November 2013 Commit Log

Number of Commits:
121
Number of Active Developers:
9
jthornoc 2013-11-27 15:11 Rev.: 51341

1) Transport Eqns are now assigned an algorithmic “stage”
2) Dependent sources of transport eqns are given the same stage.
3) Updated the add_species function to include an old or new state.
4) Set boundary conditions on all table lookup species such that the interpolated face value results in the table lookup condition
5) Adding an option extra table lookup
6) Some minor optimizations
7) Added the manifold run rate source term
8) Simplified some calls to computing diffusion terms.

762 lines of code changed in 37 files:

jsutherland 2013-11-26 17:46 Rev.: 51340

Update to conform to change in ExprLib API.

0 lines of code changed in 4 files:

harman 2013-11-26 14:19 Rev.: 51339

Reduce the BLOCKSIZE if the number of cells in a block is < blockSize^2

11 lines of code changed in 1 file:

guilkey 2013-11-25 15:05 Rev.: 51337

A few more additions to the Thomsen-Hartka water model.

0 lines of code changed in 2 files:

harman 2013-11-25 15:04 Rev.: 51336

-updated RT settings for albion.sci
-No longer sending remake email to dav. I'm sure he hasn't looked at it in years.

0 lines of code changed in 4 files:

harman 2013-11-25 13:53 Rev.: 51335

- added multi-patch tests.
- minor polishing of the ray tests

205 lines of code changed in 7 files:

guilkey 2013-11-25 13:06 Rev.: 51334

Cleaned up the .cc file, added better comments to the .h file.

22 lines of code changed in 2 files:

tsaad 2013-11-25 09:25 Rev.: 51332

remove an assertion from the scalability-test-transport-equation that caused failure on debug builds. This assertion is not needed.

0 lines of code changed in 2 files:

harman 2013-11-22 17:07 Rev.: 51331

The datum for thread indices is the patch->getExtraCellLow() not domainLo. This fixes a
very nasty multipatch bug.

Added temporary sanity check code to test the "iterators."

Removed domainLow and domainHi, since they're no longer needed.

removed code that isn't used containsCellDevice()


42 lines of code changed in 3 files:

jthornoc 2013-11-22 15:58 Rev.: 51330

This time, try allocating something real.

2 lines of code changed in 1 file:

jthornoc 2013-11-22 14:54 Rev.: 51329

Moving the filter volume calc into the Filter class.

36 lines of code changed in 6 files:

harman 2013-11-22 12:19 Rev.: 51328

update the configure line for albion.

0 lines of code changed in 2 files:

harman 2013-11-21 17:53 Rev.: 51327

Clean up for gpu vs cpu comparisons

179 lines of code changed in 8 files:

harman 2013-11-21 17:16 Rev.: 51326

Only create a new order_of_accuracy directory if it doesn't exist
Only create a new component directory if it doesn't exist.

Append a counter "Test' directories.

Stop the stopwatch after sus has executed.

28 lines of code changed in 3 files:

jsutherland 2013-11-21 15:18 Rev.: 51325

Warches fix.

1 lines of code changed in 1 file:

jsutherland 2013-11-21 15:11 Rev.: 51324

Make bigmac happy.

0 lines of code changed in 1 file:

jsutherland 2013-11-21 14:55 Rev.: 51323

First major cut at enthalpy transport with heat loss in Wasatch. We still need to couple in the radiation terms, but the hooks are in place.

347 lines of code changed in 14 files:

jsutherland 2013-11-21 14:55 Rev.: 51322

Fix a bad merge.

0 lines of code changed in 2 files:

jsutherland 2013-11-21 14:54 Rev.: 51321

Fix a few issues in the DensitySolver:

- Jacobian layout was wrong for the heat loss solver.

- Avoid copies in calls to get_bounds

- Output convergence failure summary in heat loss density solver.

- Don’t calculate the full jacobian at small and large mixture fraction
since heat loss degenerates at those points.

0 lines of code changed in 4 files:

jsutherland 2013-11-21 14:54 Rev.: 51320

A few misc changes:

- Create a default constructor for TurbulenceParameters to avoid dependence on initialization in Wasatch.cc.

- remove “forcedIDs” from GraphHelperTools since it wasn’t really being used.

