September 2012 Commit Log

Number of Commits:
113
Number of Active Developers:
16
ahumphrey 2012-09-30 13:49 Rev.: 49313

Add extra info to GPUStats DebugStream for multi-GPU nodes with non-uniform GPU models.
Also added some comments, formatting.

81 lines of code changed in 2 files:

ahumphrey 2012-09-30 10:24 Rev.: 49312

Fix output for thread DebugStream in Unified Scheduler.

5 lines of code changed in 1 file:

jsutherland 2012-09-29 16:08 Rev.: 49310

Major refactor to TaskInterface and TreeTaskExecute to fix some problems Tony was having with the modifier expressions. This is also a cleaner implementation than previously.

141 lines of code changed in 4 files:

jsutherland 2012-09-29 16:08 Rev.: 49309

modify a build order to speed up some builds a bit.

3 lines of code changed in 1 file:

awabboud 2012-09-28 13:55 Rev.: 49301

Two small fixes for digital filter generator.

16 lines of code changed in 1 file:

sadeghirad 2012-09-28 13:00 Rev.: 49300

committed updated source files and an input file regarding CBDI (conforming boundary domain interpolation)

356 lines of code changed in 11 files:

harman 2012-09-27 15:27 Rev.: 49297

coarsenNodalData_CFI() & coarsenNodalData_CFI2()
-using proper syntax when accessing an element of coarseCFI_Patches.

computeZoneOfInfluence()
- removed flawed bulletproofing

Global:
changes to instrumentation code that warns when the answers are significantly
different than know solution.

46 lines of code changed in 1 file:

harman 2012-09-27 14:57 Rev.: 49296

pudaVarsummary
- wrapper around puda -varsummary that parse the output

advect_3L_(*).tst: test files for various patch configurations
and gravitational fields.

advect_3L_(*).ups: increased particle res to avoid the dreaded numerial
singularity with linear MPM.

982 lines of code changed in 9 files:

harman 2012-09-27 13:36 Rev.: 49295

increment the nTest counter when you first find <Test>
This allows both

<replace_values>
</replace_values>
and
<replace_lines>
</replace_lines>

to be used for each test

6 lines of code changed in 1 file:

harman 2012-09-27 12:41 Rev.: 49294

remove leading space from post processing command
echo the current patch to 'scriptPath' file

3 lines of code changed in 3 files:

tsaad 2012-09-27 10:42 Rev.: 49293

nomenclature fixes.

31 lines of code changed in 1 file:

tsaad 2012-09-27 09:46 Rev.: 49292

rename the WALE model tensor.

28 lines of code changed in 4 files:

tsaad 2012-09-27 09:27 Rev.: 49291

don't do restart on the Arches isotropic turbulence case. for some reason, that input file is not generating checkpoints.

3 lines of code changed in 1 file:

tsaad 2012-09-27 09:25 Rev.: 49290

Add some documentation to the BCHelperTools functions.

95 lines of code changed in 2 files:

harman 2012-09-26 15:48 Rev.: 49287

coarseLevel_CFI_Iterator()
TREADING LIGHTLY HERE
- Both the l & h must be contained by the coarse patch
before it's considered valid iterator. This logic is also used in
coarseLevel_CFI_NodeIterator()


1 lines of code changed in 1 file:

harman 2012-09-26 14:49 Rev.: 49286

coarseLevel_CFI_NodeIterator()
- removed duplicate code
- check that the coarsePatch contains both l & h nodes.

fineLevel_CFI_iterator()
- removed redundant conditional statement.

3 lines of code changed in 1 file:

tsaad 2012-09-26 11:11 Rev.: 49285

Fix bug when running inviscid flow cases. modify energy_spectrum calculation to use Wasatch's t0 data instead of the cbc initial data.

1 lines of code changed in 1 file:

guilkey 2012-09-26 09:16 Rev.: 49284

Fix some uninitialized variable warnings pointed out to me by Tony.

