January 2016 Commit Log

Number of Commits:
108
Number of Active Developers:
15
u0407585 2016-01-31 19:33 Rev.: 54753

Added the new rate computation into the new char oxidation model. This commit shouldn't impact regression tests.

349 lines of code changed in 2 files:

harman 2016-01-29 16:13 Rev.: 54752

global: generalization
- d_timingStats -> d_runTimeStats
This infomap will hold more than just times.

SimulationController::printSimulationStats()
- output the units for each of the runTimeStats

DataArchiver::outputVariables()
- save timing info when outputting PIDX formatted files.

78 lines of code changed in 13 files:

allen 2016-01-29 15:19 Rev.: 54751

added in an example of inserting in-situ vars from a component

25 lines of code changed in 1 file:

allen 2016-01-29 15:16 Rev.: 54750

added recompile to in-situ

9 lines of code changed in 2 files:

allen 2016-01-29 15:01 Rev.: 54749

changed to use the var defined units

17 lines of code changed in 1 file:

allen 2016-01-29 14:54 Rev.: 54748

added a units to the stats

46 lines of code changed in 3 files:

tsaad 2016-01-29 14:35 Rev.: 54747

fix a bug that prevents restarts on scalar transport

4 lines of code changed in 1 file:

allen 2016-01-29 13:30 Rev.: 54746

changed to std::abs to assure coorect result

0 lines of code changed in 2 files:

allen 2016-01-29 12:42 Rev.: 54745

fixed the pointer passing

1 lines of code changed in 1 file:

allen 2016-01-29 11:41 Rev.: 54744

fixed the pointer passing

12 lines of code changed in 5 files:

derekhar 2016-01-28 15:25 Rev.: 54743

Fixed a few of the radiation solvers within the Arches-Hypre interface. Solver and precondition pfmg now works correctly.

115 lines of code changed in 2 files:

tsaad 2016-01-28 12:27 Rev.: 54741

add body force effects to the total internal energy equation.
Fix a bug in passing the body force tag to the compressible momentum equations.

44 lines of code changed in 4 files:

tsaad 2016-01-28 10:05 Rev.: 54739

change the STATE of all transported quantities to STATE_NP1 rather than STATE_NONE.
This makes things consistent with the "state" nomenclature.
This commit will NOT change the answers. The failing RT is caused by my previous commit.

27 lines of code changed in 11 files:

tsaad 2016-01-28 10:03 Rev.: 54738

Speed things up a bit for the local and nightly RT by changing all tests running mpirun -np 16 to np 8.
This will change the answers slightly on those tests.

9 lines of code changed in 1 file:

harman 2016-01-27 17:25 Rev.: 54737

Abandoned the d_usingPIDX switch in favor of

enum outputFileFormat {UDA, PIDX};

This allows for growth to other file formats.

Cleaned up some convoluted logic that was allowing p.XXXXX files to be dumped
in the checkpoints when using PIDX file format.

10 lines of code changed in 2 files:

harman 2016-01-27 16:41 Rev.: 54736

added global switch d_usingPIDX

problemSetup()
- 2 space indentation
- added {} around conditionals
- cleaned up comment
- parse DataArchiver tag for "type=PIDX", set the switch according.

The user must use:

<DataArchiver type="PIDX">

and configure with:

--with-pidx=<path to PIDX installation>

to utilize the PIDX file format.


217 lines of code changed in 2 files:

harman 2016-01-27 15:55 Rev.: 54735

DataArchiver:
- Moved the creation of the PIDX subdirectories upstream into
makeTimestepDirs(). Parallel IO working again.
- moved the creation of the vector of supported PIDX Types upstream into

PIDXOutputContext::getSupportedVariableTypes()

PIDXOutputContext
- added dividers
- added getSupportedVariableTypes() and getDirectoryName(TypeDescription::Type TD)

The majority of the heavy lifting is done.


151 lines of code changed in 4 files:

harman 2016-01-27 15:08 Rev.: 54734

Backout previous commit and punt. Bigmac won't link with:

cout << Uintah::Parallel::getMPIRank()<< "message" << endl;
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

My desktop will compile it with either gcc and clang..

6 lines of code changed in 2 files:

harman 2016-01-27 10:51 Rev.: 54733

createSubdirPlus
- added MPI rank to the warning message.


3 lines of code changed in 2 files:

harman 2016-01-27 10:42 Rev.: 54732

In prep for PIDX changes moved code that repeatedly tries to create a sub-directory upstream into the Dir class.