- misc. improved error trapping.

43 lines of code changed in 14 files:

jsutherland 2013-11-21 14:54 Rev.: 51319

- Enthalpy need not be specified for heat loss density calculation.
- fix a state on the heat loss spec for predicted scalar evaluations.

7 lines of code changed in 3 files:

harman 2013-11-21 14:05 Rev.: 51318

added code to initialize divQ, VRFlux and radiationVolQ inside the kernel.

30 lines of code changed in 3 files:

harman 2013-11-21 11:16 Rev.: 51317


Backout recent changes to stencil7 variable BoundFlux. These will be reinstated once
we have a handle on the odd behavior.

37 lines of code changed in 2 files:

ahumphrey 2013-11-20 23:21 Rev.: 51316

Copy the correct number of bytes back from the device in postD2HCopies
Cleanup some comments in Task.h

4 lines of code changed in 2 files:

tsaad 2013-11-19 16:49 Rev.: 51315

remove a warning when parsing boundary conditions. this places the burden of bulletproofing on the component developers.

0 lines of code changed in 2 files:

harman 2013-11-19 11:34 Rev.: 51314

Scattering on the GPU now runs. Answers have not been verified.

48 lines of code changed in 3 files:

harman 2013-11-19 09:11 Rev.: 51313

changed from /bin/sh -> /bin/bash more fallout from Debian using dash.

0 lines of code changed in 2 files:

harman 2013-11-18 15:56 Rev.: 51312

added bulletproofing to check for the installed perl modules.

15 lines of code changed in 1 file:

harman 2013-11-18 15:36 Rev.: 51311

added bulletproofing check for dependency xmlstarlet.

2 lines of code changed in 1 file:

ahumphrey 2013-11-18 14:49 Rev.: 51310

Fix typo in puda-varsummary code.

0 lines of code changed in 2 files:

harman 2013-11-18 14:18 Rev.: 51308

Added an initialization function for stencil7 variables

Initializing boundaryFlux = 0 in GPULand. This is just a test for GPUStencil7 support.

50 lines of code changed in 6 files:

harman 2013-11-16 15:54 Rev.: 51307

Fixed all of the redirection of stdout & stderr.
On some systems the default /bin/sh is really a symbolic link to dash (albion).
Dash is strict about redirection.


93 lines of code changed in 26 files:

harman 2013-11-16 13:34 Rev.: 51306

Global name change
Int3 -> gpuIntVector
Double3 -> gpuVector

These variables will eventually behave similar to IntVectors & Vectors.

69 lines of code changed in 5 files:

harman 2013-11-16 12:12 Rev.: 51305

fixed compile error.

Removed the hack for cellType. Now using native supported GPUGridVarialbe<int>

9 lines of code changed in 4 files:

harman 2013-11-16 11:24 Rev.: 51304

Moved some of the Int3/double3 operators upstream to GPUVector.h.

Turned on the RNGs. Now initializing the RNGs cudaState upstream of the main kernel in a separate
setupRandNum_kernel.


70 lines of code changed in 3 files:

guilkey 2013-11-15 17:35 Rev.: 51303

Adding Andy Tonge's implementation of run time specification of domain freezing.
Access this feature by adding, e.g.,:

<cpdi_lcrit> 1.25 </cpdi_lcrit>

to the MPM (flags) section of an input file.

210 lines of code changed in 13 files:

harman 2013-11-15 14:06 Rev.: 51302

The RNGs are consistent with the those in RayGPUKernel.

0 lines of code changed in 4 files:

jthornoc 2013-11-15 13:04 Rev.: 51301

Did not mean to commit these changes. I blame James.

21 lines of code changed in 2 files:

jthornoc 2013-11-15 12:21 Rev.: 51300

Adding this back in .

28 lines of code changed in 3 files:

tsaad 2013-11-15 12:00 Rev.: 51299

cleanup the embedded geometry interface and rip out boolean flags from being passed into transport equations. Instead, have those embedded in the EmbeddedGeometryHelper.

