multibox_rmcrt_coal_1L) can save (slightly different) results.
In the multibox_rmcrt_coal_1L, we saw (only) a handful of differences like this:
((A 1 vs a 0 in a couple of locations) Also note that the UDA itself compared
successfully, but the checkpoint underneath it did not...)
DIFFERENCE [int 36, 5, 0] Time: 0.0003106658 Level: 0 Patch1: 0 Patch2: 0 Material: 0 Variable: areaFractionFX
multibox_RMCRT_coal_1L.uda/checkpoints goldStandard/.../multibox_RMCRT_coal_1L.uda/checkpoints
1 0
- "#if HAVE_PIDX" is used inconsistently through a number of files. Some PIDX stuff is #if'd out, while other code
is left in and compiles, it is just not used.
- There are a lot of cleanups that can and should take place wrt the PIDX integration.
While the code passes all the local RT tests (with the exception of particle tests),
I don't believe it has been run at large scale (though it should work) on a BGQ or Quartz@llnl.
Summary of changes: (Note, see pidx_xml branch commits if you want more information.)
M CCA/Ports/ApplicationInterface.h
M CCA/Components/Application/ApplicationCommon.h
- Added the ability to record (and retrieve) the number for the last regrid time step.
M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/DataArchiver/DataArchiver.cc
- When saving as PIDX, only create/output timestep.xml on the initial (I/O) time step that occurs after the regrid.
- Fixes that allow PIDX to save correctly (and efficiently) in parallel. If you are ever trying
to trace this back, read the comments from the commit logs for the "pidx_xml" branch.
- Remove createPIDX_dirs() as it was commented out and Sid tells me that PIDX creats its own dirs and we don't need this.
- Lot of white space fixes.
M CCA/Components/Examples/RMCRT_Test.cc
M CCA/Components/PostProcessUda/PostProcess.cc
- The DataArchive (DA) queryVariables() function now also returns the number of materials for each variable.
- "else" and "else if" should be on a separate line to make it easier to read.
M CCA/Components/Models/Radiation/RMCRT/RayGPU.cc
- Differentiate the output between the GPU and non-GPU reports so the viewer knows explicitly whether the GPU code was run.
M CCA/Components/Schedulers/OnDemandDataWarehouse.h
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Cosmetics: Line up variables, use more than 80 chars per line, white space.
Add in comments denoting default param values.
M CCA/Components/Schedulers/SchedulerCommon.cc
- Cosmetics.
M CCA/Components/SimulationController/AMRSimulationController.cc
- Cosmetics: Use more white space, 80+ chars per line for better readability, etc.
M CCA/Ports/PIDXOutputContext.h
- const'ify some params.
- checkReturnCode() is a static function so mark it so.
M CCA/Ports/PIDXOutputContext.cc
- White spacee. Code alignment for readability.
M Core/DataArchive/DataArchive.h
M Core/DataArchive/DataArchive.cc
- Add in PIDX functions. Note, queryPIDXSerial() is used (currently) by standalone codes (eg: puda).
Its purpose is to wrap the setupQueryPIDX()/queryPIDX() calls that have been added to
allow PIDX to truly run in parallel. At some point it would be good to update puda/compare_uda/etc
to run in parallel...
- See previous comments from PIDX branch for more details on the PIDX communicators that are necessary
to transfer data as some data does not live on all cores and thus can't use the golbal comm.
- Rename a few functions (queryAndSetParticlePositionName()) to be more accurate as to what they do.
- There are still a number of hacks in this code that need to be addressed (eg: var_materials map).
M Core/Geometry/IntVector.h
- Mostly cosmetics...
White space for readability.
Place 1-line functions in .h on one line to make it easier to see all provided functions.
M Core/Grid/Grid.cc
- White space, variable alignment for readability.
M Core/Grid/Level.h
M Core/Grid/Level.cc
- White space, coding standard (return type on its own line).
- Fix logic error in computeVariableExtents() that did not handle periodic boundaries correctly.
This fix was suggested as probably the correct way to do it by Todd... seems to pass tests and did fix
the issue (PIDX saving a particular something or other) that led me to it.
M Core/Grid/Patch.cc
- Place "else" on its own line for readability.
M Core/Grid/Variables/GridVariable.h
- Added emitPIDX().
- Opening "{" for functions in .h files goes on same line.
M Core/Grid/Variables/GridVariableBase.h
M Core/Grid/Variables/GridVariableBase.cc
- Organize #includes.
- White space, line up vars, etc for better readability.
- Return type on its own line.
M Core/Grid/Variables/ParticleData.h
- #include ParticleSubset.h for particleIndex.
M Core/Grid/Variables/ParticleSubset.h
- Cosmetic white space.