Added a descriptive warning statement if one of the cores is having problems creating the subdir.

I'm open to suggestions on the method name

Added dividers.

149 lines of code changed in 4 files:

harman 2016-01-26 17:31 Rev.: 54731

saveLabels_PIDX()
- code cleanup and consolidation.


45 lines of code changed in 1 file:

dsunder 2016-01-26 16:13 Rev.: 54729

Add getKokkosView() to Array3

Wrap the Array3 memory with an unmanaged Kokkos::View.

148 lines of code changed in 5 files:

harman 2016-01-26 15:02 Rev.: 54728

Added support for Stencil7 & Stencil4 subtypes.

11 lines of code changed in 1 file:

harman 2016-01-25 19:14 Rev.: 54727

wrap PIDX code with

#if HAVE_PIDX
#endif

2 lines of code changed in 1 file:

harman 2016-01-25 18:48 Rev.: 54726

outputVariables()
- Moved the guts of the PIDX section to a new method (saveLabels_PIDX).
- Added method that returns a vector of saveItems with a common TypeDescription.
- Added loop over TypeDescriptions and call saveLabels_PIDX for each variable type

CC, SFCX, SFCY, SFCZ types, Vectors, doubles and int are supported. Normal output and checkpoints
are working in serial ONLY.

Needs additional testing and cleanup.

391 lines of code changed in 2 files:

harman 2016-01-25 14:22 Rev.: 54725

DataArchiver::outputVariables_PIDX()
- added {}
- removed commented out code.
- enabled checkpointed in PIDX section
- checkpointing with CC variables ONLY is working.

Directory structure is not correct for PIDX.

18 lines of code changed in 1 file:

tsaad 2016-01-25 12:05 Rev.: 54724

Fix a serious bug in the compressible flow solver.
1. Problems with the units for the gas constant (universal/specific). Must use specific gas constant.
2. The default behavior for the transport equation is to compute the diffusive flux based on the transported variable. In the case of the totalInternalEnergy, use the temperature instead.
Thanks to Mike Hansen for helping out and providing comparison datasets.

10 lines of code changed in 1 file:

harman 2016-01-25 11:36 Rev.: 54723

More generalizations inside of outputVariables+PIDX.
The variable type extents are now being accounted for.

mpirun -np 8 sus inputs/ICE/advect.ups (CCVariables only, no checkpointing) runs to completion

41 lines of code changed in 1 file:

allen 2016-01-22 17:32 Rev.: 54721

removed one dir level

1 lines of code changed in 1 file:

allen 2016-01-22 17:29 Rev.: 54720

added one more dir level

8 lines of code changed in 1 file:

allen 2016-01-22 17:28 Rev.: 54719

cleanup of the dw naming and other clean up

46 lines of code changed in 3 files:

allen 2016-01-22 17:21 Rev.: 54718

made set call controller generic

1 lines of code changed in 1 file:

allen 2016-01-22 17:13 Rev.: 54717

cleaned up dw calls

5 lines of code changed in 1 file:

allen 2016-01-22 17:12 Rev.: 54716

cleaned up file creation and reporting

17 lines of code changed in 2 files:

allen 2016-01-22 15:34 Rev.: 54715

changed dw

9 lines of code changed in 1 file:

harman 2016-01-21 17:37 Rev.: 54714

global:
- Created a method "getMaterialSubSet(level)" in SaveItem that returns the MaterialSubSet
for that variable and level.

- Replaced confusing logic with call to getMaterialSubset().

At least now the confusion is localized.


60 lines of code changed in 2 files:

harman 2016-01-21 16:44 Rev.: 54713

<< operators
output "null PatchSubset" or "null Material Subset" if they are null.

0 lines of code changed in 2 files:

harman 2016-01-21 15:07 Rev.: 54712

- PIDX directory names are now based on the timestep.

- Enable CCVarialbe<Vector> output

- Turn off PIDX debugging

- The pidxOffset is no longer hardwired to 1,1,1. Each level can have a different number of extracells.

mpirun -np 8 sus advect.ups (8 patch, CCVars only, no checkpoints) runs.

21 lines of code changed in 1 file:

cgritton 2016-01-21 14:46 Rev.: 54711

Cleaning up unused Diffusion models

1 lines of code changed in 5 files:

cgritton 2016-01-21 14:04 Rev.: 54710

Removing unused constitutive model.