155 lines of code changed in 23 files:

harman 2013-11-15 09:33 Rev.: 51298

Delete (") from dialog output. For some reason Beast.sci adds them

6 lines of code changed in 1 file:

tsaad 2013-11-15 08:19 Rev.: 51297

add some missing documentation to the new TransportEquation class

20 lines of code changed in 1 file:

jthornoc 2013-11-14 21:29 Rev.: 51296

Forgot to multiply by the volume.

0 lines of code changed in 2 files:

jthornoc 2013-11-14 20:39 Rev.: 51295

Removing reference to mm_explicit*

0 lines of code changed in 1 file:

jsutherland 2013-11-14 20:01 Rev.: 51294

Clean up a few compiler warnings in Wasatch that were showing up on gcc 4.8.

14 lines of code changed in 6 files:

jsutherland 2013-11-14 19:44 Rev.: 51293

See if this fixes Jeremy’s commit that broke the build...

4 lines of code changed in 1 file:

jsutherland 2013-11-14 19:41 Rev.: 51292

Fix a mistake in my last commit.

3 lines of code changed in 1 file:

jthornoc 2013-11-14 18:24 Rev.: 51290

Fixing a problem with the massflow inlet. The density check here was
erroneous.

24 lines of code changed in 1 file:

jthornoc 2013-11-14 18:24 Rev.: 51289

Fixing some warnings.

51 lines of code changed in 3 files:

jsutherland 2013-11-14 18:06 Rev.: 51288

Refactor transport equations in Wasatch. Transport equation classes now encapsulate the registration of relevant expressions.

868 lines of code changed in 20 files:

tsaad 2013-11-14 11:18 Rev.: 51287

fix a typo in the BCHelper documentation that James pointed out.

0 lines of code changed in 2 files:

awabboud 2013-11-14 11:11 Rev.: 51286

Change a variable name for clarification.

3 lines of code changed in 1 file:

tsaad 2013-11-14 10:58 Rev.: 51285

minor cleanup for documentation and indentation in the BCHelper

31 lines of code changed in 1 file:

awabboud 2013-11-14 10:54 Rev.: 51284

Make a fix for the reactino extent source term for embedded geometry.

0 lines of code changed in 2 files:

tsaad 2013-11-14 10:22 Rev.: 51283

Enforce density specification for ALL wasatch simulations

9 lines of code changed in 1 file:

ahumphrey 2013-11-14 09:49 Rev.: 51282

Begin GPU ParticleVariable support.

129 lines of code changed in 6 files:

tsaad 2013-11-14 09:03 Rev.: 51280

fix a bug in property evaluations. Since we don't enforce the specification of density via the input file, then assume that it is constant if no density block is specified. This will repair the failing RT. We could however enforce density specification...

3 lines of code changed in 1 file:

jsutherland 2013-11-13 16:51 Rev.: 51278

- Add ability to specify density via an analytical solution for two-stream mixing without using TabProps.
- add regression test coverage for this.

NOTE: this will break the regression tester since a new test is being added.

336 lines of code changed in 5 files:

ahumphrey 2013-11-13 16:03 Rev.: 51277

* Fix GPUReductionVariable support; adhere to default material index being -1 for ReductionVariables in general.
* Some code cleanup in Unified scheduler.

96 lines of code changed in 9 files:

jthornoc 2013-11-13 13:52 Rev.: 51274

1) Fix a warning.
2) Fix an error in the cold flow model with regards to the boundary
density value
3) Fix a sign error in the mass-balance calculator

10 lines of code changed in 3 files:

jthornoc 2013-11-13 12:15 Rev.: 51272

Cleaning up a warning.

6 lines of code changed in 2 files:

jthornoc 2013-11-13 12:15 Rev.: 51271

Don't cleanup after DQMOM equations.

0 lines of code changed in 3 files:

jthornoc 2013-11-13 12:15 Rev.: 51270

Removing the _has_been_computed bool.

50 lines of code changed in 14 files:

jthornoc 2013-11-13 12:15 Rev.: 51269

Removing an _new.

9 lines of code changed in 5 files:

ahumphrey 2013-11-12 22:17 Rev.: 51267

Finish support for GPUReductionVariable.

109 lines of code changed in 12 files:

harman 2013-11-12 18:36 Rev.: 51266

Remove quotations " from dialog output. This bug only shows up on beast.sci.