M Core/Grid/Variables/ParticleVariable.h
- White space, variable line up, etc.
- Added emitPIDX() function for particles. Note, particles do not fully work yet (on PIDX side).
And thus, this function hasn't really been tested.
M Core/Grid/Variables/ParticleVariableBase.h
M Core/Grid/Variables/ParticleVariableBase.cc
M Core/Grid/Variables/PerPatchBase.h
M Core/Grid/Variables/PerPatchBase.cc
M Core/Grid/Variables/ReductionVariableBase.h
M Core/Grid/Variables/ReductionVariableBase.cc
- Cosmetic white space. Coding standards. Etc.
M Core/Grid/Variables/Variable.h
M Core/Grid/Variables/Variable.cc
- Organize #includes.
- Use "const" on params that are const.
- Cosmetic white space, etc.
M Core/Grid/Variables/VarnameMatlPatch.h
- Pass non-changing strings by const reference (instead of copying them).
- White space for readability.
M Core/ProblemSpec/ProblemSpec.cc
- Line up vars, white space.
M R_Tester/helpers/compare_dat_files.pl
- Strip "/" from end of uda names.
- Clean up output to make it more readable (Todd I hope this doesn't break some of your scripts...)
M R_Tester/helpers/compare_dats
- White space.
M R_Tester/helpers/runSusTests.py
- Fix typo.
M StandAlone/compare_uda.cc
- White space.
- Line up vars.
- Coding standard.
- Line up case statement for better readability.
- 0 => nullptr
- query() now returns if the var was found (because PIDX has a list of all variables the simulation starts with
and the vars may not actually exist in the UDA.
- var => var_name (as it is actually the name, and not the var).
- Use 80+ columns.
M StandAlone/partvarRange.cco
M StandAlone/selectpart.cc
M StandAlone/tools/compute_Lnorm_udas.cc
M StandAlone/tools/dumpfields/dumpfields.cc
M StandAlone/tools/extractors/extractF.cc
M StandAlone/tools/extractors/extractS.cc
M StandAlone/tools/extractors/extractV.cc
M StandAlone/tools/extractors/faceextract.cc
M StandAlone/tools/extractors/lineextract.cc
M StandAlone/tools/extractors/partextract.cc
M StandAlone/tools/extractors/particle2tiff.cc
M StandAlone/tools/extractors/timeextract.cc
M StandAlone/tools/puda/AA_MMS.cc
M StandAlone/tools/puda/ER_MMS.cc
M StandAlone/tools/puda/GV_MMS.cc
M StandAlone/tools/puda/ICE_momentum.cc
M StandAlone/tools/puda/PIC.cc
M StandAlone/tools/puda/POL.cc
M StandAlone/tools/puda/asci.cc
M StandAlone/tools/puda/jacquie.cc
M StandAlone/tools/puda/jim1.cc
M StandAlone/tools/puda/jim2.cc
M StandAlone/tools/puda/jim3.cc
M StandAlone/tools/puda/pressure.cc
M StandAlone/tools/puda/puda.cc
M VisIt/interfaces/archiveInterface.cc
- queryVariables() now returns number of materials.
M StandAlone/tools/puda/varsummary.h
M StandAlone/tools/puda/varsummary.cc
- Swat some evil endls.
M build_scripts/build_pidx.sh
- FYI... Not sure if changing PIDX_TAG to "master" actually works...
M buildbot_try.sh
- Added a number of comments about use of this script.
- Fixed some typos.
- Spread command to multiple lines for readability.
2102 lines of code changed in 106 files:
Remove Oren's todo list.
0 lines of code changed in 1 file:
Hack around a hack...
Now at least this will not kill a simulation if the <BoundaryCondition>
spec is missing from <Arches>.
11 lines of code changed in 2 files:
clipping method for psNOx
43 lines of code changed in 1 file:
fixing bug in extended zeldovich mechanism
3 lines of code changed in 1 file:
Using DOUT now.
38 lines of code changed in 1 file:
Fix for potentail fatal bug when putting variables into the Datawarehouse (DW) when the variable type is
different from the type specified by the VarLabel. I'm surprised that we did not validate this previously
and more surprised that many things did not fail because of this. I'm guessing that for the most part
people didn't accidentally trigger this issue, and when it did happen, the underlying data was close enough
that it didn't cause issues.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Put in a check to validate that the variable and var label types match when allocateAndPut() is called.
Only makes this check if assertions are configured on (ie, debug builds).
M CCA/Components/Arches/ExplicitSolver.cc
- Fix error where SFCYVariable as being put into the DW as a SFCXVariable (X instead of Y).