0 lines of code changed in 4 files:

harman 2016-01-21 14:02 Rev.: 54709

Heavy construction zone:
- more work on generalization
- no longer squashing doubles into floats by default.
Relax, we'll bring that feature back once all required features are in place.
- consolidated diagnostic prints
- added comments and dividers

mpirun -np 8 sus advect.ups (8 patch, CCVars only, no checkpoints) runs.

91 lines of code changed in 1 file:

sidharth 2016-01-21 04:25 Rev.: 54706

compression disabled

4 lines of code changed in 2 files:

jholmen 2016-01-20 19:12 Rev.: 54705

* Added a Kokkos-based implementation of Poisson1::timeAdvance

52 lines of code changed in 1 file:

jholmen 2016-01-20 16:36 Rev.: 54704

* Added CXXFLAGS support and moved LDFLAGS

2 lines of code changed in 1 file:

dsunder 2016-01-20 16:21 Rev.: 54703

Improve interface to RowMajor and ColumnMajor ranges

110 lines of code changed in 1 file:

allen 2016-01-20 16:12 Rev.: 54701

clean up proc0 code

13 lines of code changed in 1 file:

allen 2016-01-20 15:56 Rev.: 54700

changed order of calls

4 lines of code changed in 1 file:

allen 2016-01-20 15:42 Rev.: 54699

added control message to alert user method was invoked.

3 lines of code changed in 1 file:

tsaad 2016-01-20 14:20 Rev.: 54697

First cut at a framework for dual time integration using a subscheduler.
The current functionality will do timeadvance within the dual time task. See: DualTime-ScalarTransportEquation.ups
This currently works on cell-centered scalar-fields (due to ghost type assumptions). Once we roll out the ExprLib dual time
iterative solver, we'll deal with integrating staggered fields.

381 lines of code changed in 6 files:

allen 2016-01-20 13:39 Rev.: 54696

added white space for readability

1 lines of code changed in 1 file:

allen 2016-01-20 13:38 Rev.: 54695

removed unneeded header

1 lines of code changed in 1 file:

allen 2016-01-20 13:34 Rev.: 54694

changed the cout to cout_doing

6 lines of code changed in 1 file:

allen 2016-01-19 19:26 Rev.: 54690

fixed warnings and case typo

14 lines of code changed in 6 files:

dsunder 2016-01-19 18:20 Rev.: 54689

Create RowMajor and ColumnMajor Ranges to which map from a linear index to a mult-dimensional index

138 lines of code changed in 1 file:

allen 2016-01-19 17:59 Rev.: 54688

custom interface for the libsim

402 lines of code changed in 1 file:

harman 2016-01-19 17:22 Rev.: 54687

DataArchiver::outputVariables() PIDX section
Removed redundant code;
- Only compute the size of the block of memory you're allocating once
- added {}
- added dividers

mpirun -np 8 sus -mpi advect.ups (8 patches) runs.

54 lines of code changed in 1 file:

harman 2016-01-19 16:31 Rev.: 54686

DataArchiver::outputVariables() PIDX section

Removed redundant code.
Only need to compute the total number of cells on a level once.

68 lines of code changed in 1 file:

tsaad 2016-01-19 16:19 Rev.: 54685

Allow one to specify the solve frequency for HypreSolver.
Simply add: <solveFrequency spec="OPTIONAL INTEGER"/>
to your spec and then use it in your input file.
More options can be added (solve at timestep 0?, disable carry forward of solution variable?...)

21 lines of code changed in 2 files:

allen 2016-01-19 15:51 Rev.: 54684

added new visit state vars

40 lines of code changed in 1 file:

allen 2016-01-19 15:50 Rev.: 54683

moved the analysis over to a global struct for commication with VisIt

47 lines of code changed in 2 files:

allen 2016-01-19 15:49 Rev.: 54682

move the controllers over to the new sim stat vars

30 lines of code changed in 4 files:

allen 2016-01-19 15:48 Rev.: 54681

added new visit state vars

4 lines of code changed in 1 file:

allen 2016-01-19 15:41 Rev.: 54680

added additional support for the custom UI

269 lines of code changed in 5 files:

dsunder 2016-01-19 14:00 Rev.: 54677

Initialize Kokkos in the MPIScheduler if UINTAH_ENABLE_KOKKOS is defined

22 lines of code changed in 2 files:

jas 2016-01-19 12:39 Rev.: 54675

Add question about PIDX as a comment.