18 lines of code changed in 3 files:

jsutherland 2013-11-12 16:42 Rev.: 51265

Adopt a new approach for density calculation. The previous approach attempted to handle all cases in one density calculation expression. It has become clear that this is not feasible. This commit adopts a more fine-grained approach that will force us to write more expressions for different models, but should be a bit easier to maintain.

Also use unwinding for the variable density advection test cases since that is the only stable convection method for long times.

Note that this commit will break 4 wasatch tests, since numerical differences are introduced.

560 lines of code changed in 3 files:

tsaad 2013-11-12 13:58 Rev.: 51263

separate the implementation of ExprAlgebration from the header file.

137 lines of code changed in 5 files:

ahumphrey 2013-11-11 17:17 Rev.: 51262

Cleanup some debug output.

5 lines of code changed in 2 files:

ahumphrey 2013-11-11 16:57 Rev.: 51261

* Working support for GPU ReductionVariables.
* Also made OnDemandDataWarehouse aware of "SingleDevice" DebugStream when creating GPU Datawarehouses.

398 lines of code changed in 8 files:

harman 2013-11-11 16:06 Rev.: 51260

added more stopwatches.
Minor changes to random number generators.

20 lines of code changed in 1 file:

ahumphrey 2013-11-11 13:02 Rev.: 51259

The beginnings of an inheritance hierarchy for GPU Variables.

123 lines of code changed in 3 files:

ahumphrey 2013-11-11 12:14 Rev.: 51258

Add support for GPU Stencil7.
Add additional cuda_testdefs macro for range checking on the GPU when SCI_CUDA_ASSERTION_LEVEL >= 3

79 lines of code changed in 4 files:

ahumphrey 2013-11-11 11:52 Rev.: 51257

Put GPUVector code within SCIRun namespace and add header guard.
Add using namespace directive accordingly to RayGPU kernel and header.

13 lines of code changed in 3 files:

harman 2013-11-11 09:15 Rev.: 51256

Removed dead code that emailed John and Alan.

0 lines of code changed in 2 files:

tsaad 2013-11-10 16:42 Rev.: 51255

remove a cout statement

0 lines of code changed in 1 file:

ahumphrey 2013-11-10 14:14 Rev.: 51254

Some cosmetic and debug output changes.

19 lines of code changed in 4 files:

ahumphrey 2013-11-10 11:35 Rev.: 51253

Add Unified Scheduler support for automatic copying of generic GridVariables to the GPU. This support can be easily extended to Stencil7, ParticleVariable, etc with an expanded inheritance heirarchy of "GPUVariables":

GPUVariable
|------GPUGridVariableBase
| |------GPUGridVariable<T>
|------GPUReductionVariableBase
| |------GPUReductionVariable<T>
|------GPUStencil7Base
| |------GPUStencil7<T>
|------GPUParticleVariableBase
| |------GPUParicleVariable<T>

* Need to implement a cleaner way to "getRegion" for RMCRT. This works for now.
* Also some small changes to the UnifedSchedulerTest example.
* Fix typo in RayGPU.cc

402 lines of code changed in 6 files:

jsutherland 2013-11-08 21:01 Rev.: 51252

Maintenance on TabProps interface in preparations for more changes.

- clone interpolants into builders in a more robust way. This should prevent some memory corruption that could otherwise occur.

- make the user interface a bit more consistent.

75 lines of code changed in 11 files:

harman 2013-11-08 18:05 Rev.: 51251

Added a bare bones Makefile.

58 lines of code changed in 2 files:

harman 2013-11-08 16:52 Rev.: 51250

removed proprietary Makefile.

99 lines of code changed in 1 file:

harman 2013-11-08 16:44 Rev.: 51249

Added standAlone code to test the CUDA RNG and Mersene Twister RNG
Octave script to plot for eyeball verification.

807 lines of code changed in 4 files:

tsaad 2013-11-08 14:38 Rev.: 51248

fix watches. for real.

4 lines of code changed in 3 files:

tsaad 2013-11-08 14:12 Rev.: 51247

revert my previous commit

1 lines of code changed in 1 file:

tsaad 2013-11-08 13:53 Rev.: 51246

fix warches

2 lines of code changed in 1 file:

tsaad 2013-11-08 12:49 Rev.: 51245

create expressions to handle coordinates instead of traditional Uintah tasks.