M CCA/Components/Arches/SourceTerms/RMCRT.cc
- Fix error where abskg and sigmaT4 were being put into the DW as doubles before being converted into float vars
in RMCRT later on.
M Core/Grid/Variables/GridVariable.h
- Add some whitespace and use {} for one line if statements.
61 lines of code changed in 4 files:
Replacing an inadvertent template parameter with the constant type.
1 lines of code changed in 1 file:
Added performance testing code for Matrix3 methods.
-A. Gaia
121 lines of code changed in 2 files:
Addressing more compiler warnings
5 lines of code changed in 3 files:
Fixed instances where GraphHelper was forward declared as a Class rather than a Struct.
14 lines of code changed in 11 files:
Taking care of compiler warnings
12 lines of code changed in 9 files:
Remove unused TaskGraph data structure. This was a remnant from the old topological sort, which has since been removed along with supporting code.
16 lines of code changed in 3 files:
Fixing yesterday's "fixing" of the logic in the extraCell bulletproofing.
3 lines of code changed in 1 file:
turb viscosity at extra cell, fixing ups file
1 lines of code changed in 1 file:
fixing a bug in BC
8 lines of code changed in 5 files:
fxing BC
4 lines of code changed in 1 file:
Working in BC for Helium plume
215 lines of code changed in 11 files:
HyperStencil7 class:
- now using m_ for member variables.
145 lines of code changed in 1 file:
Added scheduleRestartInitialization() to the solver infrastructrure.
If you need a solver related variable from the old_DW and it isn't checkpointed then
create it in this task.
It's currently disabled in hypre.
57 lines of code changed in 11 files:
cleaned up the var naming
81 lines of code changed in 3 files:
removed the node info
4 lines of code changed in 1 file:
new names for the machine info
7 lines of code changed in 1 file:
Fixed a logic error in the extraCell bulletproofing code.
1 lines of code changed in 1 file:
added machine memory
18 lines of code changed in 3 files:
Reverted yet another file.
643 lines of code changed in 1 file:
added machine vars
117 lines of code changed in 1 file:
Removed code"hoops" that were jumped through so the hypreSolver could use the timestep.
SolverInterface.h:
-Formatting and added setWhichOldDW() and getWhichOldDW() methods
HypreSolver.cc
- Just get the timestep from the datawarehouse, either old_DW or parentOldDW. No more transferForwards (hoops).
impICE.cc
- removed scheduling the timestepLabel needed for Hypre. That is handled by hypreSolver.
ICE.cc
- formatting.
73 lines of code changed in 4 files:
fixed a few typos
1 lines of code changed in 1 file:
cleanup
69 lines of code changed in 37 files:
Added some files I forgot in the last commit. Oops.
838 lines of code changed in 4 files:
In Wasatch:
1. Made expressions for calculating energy transfer terms due to devolatilization, char reactions, and evaporation gpu-runnable.
2. Improved test coverage of coal models
3. Replaced elemental hydrogen in CPD model with diatomic hydrogen
4. removed a cantera file with a faulty chemical mechanism from the inputs directory
454 lines of code changed in 76 files:
rolled back changes to r58119
5834 lines of code changed in 108 files:
In Wasatch:
1. Made expressions for calculating energy transfer terms due to devolatilization, char reactions, and evaporation gpu-runnable.
2. Improved test coverage of coal models
3. Replaced elemental hydrogen in CPD model with diatomic hydrogen
4. removed a cantera file with a faulty chemical mechanism from the inputs directory
1292 lines of code changed in 46 files:
fix absently minded move
640 lines of code changed in 17 files:
Update copyright date.
2959 lines of code changed in 35 files:
changed logic for getting delta t fo subtaks
19 lines of code changed in 2 files:
Added RT test with mass/enthalpy conservation in the case of slagging walls.
3 lines of code changed in 1 file:
Adding a no-pressure-solve version of the DQMOM char example.
Adding some bullet proofing.
202 lines of code changed in 1 file:
Added new regression test showing mass and energy conservation for coal problems.
19 lines of code changed in 1 file:
This commit adjust the enthalpy balance, and ash mass balance for conservation. This commit will not change the answers.
506 lines of code changed in 5 files:
begin to treat Sole varibales as first class vars
2 lines of code changed in 1 file:
cleanup of depencendies to applications
302 lines of code changed in 6 files:
removed need for calls to shared state for the time step and sim time
3327 lines of code changed in 23 files:
begin to treat Sole varibales as first class vars
308 lines of code changed in 1 file:
* Get views after setup for boundedRayLength.
770 lines of code changed in 1 file:
Changed variable name modfies_hypre -> isFirstSolve and made a small change in the scheduling logic.
The hyper_solver_label was never modified. The scheduling logic changed after the first pass
through the solver, thus the name change.