1 lines of code changed in 1 file:

harman 2016-01-19 10:41 Rev.: 54674

DataArchiver::outputVariables()
Formatting changes mainly to PIDX section:
- removed tabs.
- added {}
- 2 space indentation
- tighten up where variables are defined.

advect.ups and advect2mat.ups run.

252 lines of code changed in 1 file:

u0407585 2016-01-18 15:27 Rev.: 54672

Created a copy of the old char oxidation model for the implementation of Phils new char oxidation model.

777 lines of code changed in 5 files:

guilkey 2016-01-17 17:30 Rev.: 54671

Fix the generalized vortex output so that it gives results for all timesteps,
not just the last one.

10 lines of code changed in 1 file:

guilkey 2016-01-17 10:49 Rev.: 54669

Fixing the failing ImpMPM RT tests.

1 lines of code changed in 1 file:

guilkey 2016-01-15 19:16 Rev.: 54667

Further merging, mostly formatting at this point

11 lines of code changed in 2 files:

guilkey 2016-01-15 17:27 Rev.: 54664

Merging code in from the ARL branch.

421 lines of code changed in 19 files:

ahumphrey 2016-01-15 17:13 Rev.: 54663

Fix more c++11-related warnings.

1.) Fix forward declaration of SimulationTime declared as a struct but defined as a class

2.) match delete[] with new[] (should fix a small memory leak)

2 lines of code changed in 3 files:

ahumphrey 2016-01-15 14:12 Rev.: 54662

Add public access modifier. Forgotten in previous commit to fix CellInformation, declared as a class but defined as a struct warning.

1 lines of code changed in 1 file:

ahumphrey 2016-01-15 13:56 Rev.: 54661

Fix incompliant c++11 code flagged by clang compiler:1.) explicit instantiations need to be in namespaces2.) match delete[] with new[] (should fix a small memory leak)3.) disambiguate method call in Socket class4.) fix CellInformation, declared as a class but defined as a struct

58 lines of code changed in 5 files:

allen 2016-01-14 15:15

moved the timing stat over to infomapper

4 lines of code changed in 3 files:

allen 2016-01-14 15:01 Rev.: 54657

moved the timing stat over to infomapper

238 lines of code changed in 10 files:

allen 2016-01-14 14:51 Rev.: 54656

converted over to new infomapper and moved callbacks

122 lines of code changed in 2 files:

allen 2016-01-14 14:48 Rev.: 54655

clean up adding lots of const when possible

40 lines of code changed in 1 file:

ahumphrey 2016-01-14 13:46 Rev.: 54654

Add complete set of subscheduler timings to the parent scheduler, and reset complete set of subscheduler timings.

27 lines of code changed in 2 files:

allen 2016-01-14 12:57 Rev.: 54653

a new template class - a std:map on steriods

200 lines of code changed in 1 file:

tsaad 2016-01-14 12:29 Rev.: 54652

This is embarrassing...
Fix several bugs in the refactor that was done for the compressible flow formulation:
1. Fix sign error for the dissipation function. Note that Wasatch computes the strain tensor and then constructs the stress tensor as needed on the fly. This was the source of the sign error issue. (Thanks to Mike Hansen who suspected an issue with the diffusive terms).
2. Fix how the stress tensor is calculated in the dissipation function. One must not forget to multiply the strain tensor by the viscosity and also subtract the dilatation from the normal strain.
3. This one is bad. The dilatation and the density were swapped in the construction of the stress tensor in the momentum rhs.
This commit will break every single Wasatch test that solves the Navier-Stokes equations.

59 lines of code changed in 9 files:

ahumphrey 2016-01-13 14:39 Rev.: 54651

"-std=c++11" is a valid option for NVCC compiler in CUDA versions >=7.0, so pass it directly to NVCC and bypass the -Xcompiler prefix (for host compilation phase).

NOTE: With this commit one can pass -std=c++11 (via CXXFLAGS for example) to Uintah at configure time and both CPU and GPU builds will complete successfully with all components enabled. Commits, r53598, r53517, etc addressed the previous issues the infrastructure had. Clang may kick up a few more. This should effect no component yet, simply adds the ability to use C++11. Once this settles, we can enforce using a C++11 compliant compiler at configure time with an M4 macro. This shouldn't be an issue as the C++11 standard is over 5 years old actually. We shouldn't need to support a compiler that old??

6 lines of code changed in 1 file:

jthornoc 2016-01-12 18:36 Rev.: 54649

Perform the variable stats task at the very end.