471 lines of code changed in 15 files:

harman 2013-11-08 12:32 Rev.: 51244

converted a few variables that I missed in last commit.
int3 -> Int3

8 lines of code changed in 3 files:

jsutherland 2013-11-08 12:16 Rev.: 51243

Use new convenience function for generating TagLists in a few places.

11 lines of code changed in 4 files:

jsutherland 2013-11-07 16:18 Rev.: 51241

Back out Dav's changes on BoundaryCondition.cc, which was breaking regression tests on Warches.

0 lines of code changed in 1 file:

jsutherland 2013-11-07 16:17 Rev.: 51240

I am backing out Dav's recent changes entirely on Grid.cc. These broke Wasatch even after my first attempt at repairing them.

14 lines of code changed in 1 file:

harman 2013-11-07 13:53 Rev.: 51239

Global:
changed int3 -> Int3
changed double3 -> Double3
So you can use [] operators.

removed the temporary functions getElement() and updateElement() which
operated on an element of a int3 or double3.

Answers do not change for rmcrt_test_1L.ups

79 lines of code changed in 2 files:

harman 2013-11-07 10:23 Rev.: 51238

Ray.cc:
moved initialization of d_DcellType from initProperties() to setBoundaryConditions

RayGPU.cc
increase the size of the printf buffer by 10X. Needed for debugging.

RayGPUKernel.cu
fixed Z-slices looping limits
changes to printf statements
turned on the while( intensity > threshold) loop
helper functions updateElement()
added break statements

81 lines of code changed in 3 files:

jsutherland 2013-11-06 19:11 Rev.: 51237

Here is my shot at fixing what Dav was trying to do.
Really, we should be using something like numeric_limits here.

6 lines of code changed in 1 file:

jsutherland 2013-11-06 17:53 Rev.: 51236

Modifications to density calculation:

- decrease maximum iteration count to 5. It seems that for most situations, we converge in 1-3 iterations. Otherwise, it doesn't converge at all.

- obtain bounds on solution variable from the table to use for scaling the error residual as well as prevent the newton solve from going out of bounds.

- use analytic jacobians rather than numeric.

18 lines of code changed in 2 files:

dav 2013-11-06 16:40 Rev.: 51235

Add 'show_zlib' target for help in debugging when multiple zlibs are linked in. (Note, this shouldn't happen due to a fix in a previous commit, but just in case.)

0 lines of code changed in 2 files:

dav 2013-11-06 16:35 Rev.: 51234


M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/DataArchiver/DataArchiver.cc
M Core/Grid/Task.h

- Fix some indentation - add white space to make reading easier.

M CCA/Components/Arches/BoundaryCondition.cc

- Validate that all faces have been specified.

M Core/Grid/Grid.cc

- Fix for adding 'epsilon' to large numbers.

M Core/Grid/Variables/VarLabel.h
M Core/Grid/Variables/VarLabel.cc

- Remove 'using' syntax from .h file.
- Indent and use white space for easier reading.
- Use 'd_' for class variable: d_defaultCompressionMode
- Swat some evil 'endl's. :)

M Core/Math/Short27.h
M Core/Math/Matrix3.h

- Added some white space.


286 lines of code changed in 13 files:

harman 2013-11-06 13:22 Rev.: 51232


Added a double verion of cellType since GPUGridVariables only support doubles at this time.
This hack creates polution but should not influence the results.

The CPU & GPU code is heavily instrumented for direct comparisons.

133 lines of code changed in 5 files:

jsutherland 2013-11-06 12:28 Rev.: 51231

Remove obsolete flag to tabprops build.

0 lines of code changed in 1 file:

jsutherland 2013-11-06 12:28 Rev.: 51230

It appears that the is_sorted method on ComputeSet differs from the STL implementation. So I just cleaned up a few things to make it a bit more compact and const-correct.

0 lines of code changed in 2 files:

tsaad 2013-11-05 10:34 Rev.: 51226

fix single-patch bug with the varden mms test

0 lines of code changed in 2 files:

harman 2013-11-04 16:13 Rev.: 51224

get() & getModifiable()

If an error is thrown only print the error on thread 0 & block 0.