11 lines of code changed in 1 file:

tsaad 2012-09-26 00:00 Rev.: 49282

Add Vreman turbulence model.

312 lines of code changed in 8 files:

jsutherland 2012-09-25 12:20 Rev.: 49278

Put a use-tip in the environmental flags file.

4 lines of code changed in 1 file:

tsaad 2012-09-25 12:19 Rev.: 49277

rip out an unused temporary field and optimize the calculation of the WALE model expression.

6 lines of code changed in 1 file:

tsaad 2012-09-25 11:55 Rev.: 49276

fix the RT isotropic turbulent test case for Arches.

51 lines of code changed in 1 file:

awabboud 2012-09-25 10:37 Rev.: 49274

make the moment reduction for stability continue to decrease the moment order until a positive result or the number of moments is 2.

99 lines of code changed in 1 file:

jsutherland 2012-09-24 19:18 Rev.: 49273

more doxygen fixes.

6 lines of code changed in 3 files:

jsutherland 2012-09-24 19:09 Rev.: 49272

Fix a typo

1 lines of code changed in 1 file:

jsutherland 2012-09-24 19:08 Rev.: 49271

Fix a bunch of documentation that was causing trouble for Doxygen.
There are still a ton of doxygen warnings to be cleaned up…

34 lines of code changed in 16 files:

ihunsaker 2012-09-24 16:25 Rev.: 49270

Added flag to turn off reflections for DOM
comparisons. Added flag to turn off solving
of divQ for computations where only q is
desired.

13 lines of code changed in 2 files:

harman 2012-09-24 15:44 Rev.: 49269

computerInternalForce_CFI()
rewrote it to work for multiple underlying coarse patches.

Lots of instrumentation and validation code.



291 lines of code changed in 2 files:

tsaad 2012-09-24 15:27 Rev.: 49267

Fix typo in constant Smagorinsky model. I was multiplying the turbulent viscosity by a factor of two which was producing inconsistent results with experimental data.

31 lines of code changed in 2 files:

jthornoc 2012-09-24 13:26 Rev.: 49265

Adding an interface to RadProps. This isn't currently functioning.

80 lines of code changed in 3 files:

harman 2012-09-24 13:18 Rev.: 49264

Now transferring any directory inside of an uda. This will pickup lineExtract and
particleExtract.

Made make the default command

0 lines of code changed in 2 files:

beckvermit 2012-09-24 08:59 Rev.: 49263

Changes made in Modified JWL eos to keep from having a negative pressure. Rho_ref was initialized twice so the computed value was not used. ConvectiveBurning.ups changed to use modified eos and propagation_burning.m made more accurate

4 lines of code changed in 3 files:

austin 2012-09-23 13:49 Rev.: 49262

Fixed minor issue with p.scalefactor. Was submitted with indexing from 1 not 0. This resulted in the 3,3 compoenent being garbage. This has been resolved and p.scalefactor is now computed correctly. -Dave A.

4 lines of code changed in 1 file:

austin 2012-09-22 13:10 Rev.: 49260

Changed p.scalefactor to matrix3 consistent with particle deformation and scaling. Allows use of deformed glyph patch.
-Dave A.

3 lines of code changed in 2 files:

tsaad 2012-09-21 21:16 Rev.: 49258

additional check in readfromfile expression to handle files that may have empty lines at the end.

2 lines of code changed in 1 file:

dav 2012-09-21 15:38 Rev.: 49257

Need to link in Core/IO for gz getDouble function. Also alphabetized list of libs and removed several duplicates.

9 lines of code changed in 1 file:

ahumphrey 2012-09-21 14:42 Rev.: 49256

Allow all schedulers to override the default via SCI_DEBUG env var or via XML in input files.
Also document these new debug vars in environmentalFLags.txt.
Fix two spots where only 1 thread was disallowed when using Unified Scheduler.

62 lines of code changed in 4 files:

tsaad 2012-09-21 13:58 Rev.: 49254

allow Wasatch's readFromFile expression to read gzip files. Change the existing test-case data file to gzip and delete the old data file. Add fclose to the Arches cbc matlab script.

24 lines of code changed in 1 file:

jthornoc 2012-09-21 09:39 Rev.: 49253

Fix missing initialization of new bool from Tony's previous commit.

1 lines of code changed in 1 file:

tsaad 2012-09-21 08:21 Rev.: 49252

add missing ; to Jeremy's commit. This should fix the buildbot problem.

1 lines of code changed in 1 file:

jthornoc 2012-09-20 23:39 Rev.: 49251

Fix a warning.

1 lines of code changed in 1 file:

harman 2012-09-20 16:18 Rev.: 49250

turned off advect_3L_3D until I can straighten it out.

1 lines of code changed in 1 file:

tsaad 2012-09-20 15:45 Rev.: 49249

Add an initialization funtion to Arches that allows it to read SFCX,Y,Z data to initialize the velocity field. This is illustrated in the updated isotropic turbulence case. scripts that generate a tke spectrum from (u,v,w) data using lineextract will follow.

120 lines of code changed in 2 files:

jsutherland 2012-09-20 13:13 Rev.: 49248

Eliminate redundant output in parallel.

1 lines of code changed in 1 file:

harman 2012-09-20 09:42 Rev.: 49247

coarseLevel_CFI_NodeIterator(),
fineLevel_CFI_Iterator()
-variable name change f_lo/hi_patch -> c_lo/hi_patch

fineLevel_CFI_NodeIterator()
- gutted it and started over. Now using CC version of
fineLevel_CFI_iterator to determine if it's the right
coarse & fine patch pair before returing the NodeFaceIterator.


37 lines of code changed in 1 file:

awabboud 2012-09-20 09:10 Rev.: 49246

Added in a numerical fix to help stability of QMOM problems.

229 lines of code changed in 2 files:

jthornoc 2012-09-19 21:40 Rev.: 49245

Adding transform for the 4 stream (3 streams + inert) mixing.

70 lines of code changed in 1 file:

jthornoc 2012-09-19 20:39 Rev.: 49244

1) Added a new filtering operation that doesn't use PETSC. Still need to verify.
2) Fixing the stripping factor in the Westbrook/Dryer model to use the CstarStrip mixture fraction.
3) Fix the rate term to account for diluent.

100 lines of code changed in 10 files:

harman 2012-09-19 16:29 Rev.: 49243

someone take the keyboard away from me.....

1 lines of code changed in 1 file:

harman 2012-09-19 16:28 Rev.: 49242

Fixed some poor coding.

6 lines of code changed in 1 file:

cam 2012-09-18 09:32 Rev.: 49241

add proper header guard, include climits

4 lines of code changed in 1 file:

cam 2012-09-17 21:38 Rev.: 49240

1) fix spreadsheet not working for CC_Mesh (was caused by proc_id), 2) cleanup getBounds, 3) set mesh->containsExteriorGhostBoundaryCells to false since it's no longer used

67 lines of code changed in 2 files:

harman 2012-09-17 17:10 Rev.: 49239

Corrected the task names for ExecTimes

7 lines of code changed in 1 file:

harman 2012-09-17 16:01 Rev.: 49238

advect_3L_3D.ups: added <minimum_mass_for_acc> 1.0e-15 </minimum_mass_for_acc>

AMRMPM:
-computeInternalForce is now done in 3 tasks. The first task is
using standard MPM over each level. Next, the internal force is computed
along the CFI with computeInternalForce_CFI on only the fine levels. Finally,
the internal force on the fine level is copied to the coarse level nodes that
are overlapping. This works for pure translation problems.

- added lots of instrumentation

409 lines of code changed in 2 files:

harman 2012-09-17 14:25 Rev.: 49237

For AMRMPM
- renamed findCellAndWeights -> findCellAndWeights_CFI
- added findCellAndWeightsAndShapeDerivatives_CFI

202 lines of code changed in 4 files:

ahumphrey 2012-09-17 08:07 Rev.: 49235

Change the default scheduler to be the Unified Scheduler.
All previous schedulers may still be invoked explicitly via command line.

68 lines of code changed in 6 files:

jthornoc 2012-09-16 12:40 Rev.: 49234

Turns out throwing an error here isn't the right idea. Now just
printing a notice to the user instead.

1 lines of code changed in 1 file:

jthornoc 2012-09-16 09:42 Rev.: 49233

Missing initialization.

3 lines of code changed in 1 file:

jthornoc 2012-09-16 09:14 Rev.: 49232

Fixing a few problems with Tony's earlier commit re: warnings in Arches.
Some function calls were commented out leading to runtime errors.

15 lines of code changed in 7 files:

jthornoc 2012-09-14 22:33 Rev.: 49231

Adding flammability limits to the westbrook dryer model.

141 lines of code changed in 2 files:

jthornoc 2012-09-14 10:52 Rev.: 49229

1) (from Dav) Updated a few sub.mk's to include Z_LIBRARY.
2) Added some hooks for the new and improved filtering operation.

73 lines of code changed in 5 files:

tsaad 2012-09-14 10:47 Rev.: 49228

add hooks to Arches to calculate a turbulent viscosity from Wasatch. I still have to hook the turbulent viscosity to the ARCHES solver.

31 lines of code changed in 3 files:

tsaad 2012-09-14 09:37 Rev.: 49227

remove typename and use scinew. this should fix bigmac buildbot error.

5 lines of code changed in 1 file:

tsaad 2012-09-14 09:33 Rev.: 49226

rip out a few cout statements.

2 lines of code changed in 1 file:

tsaad 2012-09-14 09:25 Rev.: 49225

Improve the turbulence interface for Wasatch and add a few helpful funcations to streamline the addition of the WALE model to Arches.

122 lines of code changed in 10 files:

awabboud 2012-09-14 09:08 Rev.: 49224

make casting explicit to silence warning.

0 lines of code changed in 2 files:

harman 2012-09-14 09:02 Rev.: 49223

Now parsing sus command line options and using them.
Added bulletproofing for running gpu runs.

34 lines of code changed in 1 file:

tsaad 2012-09-14 08:37 Rev.: 49222

add debug flag to Wasatch BCs to reduce output.

4 lines of code changed in 1 file:

harman 2012-09-13 15:36 Rev.: 49221

Turned impHotBlob test back on.

1 lines of code changed in 1 file:

harman 2012-09-13 15:32 Rev.: 49220

-Add a little more info to user when requesting a timestep restart.

- removed redundant version of readParameters()
added missing getWithDefault(maxiterations......) line

5 lines of code changed in 2 files:

amir 2012-09-13 15:04 Rev.: 49218

Add regression test for scalar closure model

7 lines of code changed in 1 file:

harman 2012-09-13 13:35 Rev.: 49217

Throw an exception if on a timestep that is being restarted delT drops below
delt_min or is 0.

19 lines of code changed in 1 file:

austin 2012-09-13 09:22 Rev.: 49216

Added <exactDeformation> flag for use with prescribed deformation. Requires that max timestep size be set to the largest (and this should be the first) steps size within time_defgrad_rotation or its equivalent. Also set min timestep size to the min within the same prescribed file. This will force the deformation history to be reproduced exactly as outlined in the prescribed fdeformation file. Used with single element histories. Currently the addition of superimposed rotations is not tested with this functionality but is implemented in a consistent manner with the F update.
-Dave Austin

35 lines of code changed in 3 files:

tsaad 2012-09-13 09:21 Rev.: 49215

silence a few warnings.

7 lines of code changed in 2 files:

austin 2012-09-12 16:25 Rev.: 49214

Checking that this works. -Dave A.

0 lines of code changed in 2 files:

jas 2012-09-12 14:22 Rev.: 49209

Squashed commit of the following:

commit 1b507b7b8b43195401670b257ea11fc41193a7f2
Author: John Schmidt <john.schmidt@utah.edu>
Date: Wed Sep 12 15:19:31 2012 -0600

Use the Struct versions for GMRES and PCG which eliminates the
HYPRE_Solver casting that was occuring.

Use a pointer to the solver and precond_solver in the hypre_solver_struct.

157 lines of code changed in 2 files:

tsaad 2012-09-12 10:31 Rev.: 49208

cleanup a bunch of warnings in Arches - Jeremy, can you do a sanity check? I commented the offending statements.

21 lines of code changed in 7 files:

harman 2012-09-12 09:06 Rev.: 49207

problemSetup()
- consistency with RMCRT_test::problemSetup()

29 lines of code changed in 2 files:

harman 2012-09-11 16:42 Rev.: 49206

Give the user plenty of rope by turnoff boundary conditions bulletproofing of the
input file.

14 lines of code changed in 1 file:

ahumphrey 2012-09-11 15:48 Rev.: 49205

Fix a deadlock.
Turns out that: task->getTask()->usesMPI() doesn't seem to ever return true, although it's defined and used throughout the framework.
Need to find out if d_usesMPI is ever set for a task.

2 lines of code changed in 1 file:

ahumphrey 2012-09-11 15:05 Rev.: 49204

Add SingleProcessor Scheduler functionality to Unified Scheduler.

56 lines of code changed in 2 files:

tsaad 2012-09-11 14:37 Rev.: 49203

Upgrade Wasatch boundary conditions to use expressions and hence become part of the graph. This will give us the flexibility of defining random dependencies at boundaries. There is work to be done on properly accessing the coordinate fields and that will be the next stage of development. Also update Arches.cc for the Wasatch time advance to account for this change in BC treatment. Finally, cleanup a few warnings in Arches.

411 lines of code changed in 8 files:

ahumphrey 2012-09-11 12:49 Rev.: 49200

Consolidate threaded task execution logic in Unified Scheduler.
* Added some nice comments to explain what's going on here
Update input file for UnifiedSchedulerTest component.

207 lines of code changed in 2 files:

harman 2012-09-11 07:55 Rev.: 49198

changed directory name

0 lines of code changed in 2 files:

ahumphrey 2012-09-10 16:53 Rev.: 49197

Some last refinements to the original GPU scheduler. This is necessary to compare results when using the Unified scheduler

13 lines of code changed in 1 file:

tsaad 2012-09-10 15:55 Rev.: 49196

add copyright info. move things around after the solverparams fix.

753 lines of code changed in 34 files:

jas 2012-09-10 14:45 Rev.: 49195

Fix memory leaks.

21 lines of code changed in 6 files:

ahumphrey 2012-09-10 12:08 Rev.: 49194

Work on memory leak in GPU Scheduler. Also do some formatting / update debug output.

259 lines of code changed in 1 file:

ahumphrey 2012-09-10 11:36 Rev.: 49193

Add test component for Unified Scheduler.

597 lines of code changed in 5 files:

ahumphrey 2012-09-10 10:14 Rev.: 49192

Unified Scheduler:
* Do some memory management on CUDA Stream and Event queues.
* Enhance GPUStats debug stream.

23 lines of code changed in 4 files:

harman 2012-09-08 15:37 Rev.: 49191

No longer scheduling pseudoCFD task. It's just causing confusion at this point.

2 lines of code changed in 1 file:

ahumphrey 2012-09-07 17:33 Rev.: 49190

Make CUDA stream and event containers thread safe.
Cleanup some dead code.
Further refinement on GPUStats debug stream.

10 lines of code changed in 3 files:

ahumphrey 2012-09-07 17:12 Rev.: 49189

Fix non-CUDA configuration compiler error.

6 lines of code changed in 2 files:

ahumphrey 2012-09-07 16:49 Rev.: 49188

Clear GPU-DB maps, etc after each timestep, this fixes D2H copy bug.
Also add more detailed GPU-related debug info.

This is largely working now.

20 lines of code changed in 1 file:

ahumphrey 2012-09-07 16:09 Rev.: 49187

Unified Scheduler: protect some critical sections, lock some GPU-related data structures.

62 lines of code changed in 2 files:

ahumphrey 2012-09-07 12:03 Rev.: 49186

Fix GPU logic in Unified Scheduler. Also some other small formatting/style mods.

28 lines of code changed in 1 file:

ahumphrey 2012-09-06 20:14 Rev.: 49183

Fix Unified scheduler compiler error.

8 lines of code changed in 1 file:

ahumphrey 2012-09-06 17:53 Rev.: 49182

Unified Scheduler: Add logic to run with or without GPU support via command line switch.

23 lines of code changed in 1 file:

harman 2012-09-06 17:32 Rev.: 49181


problemSetup()
- changed getWithDefault(shouldSetBCs) -> get(shouldSetBCs)

2 lines of code changed in 1 file:

harman 2012-09-06 13:54 Rev.: 49178

Updates from Scott Bardenhagen.

*This should not change the answers.

39 lines of code changed in 2 files:

harman 2012-09-06 13:11 Rev.: 49177

Changed how clamps are applied. If a cell contains a particle then apply clamp,
otherwise initialize it to either 0 or the clamp min value.

35 lines of code changed in 1 file:

ahumphrey 2012-09-06 11:24 Rev.: 49176

Add GPU related logic and locks to Unified scheduler.

234 lines of code changed in 5 files:

wyxpuma 2012-09-05 22:47 Rev.: 49175

fix the mass balance problem due to new_den calculation error

1 lines of code changed in 1 file:

harman 2012-09-05 15:27 Rev.: 49174

Fixed how matls indicies were being read in.
-m all, -m 0, -m 1, -m 0 1

now work

7 lines of code changed in 1 file:

harman 2012-09-05 14:27 Rev.: 49173

Added optional user flag

<shouldSetBCs> true </shouldSetBCs>

to control setting the boundary conditions.

7 lines of code changed in 2 files:

tsaad 2012-09-05 13:24 Rev.: 49172

Task checksum reports the wrong number of processors since process rank is counted from 0 not 1. fix that.

1 lines of code changed in 1 file:

jas 2012-09-05 09:54 Rev.: 49171

Delete hypre_solver_label and fix memory leak.

1 lines of code changed in 1 file:

awabboud 2012-09-05 09:36 Rev.: 49170

Fix to aggregation coefficient for embedded geometry since rho = 0 in intrusions.

2 lines of code changed in 1 file:

dav 2012-09-04 15:17 Rev.: 49168


Update compare_uda (and the Regression Tester's use of it) to be able
to print out the first error for each variable (instead of just dieing
after the very first difference is found).

Use the new '-concise' flag in addition to the already existing
'-as_warnings' flag in the RT.

M StandAlone/compare_uda.cc

* Cleaned up some formatting. (Truly, white space is your friend.
and single letter variable names are NOT (especially if they
are used for more then a few lines in a for loop).)
* Added the -concise flag. (Note, even though the diff will have a bunch
of lines, the only 'real' additions are about 10 lines dealing with the
'-concise' flag.)

M R_Tester/helpers/compare_sus_runs_by_udas

* Add the -as_warnings and -concise flags to the compare_uda runs.


118 lines of code changed in 3 files:

jas 2012-09-04 09:17 Rev.: 49167

Turn off impHotBlob temporarily.

1 lines of code changed in 1 file:

ahumphrey 2012-09-04 08:42 Rev.: 49166

Some formatting.

944 lines of code changed in 3 files:

jthornoc 2012-09-02 22:25 Rev.: 49164

Intrusion boundary conditions for DQMOM.

74 lines of code changed in 4 files:

tsaad 2012-09-01 12:55 Rev.: 49162

remove a cout statement.

0 lines of code changed in 1 file:

August 2012 »

Generated by StatSVN 0.7.0