86 lines of code changed in 4 files:

allen 2016-01-12 14:38 Rev.: 54647

made the min max struct public

9 lines of code changed in 1 file:

allen 2016-01-12 14:38 Rev.: 54646

moved includes to the cc

5 lines of code changed in 2 files:

allen 2016-01-12 14:36 Rev.: 54645

added access for data analysis and split custom ui calls

527 lines of code changed in 7 files:

allen 2016-01-11 16:04 Rev.: 54644

clean up of AMR SIm Ctrl and moved code into the libsim area

357 lines of code changed in 7 files:

allen 2016-01-11 16:01 Rev.: 54642

added flag for adjust delT so it is possible to skip

5 lines of code changed in 2 files:

ahumphrey 2016-01-11 13:03 Rev.: 54641

Partial revert of r54638. and generate new configure script

7 lines of code changed in 1 file:

jas 2016-01-08 15:45 Rev.: 54640

Update copyright date to 2016.

2256 lines of code changed in 3414 files:

bpeterson 2016-01-08 14:17 Rev.: 54639

Some GPU debugging tweaks in Unified Scheduler

52 lines of code changed in 1 file:

ahumphrey 2016-01-08 12:21 Rev.: 54638

For GPU builds:

1.) now support compute capability 5.0 & 5.2 (Maxwell)
2.) no longer support sm_2.*
2.) compile debug builds with -O0 (-m64 -g -G -O0 passed to NVCC)

5 lines of code changed in 1 file:

tsaad 2016-01-08 08:48 Rev.: 54637

OCD-related formatting

14 lines of code changed in 1 file:

guilkey 2016-01-07 17:58 Rev.: 54636

Merging some of my fine changes from the branch in with Todd's fine changes to
the trunk. Will do the reverso next week.

63 lines of code changed in 2 files:

tsaad 2016-01-07 17:06 Rev.: 54635

add a zero-Neumann condition on the Density at walls to avoid negative values of temperature in extra cells.

66 lines of code changed in 1 file:

mcconnell 2016-01-07 16:20 Rev.: 54634

Removed some debugging code included in the last commit.

2 lines of code changed in 1 file:

mcconnell 2016-01-07 16:13 Rev.: 54633

A tag for the solution variable RHS is now passed to WasatchCore::TimeStepper::add_equation instead of an Expr::ExpressionID. The previous implementation was unsafe for expressions that compute multiple fields.

62 lines of code changed in 3 files:

tsaad 2016-01-07 14:47 Rev.: 54632

Revert "add 2 regression tests for compressible wall boundary conditions"

This reverts commit 14d7574aa011d4a41042d8999dd5de38a0026721.

0 lines of code changed in 1 file:

tsaad 2016-01-07 10:40 Rev.: 54631

get rid of a carriage return that prevents make gold_standards from running when MPIRUN is not set as an environmental variable.

1 lines of code changed in 1 file:

tsaad 2016-01-07 09:26 Rev.: 54630

add 2 regression tests for compressible wall boundary conditions

4 lines of code changed in 1 file:

tsaad 2016-01-06 16:04 Rev.: 54629

Wall boundary conditions for compressible flows. setup the framework for parsing and specifying boundary conditions.
Currently need to specify the BC for the conserved total internal energy. Next we will provide support for specifying temperature rather than energy at walls.

180 lines of code changed in 3 files:

harman 2016-01-05 15:47 Rev.: 54628

operator<<
- now outputting level index.

8 lines of code changed in 1 file:

harman 2016-01-05 13:52 Rev.: 54627

global:
added
Ghost::GhostType d_gac;
Ghost::GhostType d_gan;
Ghost::GhostType d_gn;

problemSetup()
- added bulletproofing to catch when the improper number of extra Cells is set when GIMP is used.

136 lines of code changed in 2 files:

bpeterson 2016-01-04 18:51 Rev.: 54626

Adding in another couple that got missed.

839 lines of code changed in 2 files:

bpeterson 2016-01-04 18:39 Rev.: 54625

Commiting two files that got missed

305 lines of code changed in 2 files:

bpeterson 2016-01-04 18:21 Rev.: 54624

All updates from the gpu_dev branch merged back into trunk.

9194 lines of code changed in 39 files:

guilkey 2016-01-01 14:52 Rev.: 54620

Add pArea label from ARL branch code.

10 lines of code changed in 2 files:

guilkey 2016-01-01 14:38 Rev.: 54619

Bringing some of the ARL changes into the trunk.

282 lines of code changed in 4 files:

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