19 lines of code changed in 1 file:

harman 2013-11-04 15:32 Rev.: 51223

removed MPMARCHES from buildbot

0 lines of code changed in 2 files:

tsaad 2013-11-04 15:31 Rev.: 51222

trying to remove MPMArches RT from executing

0 lines of code changed in 1 file:

harman 2013-11-04 15:12 Rev.: 51221

BC_bulletproofing()
- Thrown an exception if the pressure BC is specified more than once for a face.

0 lines of code changed in 2 files:

tsaad 2013-11-04 13:38 Rev.: 51220

add regression test for clipping with intrusions

3 lines of code changed in 1 file:

tsaad 2013-11-04 13:35 Rev.: 51219

Fix clipping inside intrusions. (use modifier expressions instead of process_after_evaluate for clipping).

102 lines of code changed in 2 files:

jsutherland 2013-11-04 10:54 Rev.: 51218

Fix a failing test by going back to std::is_sorted()

0 lines of code changed in 2 files:

guilkey 2013-11-04 10:28 Rev.: 51217

Add option to tile frames top and bottom or side by side

2 lines of code changed in 1 file:

harman 2013-11-03 15:49 Rev.: 51216


The user must specify the material when using inletVelocity profile BCs.
Only apply the BC to that matl.

Set the default value for addVariance = false.

0 lines of code changed in 8 files:

tsaad 2013-11-02 17:48 Rev.: 51215

fix a very bad bug in applying density boundary conditions for variable density problems. Also repair a fundamental mistake in the varden mms case. this commit will break that test.

1 lines of code changed in 1 file:

tsaad 2013-11-02 17:00 Rev.: 51214

consolidate boundary conditions and separate implementation from class definition to speed compilation a bit.

1256 lines of code changed in 30 files:

jsutherland 2013-11-02 09:51 Rev.: 51213

Oops - forgot this file changes in an earlier commit:

It appears that there is an implementation of is_sorted within Uintah that can clash with the one in STL. While I was tempted to rip this out, I instead just deactivated it on APPLE platforms to get us further on compiling debug builds of Uintah on the new Mac OS (Mavericks) with the latest XCode.

Framework developers: we should look into this to see if the separate implementation is really necessary.

0 lines of code changed in 2 files:

jsutherland 2013-11-02 09:49 Rev.: 51212

It looks like ComputeSet implements an is_sorted member function. Switch to use that where applicable.

2 lines of code changed in 1 file:

jsutherland 2013-11-02 09:49 Rev.: 51211

It appears that there is an implementation of is_sorted within Uintah that can clash with the one in STL. While I was tempted to rip this out, I instead just deactivated it on APPLE platforms to get us further on compiling debug builds of Uintah on the new Mac OS (Mavericks) with the latest XCode.

Framework developers: we should look into this to see if the separate implementation is really necessary.

1 lines of code changed in 1 file:

tsaad 2013-11-01 21:47 Rev.: 51210

forgot to commit the vardenMMS expressions

522 lines of code changed in 2 files:

tsaad 2013-11-01 21:06 Rev.: 51209

separate the variable density MMS expressions into header and implementation files for clarity and to speed-up compilation time.

4 lines of code changed in 6 files:

jsutherland 2013-11-01 17:52 Rev.: 51208

Silence a few warnings.

0 lines of code changed in 4 files:

tsaad 2013-11-01 13:16 Rev.: 51206

Fix yet another bug related to the silly cast from Point to Vector. This is likely a costly fix since I opted for creating a vector instead of a cast by adding a sister function called toVector() opposed to asVector(), which does the cast. This will hopefully fix other issues that we were having when using unions/differences on boundaries...

0 lines of code changed in 4 files:

jas 2013-11-01 09:44 Rev.: 51204

Remove obsolete Mixing library

1 lines of code changed in 1 file:

jsutherland 2013-11-01 09:13 Rev.: 51203

Fix another namespace clash.

2 lines of code changed in 1 file:

jsutherland 2013-11-01 09:13 Rev.: 51202

Turn off a test in Warches.
It looks like this test uncovered a bug in the BC treatment - perhaps in the framework.
We are going to turn it off until that gets sorted out...

0 lines of code changed in 2 files:

October 2013 »

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