43 lines of code changed in 19 files:
change for perpatch data
79 lines of code changed in 1 file:
name change
1084 lines of code changed in 7 files:
added templates the header
0 lines of code changed in 4 files:
lib name change
1 lines of code changed in 1 file:
split the interfaces and renamed files/dir
2970 lines of code changed in 16 files:
Removed sharedState from SolverParameters::readParameters(). It's not used.
HypreSolver.h
_ removed setSolveFrequency() and getSolveFrequency. The solve frequency is handled by the parameters.
BuildBotTry:
Changed #!/bin/csh -> #!/bin/csh -f
This fixed a oddball error.
32 lines of code changed in 23 files:
Passing arches down to the task factories.
106 lines of code changed in 39 files:
Passing reference to Arches down into the NLSolver.
53 lines of code changed in 7 files:
moved Todd'd print to here
25 lines of code changed in 2 files:
added Patch mesh
171 lines of code changed in 1 file:
removed duplicate print tasks, added deletes
0 lines of code changed in 4 files:
name cleanup
3 lines of code changed in 3 files:
added override to not scrub
13 lines of code changed in 1 file:
removed unneed header file
0 lines of code changed in 1 file:
Document remaining Douts.
19 lines of code changed in 8 files:
For infrastructure: Update existing DebugStreams and Dout objects to be constructed with a desription matching that found in environmentalFlags.txt. EnvironmentalFlags,txt itself also updated.
Components can individually go in and do this same thing now, ultimately deprecating and eventually removing environmentalFlags.txt (hopefully).
66 lines of code changed in 21 files:
Formatting:
- added horizontal and vertical space.
- added {} after conditional statements
- added __________________________________
- alignment were appropriate
178 lines of code changed in 2 files:
Convert user inputs string for the solver and preconditioner type from mixed case to lower case.
Changed conditionals to compare against lower case strings.
41 lines of code changed in 2 files:
DOUT.Hpp
- added DOUTR0() macro which prints on rank 0 all threads.
impICE.cc
- using DOUTR0 instead of proc0cout(), needed for threaded scheduler.
15 lines of code changed in 2 files:
Added constructors that initialize the elementss of the stencils
0 lines of code changed in 4 files:
Make sure to set SimulationState MaterialSet objects to nullptr in SimulationState::clearMaterials(). This was causing the problem with the Switcher and IMPM, etc. Valgrind gives the failing Switcher tests a clean bill of health now.
A few other minor, cosmetic changes.
23 lines of code changed in 6 files:
RT for OFC kokkos
1 lines of code changed in 1 file:
Intrusion for kokkosolver
69 lines of code changed in 4 files:
added patch mesh
122 lines of code changed in 1 file:
removed warnings
2 lines of code changed in 2 files:
fixing initialization and define variables inside of parallel_for
63 lines of code changed in 1 file:
Changed the hottel soot model to a new model, advocated by David Lignell, and Modest.
0 lines of code changed in 2 files:
added labels
2 lines of code changed in 1 file:
updated RT test, change name of list of models
523 lines of code changed in 11 files:
char model ps implimented in explicit solver
40 lines of code changed in 3 files:
Kokkos DQMOM with drag model
47 lines of code changed in 5 files:
abs -> fabs for portability.
Since AtomicTask now derives from Task, use its protected members for task name and matl rather than create its own.
31 lines of code changed in 8 files:
Remove code that Allen commented.
0 lines of code changed in 1 file:
removed the shared state from the radiation model and re-invoked the in-situ
106 lines of code changed in 14 files:
re-invoked the in-situ
144 lines of code changed in 4 files:
changed init order to remove RT warning and initialized a value
3 lines of code changed in 2 files:
Add Dout to sus to enable printing the environment out when sus loads up.
Reports after the MPI runtime is initialized.
10 lines of code changed in 3 files:
poked a temporary hole in the scheduler interface to get the application
10 lines of code changed in 2 files:
Cleanup UintahParallelComponent
0 lines of code changed in 4 files:
removed ICE models interface from the ModelInterafce, added HEChem interface and removed used methods
290 lines of code changed in 27 files:
Remove redundant code in SimulationState::clearMaterials.
With the switcher component, this was incorrectly decrementing the ref count on material sets, which is likely the reason ComputeSubsets were being deleted prematurely and subsequently casusing double delete issues when switching occurred. This problem would not manifest in anything but the switcher, as clearing materials only happened implicitly by the infrastructure via SimulationState DTOR. Switcher was calling it explicitly in Switcher::needRecompile().
Some other cleanup, e.g 0->nullptr, braces, white space, etc.
139 lines of code changed in 7 files: