May 2015 Commit Log

Number of Commits:
112
Number of Active Developers:
10
harman 2015-05-29 16:52 Rev.: 53566

Added tst file to run RMCRT:DataOnion (2L) with various patch configurations
on coarse and fine levels. This is used to perform cpu vs gpu comparisons
over a wide range of patch layouts.

327 lines of code changed in 2 files:

harman 2015-05-29 16:22 Rev.: 53565

Removed (using namespace *) from include files.


26 lines of code changed in 57 files:

harman 2015-05-29 13:25 Rev.: 53564

removed "using namespace *"

0 lines of code changed in 2 files:

harman 2015-05-29 13:20 Rev.: 53563

removed "using namespace *" from include files.


13 lines of code changed in 19 files:

tsaad 2015-05-29 10:01 Rev.: 53562

Simplify how the density is computed from
rho*f. This will cause some roundoff errors
due to the change in algebraic operations.

3 lines of code changed in 1 file:

tsaad 2015-05-28 11:16 Rev.: 53559

Propagate the solvability constraint through Wasatch.
This is controlled by the user: Simply add <EnforceSolvability/> to the <Pressure> xml block.
Start deprecating the reference pressure setup and replace with
the new approach.
Loosen up the tolerance on a few tests to help Hypre converge.
This commit will fail a few RT tests with machine diffs.

56 lines of code changed in 4 files:

jas 2015-05-28 10:53 Rev.: 53558

Reapply revision 53556.

1 lines of code changed in 1 file:

jas 2015-05-28 09:26 Rev.: 53557

Revert c++-11 namespace changes.

1643 lines of code changed in 389 files:

guilkey 2015-05-27 23:41 Rev.: 53556

Taking out the Collide test for now. It is failing oddly, like maybe I'm
creating duplicate particleIDs?

1 lines of code changed in 1 file:

jas 2015-05-27 15:46 Rev.: 53555

Remove backup file.

0 lines of code changed in 1 file:

jas 2015-05-27 15:34 Rev.: 53554

Explicit namespace usage as part of the transition to c++-11.

2566 lines of code changed in 250 files:

jas 2015-05-27 15:33 Rev.: 53553

Explicit namespace specification as we transition to c++-11.

515 lines of code changed in 32 files:

tsaad 2015-05-27 12:29 Rev.: 53552

remove a couple of cout statements

0 lines of code changed in 1 file:

tsaad 2015-05-27 12:02 Rev.: 53551

allow the solvability constraint to work with multistage integration.
The issue stems from doing multiple reductions on the same
variable - something that Uintah doesn't allow.
Therefore, one needs to use a different varlabel everytime
a reduction is required, on a given variable, within the same timestep.

55 lines of code changed in 1 file:

tsaad 2015-05-27 09:01 Rev.: 53550

Forgot to delete varlabel.
Remove check for periodicity from the task that enforces solvability.
The user/developer must determine when to call that task.

4 lines of code changed in 1 file:

tsaad 2015-05-26 16:20 Rev.: 53549

Add a top-level task to the Solver base class that allows users/developers to set a reference value
for the Poisson equation.
The function is super simple to use given a solver instance:

solver.scheduleSetReferenceValue( level, sched, matls, xLabel, refCell, refValue)

xLabel is the varlabel of the solution vector (e.g. pressure)
refCell is an IntVector designating the reference cell and defaults to [0,0,0]
refValue is a double designating the reference value and defaults to 0.0

This task MUST be called AFTER scheduleSolve

102 lines of code changed in 1 file:

tsaad 2015-05-26 14:37 Rev.: 53548

remove and un-necessary const_cast from the HypreSolver

2 lines of code changed in 1 file:

guilkey 2015-05-26 12:51 Rev.: 53546

Remove the finalParticleUpdate call for the scalar diffusion model, as it is all
currently empty.

43 lines of code changed in 2 files:

guilkey 2015-05-26 12:44 Rev.: 53545

Use code reuse to reduce duplicate code where possible.

336 lines of code changed in 12 files:

guilkey 2015-05-26 11:42 Rev.: 53543

Replace use of zeroth_matl with Todd's d_one_matl, which is effectively the
same thing. This hopefully fixes the memory leak identified by the RT.

3 lines of code changed in 1 file:

tsaad 2015-05-26 11:40 Rev.: 53542

Add a top-level task to the linear solver that enforces the solvability condition for the Poisson equation in periodic problems.
This task can be called by ALL components given an instance of a solver.
It will only execute on periodic problems (all 3 dimensions).
Simply use: solver.scheduleEnforceSolvability<rhsType >(level, sched, matls, rhs_label)
where rhsType is the Uintah data type of the Poisson rhs: e.g. CCVariable<double> etc...
This task MUST be called before the scheduleSolve task.

116 lines of code changed in 1 file:

jas 2015-05-22 10:26 Rev.: 53541

Remove the commented out <omp.h> since we are not using any omp calls.

0 lines of code changed in 1 file:

dav 2015-05-21 17:52 Rev.: 53540


Added --with-pokitt=DIR for James Sutherland.

126 lines of code changed in 3 files:

harman 2015-05-21 17:19 Rev.: 53539

Added #ifs around code that doesn't compile on titan.
That machine is using cuda 5.5.


7 lines of code changed in 1 file:

dav 2015-05-21 16:39 Rev.: 53538

Talked to John and omp.h (OpenMP) is not needed in this file. Removing it to fix Mac build.

1 lines of code changed in 1 file:

guilkey 2015-05-21 15:57 Rev.: 53537

Added the tasks needed for scalar diffusion on a single level. Still need to
add the corrections for the CFI.

451 lines of code changed in 5 files:

guilkey 2015-05-21 15:55 Rev.: 53536

Add a short AMR test to the nightly RT.

2 lines of code changed in 1 file:

guilkey 2015-05-21 15:48 Rev.: 53535

Add concentration as an option for geometry piece attributes.

1 lines of code changed in 1 file:

guilkey 2015-05-21 14:07 Rev.: 53534

Fix the diffusion models, at least the ones needed for nano_pillar2_2d.ups, so
that we can run that problem on multiple patches and on multiple processors.
Now doing this in the trunk version.

45 lines of code changed in 6 files:

jas 2015-05-21 13:47 Rev.: 53533

For once per proc task, turn off all but one thread.

59 lines of code changed in 1 file:

guilkey 2015-05-21 10:42 Rev.: 53530

Delete the VarLabels associated with the reduction on the refinement flags.

6 lines of code changed in 1 file:

tsaad 2015-05-21 09:51 Rev.: 53529

clip the density when using the (closed form) mixing model

16 lines of code changed in 2 files:

harman 2015-05-20 16:07 Rev.: 53528

Ray.cc: updateSumI_ML()
- consistent debugging output with GPU code

RayGPU.cuh + RayGPUKernel.cu
- Pass regionLo and regionHi into the kernel instead of using levelP.
These quantities vary on a per patch basis. levelP is copied to global memory
and regionLo/Hi should be in shared memory.


55 lines of code changed in 3 files:

u0407585 2015-05-20 14:04 Rev.: 53524

Fixed boundary condition bug, when using inert stream.

1 lines of code changed in 1 file:

guilkey 2015-05-20 09:45 Rev.: 53522

Remove duplicate addition of scalar diffusion model in the outputProblemSpec.
The removed one was not inside of a conditional.

0 lines of code changed in 1 file:

guilkey 2015-05-19 16:09 Rev.: 53521

Require MPMRefineCell for d_one_matl (matl 0) only.

1 lines of code changed in 1 file:

tsaad 2015-05-19 15:35 Rev.: 53520

add a field that tags the points where the density-mixture fraction nonlinear solver failed to converge.
This will help us visualize where these unconverged points occur.

34 lines of code changed in 6 files:

guilkey 2015-05-19 15:18 Rev.: 53519

Minor tidying.

9 lines of code changed in 3 files:

guilkey 2015-05-19 15:18 Rev.: 53518

Perform a reduction on the refine flags so that a rectangular region for refinement can
be created, thereby preventing inside corners, which the infrastructure will not tolerate
for NC variables.

242 lines of code changed in 5 files:

jas 2015-05-19 13:46 Rev.: 53517

C++11 cleanups.

59 lines of code changed in 11 files:

guilkey 2015-05-19 12:09 Rev.: 53516

Fix, I hope, the deletion of the scalar diffusion model.

2 lines of code changed in 1 file:

ahumphrey 2015-05-19 10:46 Rev.: 53515

Do not throw exception when fine-level halo used in GPU::RMCRT_DO. This is all working properly now.

0 lines of code changed in 1 file:

harman 2015-05-19 10:10 Rev.: 53514

Deleted GPU.py. Those a managed by each component.

runSusTests.py: reset SCI_DEBUG on each test.

startTester: removed GPU.py tests from albion and cyrus.

8 lines of code changed in 3 files:

ahumphrey 2015-05-18 17:32 Rev.: 53513

Get rid of operator new calls on device. Use compile time constant to size arrays for now.

4 lines of code changed in 1 file:

guilkey 2015-05-18 17:22 Rev.: 53512

Put deletion of scalar diffusion model inside of a conditional.

3 lines of code changed in 1 file:

harman 2015-05-18 16:05 Rev.: 53511

If a test is using a GPU set the environmental flag
SCI_DEBUG SingleDevice:+
and for it to run on 1 gpu.

3 lines of code changed in 1 file:

harman 2015-05-18 15:18 Rev.: 53510

Throw an exception if the user is trying to use multiple GPUs. The simulation chugs along
as if it's working when really the some of the GPU kernels are being skipped. This was
observed on a machine with two different GPUs and may not hold when the GPUs are the same make/model.

10 lines of code changed in 1 file:

guilkey 2015-05-18 13:59 Rev.: 53509

Added flags for turning on/off scalar diffusion.

19 lines of code changed in 2 files:

harman 2015-05-18 13:25 Rev.: 53507

- fixed compiler warnings.
- added patch.print() call
- removed a weed

2 lines of code changed in 1 file:

harman 2015-05-18 13:04 Rev.: 53506

added patchParams:print(). Useful for debugging

7 lines of code changed in 1 file:

guilkey 2015-05-18 12:35 Rev.: 53503

Adding models for the ARL project.

4432 lines of code changed in 27 files:

tsaad 2015-05-18 11:50 Rev.: 53502

spring cleaning: rip out ALL STATE_N specification in all Wasatch input files.
There should NO need to use STATE_N. One should use STATE_DYNAMIC
instead.

3 lines of code changed in 1 file:

harman 2015-05-18 09:37 Rev.: 53501

removed test. Input file no longer exists

5 lines of code changed in 1 file:

jsutherland 2015-05-15 13:22 Rev.: 53500

minor cleanup; use min/max rather than cond.

29 lines of code changed in 1 file:

harman 2015-05-15 11:15 Rev.: 53499

Removed RMCRT_test_1L from the GPU python script. That ups is tested in Examples.py.
We should consider removing the GPU.py script. I'm not sure the tests are still relevant.


2 lines of code changed in 1 file:

harman 2015-05-15 10:24 Rev.: 53498

scheduleInitialize()
added requires for radiationVolq.

8 lines of code changed in 1 file:

tsaad 2015-05-15 09:32 Rev.: 53497

Fix minor bug in momentum rhs dependencies - require density only when body forces are needed

5 lines of code changed in 1 file:

harman 2015-05-14 17:23 Rev.: 53496

added gpu workaround script which modifies an input file so it will hobble through the gpu RT tests
calc_frequency -> 1
halo -> [0,0,0]

Examples.py
- Call the gpuWorkAround script on gpu tests.

6 lines of code changed in 1 file:

harman 2015-05-14 16:27 Rev.: 53495

RMCRTCommon:
updateSumI() mimic debugging output for gpu code for direct comparison with cpu results.
Variable name change face->dir, consistent with cpu code.

Ray.cc:
update TO DO list
sched_rayTrace() and sched_rayTrace_dataOnion()
- throw an exception if calc_frequency > 1. This is another big infrastructure issue.

RayGPUKernel.cu
update TO DO list

RayGPU.cc
rayTraceGPU()
- In doCarryForward block added transferFrom() calls. These will be used once
the GPUDW transferFrom issue is fixed.

164 lines of code changed in 4 files:

harman 2015-05-14 13:54 Rev.: 53494

Now running GPU nightly regression testing on cyrus.mech

27 lines of code changed in 2 files:

jas 2015-05-14 13:42 Rev.: 53493

Add check for C++-11 compiler.

105 lines of code changed in 1 file:

jas 2015-05-14 13:30 Rev.: 53492

Fixes for c++-11 with g++ 5.1.

0 lines of code changed in 2 files:

derekhar 2015-05-14 13:24 Rev.: 53491

Fixed thread saftey issues in Yamamoto coal devolitalization model.

5 lines of code changed in 2 files:

jas 2015-05-14 13:20 Rev.: 53490

Fixes for c++-11 with g++ 5.1.

0 lines of code changed in 2 files:

harman 2015-05-14 10:52 Rev.: 53489

Initialize d_halo to -9,-9,-9

problemSetup:GPU bulletproofing
- only check for halo violation if algorithm == dataOnion

Minor debugging tweaks.

19 lines of code changed in 2 files:

jas 2015-05-14 10:44 Rev.: 53488

Change for c++-11.

0 lines of code changed in 2 files:

harman 2015-05-13 17:24 Rev.: 53487

Moved the code that increases the cuda prinf buffer upstream to problemSetup. You only
want to do this once.

19 lines of code changed in 2 files:

harman 2015-05-13 17:17 Rev.: 53486

Added checkBounds() instead of using cuda_testdefs: CHECK_INSIDE. The output now
includes the variable pointer. If you add

new_dw->print();

inside of the kernel you can cross reference the pointer with the variable.


0 lines of code changed in 2 files:

derekhar 2015-05-13 15:04 Rev.: 53485

Fixed thread saftey issues in RichardsFletcher Devolitalization coal model.

107 lines of code changed in 3 files:

jas 2015-05-13 15:04 Rev.: 53484

Changes required to use c++-11.

217 lines of code changed in 46 files:

derekhar 2015-05-13 13:36 Rev.: 53483

Added a missing initialize for radVolQ. Now rmcrt can run with caol problems.

6 lines of code changed in 2 files:

jsutherland 2015-05-13 13:25 Rev.: 53482

Misc. cleanup, including removal of a few zeroing operations that were unnecessary.

77 lines of code changed in 5 files:

harman 2015-05-13 09:24 Rev.: 53481

delete abskgLabel if using FLOATS. Thanks Derek.

3 lines of code changed in 1 file:

harman 2015-05-12 16:57 Rev.: 53480

RayGPU.cuh
- added operator > and operator < for GPUIntVector.

GPUVariableSanityCK()
- only compile if assertion level > 0
- if variable bounds are exceeded then print a warning and escape.


rayTraceDataOnionKernel()
- turn off raytracing. Currently crashing on 3rd timestep for some memory related issue.
- turn off the delete(GPUVariable) calls. . cuda-memcheck is throwing an error on them.
- added GPUVariableSanityCK() calls.


96 lines of code changed in 2 files:

harman 2015-05-12 15:56 Rev.: 53479

removed print statement that clutters the mind.

0 lines of code changed in 1 file:

harman 2015-05-12 15:54 Rev.: 53478

added const getLowIndex() and const getHighIndex()

18 lines of code changed in 1 file:

harman 2015-05-12 15:47 Rev.: 53477

add $MPIRUN to the path

2 lines of code changed in 1 file:

derekhar 2015-05-12 15:46 Rev.: 53476

Removed global variable in property calculator that is no longer used.

0 lines of code changed in 1 file:

derekhar 2015-05-11 16:46 Rev.: 53475

Fixed thread safety issues in coal models, and in hottel-sarofim radiation properties.
This commits also removes ambiguous calls to isnan and isinf which cause compile errors in c++11.

53 lines of code changed in 14 files:

tsaad 2015-05-11 16:33 Rev.: 53474

minor fix to get Wasatch to build with c++11

1 lines of code changed in 1 file:

jthornoc 2015-05-11 15:22 Rev.: 53473

Fix thread safety issues.

22 lines of code changed in 7 files:

tsaad 2015-05-11 15:15 Rev.: 53472

Major Commit. Simplify the user specification of nametags. From now on, the state of a variable is optional. When a state is NOT specified, we default to STATE_NONE.
Before this commit, STATE_NONE occurred in 88% of all expressions (~ 1700 occurrences) in all of the Wasatch input files.

6 lines of code changed in 1 file:

harman 2015-05-11 15:07 Rev.: 53471

gpu_stats formatting and now outputting the nCells. It's much easier to follow.

22 lines of code changed in 1 file:

jthornoc 2015-05-11 14:56 Rev.: 53470

Wrapping up reference pressure implementation.
The user now can remove dimensions from the pressure solve by specifying
the dimensions in the input file. This allows for 2D and 1D, periodic,
variable density problems to work.

153 lines of code changed in 2 files:

jthornoc 2015-05-11 14:56 Rev.: 53469

Use a SMALLNUM when worried about divide by zero problems (Thanks,
Todd/Dav, for pointing this out.)

Get the reference pressure working for two-d problems.

127 lines of code changed in 3 files:

jthornoc 2015-05-11 14:56 Rev.: 53468

Comments.
For SampleTask, using the cleaner interface for computing variables.

6 lines of code changed in 2 files:

harman 2015-05-11 11:38 Rev.: 53465

postH2DCopies()
- simplified logic for deciding if a variable is a "levelItem."
- Moved H2dRequiresLock up stream, needed to avoid issues when multiple threads
query existsLevelDB() simultaneously. Kudos to Dav for helping on this!

preallocateDeviceMemory() & postD2HCopies()
- gpu_stats: Added the number cells in the x,y,z dirs.



137 lines of code changed in 1 file:

harman 2015-05-11 11:12 Rev.: 53463

rayTraceKernel:
- now using getLevel() instead of get() This avoid getRegion() which we know is slow for large patch counts.
- Passing level index into the kernel

added operator != for GPUIntVectors

Added GPUVariableSanityCK()
- Does variable exist and have the proper extents and doesn't contain INFs or NANs

** This commmit will break the GPU:RMCRT 1L tests. It is the right thing to do but there are issues in the unified scheduler
that need to be sorted out. **


107 lines of code changed in 3 files:

harman 2015-05-11 09:24 Rev.: 53462

added environmental variable MPIRUN for albion.sci

3 lines of code changed in 1 file:

harman 2015-05-08 20:13 Rev.: 53460

Include GPU tests in the Nightly RT.

4 lines of code changed in 1 file:

harman 2015-05-08 16:23 Rev.: 53459

Use albion.sci for GPU:RMCRT tests

7 lines of code changed in 2 files:

tsaad 2015-05-08 14:46 Rev.: 53458

fix bug in my previous commit that broke the buildbot

3 lines of code changed in 1 file:

harman 2015-05-08 10:54 Rev.: 53456

allocateAndPut()
- added comments

4 lines of code changed in 1 file:

tsaad 2015-05-08 09:52 Rev.: 53455

propagate information about the new gaussian model for alpha
into the 1D and 2D Varden MMS'.
Cleanup a few things in the 2D MMS for better readability
and code reusability.

34 lines of code changed in 4 files:

harman 2015-05-08 09:09 Rev.: 53454

Added getLowIndex() and getHighIndex()

22 lines of code changed in 3 files:

tsaad 2015-05-07 15:16 Rev.: 53449

repair bug when parsing tabulated properties that prevented restarts from working properly

1 lines of code changed in 1 file:

tsaad 2015-05-07 11:49 Rev.: 53442

Add a regression test for a 2d laminar jet using the previously committed smooth impulse model for alpha.

2 lines of code changed in 1 file:

tsaad 2015-05-07 11:43 Rev.: 53441

Add a Gaussian type model for the variable density blending coefficient alpha.
This Gaussian model will produce a smooth version of the impulse model.
The smoother impulse can be shown to help suppress wave intermittency
that was observed in some varden jet simulations.

16 lines of code changed in 4 files:

harman 2015-05-07 09:53 Rev.: 53440

Comment out varLabelNames section. Something isn't right and it isn't needed right now.

3 lines of code changed in 1 file:

harman 2015-05-07 09:48 Rev.: 53439

Now outputting MPI rank and threadID in taskdbg statements. You can now
grep <rank>.<ID> so watch what each thread is doing.

The getRankThread() function should be moved upstream so others can use it.



10 lines of code changed in 1 file:

tsaad 2015-05-07 09:19 Rev.: 53438

add a (non reacting) 2d MMS varden test using (1) single velocity predictor, (2) tabulated properties, (3) and a reference pressure.
This holds up all the way without any convergence issues with the density-mixture fraction solver

2 lines of code changed in 1 file:

guilkey 2015-05-06 15:48 Rev.: 53437

Additional tortuous logic to:

1. Allow for more than two levels.
2. Keep fine patches with particles from being deleted, even if they
don't have refine flags set on them (otherwise the particles on them
disappear as well).
3. Refine particles as they move into finer levels, so that particle size
doesn't exceed cell size.

64 lines of code changed in 2 files:

harman 2015-05-06 15:05 Rev.: 53436

display()
- moved patchset output to the end of the line.
- identify tasks that are GPU tasks.

9 lines of code changed in 1 file:

tsaad 2015-05-06 14:29 Rev.: 53435

(1) fix bug in the reference-pressure treatment that was due to a typo
(2) convert all 2D variable density tests to use 1 cell in the irrelevant direction.
(3) update said tests to use the 2D laplacian instead of the 3D version
This will break the RT. Will also lead to noticeable speedups.

3 lines of code changed in 1 file:

tsaad 2015-05-06 12:28 Rev.: 53431

Once and for all, fix the reference pressure dilemma in Wasatch.

86 lines of code changed in 1 file:

harman 2015-05-06 11:17 Rev.: 53430

Initialize the cudaStream to NULL.

<< operator:
- if a task is using the cuda stream then output the stream address.


7 lines of code changed in 1 file:

tsaad 2015-05-06 10:38 Rev.: 53429

if hypre solver is SMG, then throw exception when periodic resolutions are not a power-of-two. Otherwise, throw a warning.

11 lines of code changed in 1 file:

tsaad 2015-05-06 09:56 Rev.: 53428

Prevent the HypreSolver interface from throwing an exception when using one cell in any given periodic direction. This will Wasatch and other components to use one cell only in directions that are not being solved for. Also, this will significantly reduce the logic associated with setting reference pressures.

3 lines of code changed in 1 file:

harman 2015-05-05 16:37 Rev.: 53427

Removed heat equation. It doesn't run and is a copy & paste of Poisson1 which does run

0 lines of code changed in 4 files:

ahumphrey 2015-05-05 12:34 Rev.: 53426

Cleanup TaskDBG output in threaded schedulers, reporting in ThreadedMPI and Unified schedulers has not been consistent. Also restrict thread-specific debugstream output.

20 lines of code changed in 4 files:

harman 2015-05-01 12:19 Rev.: 53423

Prepend all gpustats output with mpirank.threadID information. For example:

0.0 Post H2D copy of REQUIRES ( abskg), L-1, patch: 1, size (bytes) = 157216 from 0x168eb90 to 0x1304a40000, using stream 0x7f44d80008c0
0.1 Post H2D copy of REQUIRES ( abskg), L-1, patch: 2, size (bytes) = 157216 from 0x16eeb10 to 0x1304a66800, using stream 0x1bc5880

Useful when debugging thread issues.


44 lines of code changed in 2 files:

harman 2015-05-01 10:14 Rev.: 53422

postH2DCopies()
- output cuda stream pointer in DebugStream gpuStats
- removed repetitive calls to dw->getGPUDW()

30 lines of code changed in 1 file:

April 2015 »

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