February 2016 Commit Log

Number of Commits:
105
Number of Active Developers:
15
dsunder 2016-02-29 16:25 Rev.: 54933

add operator()(i,j,k) to Array3 if Kokkos is NOT enabled

9 lines of code changed in 1 file:

tsaad 2016-02-26 16:45 Rev.: 54921

Fix a bug that showed up when using a GPU build in CPU-only mode.

5 lines of code changed in 1 file:

tsaad 2016-02-26 10:20 Rev.: 54914

fix typo in a comment

1 lines of code changed in 1 file:

guilkey 2016-02-25 17:40 Rev.: 54911

Implement new modes of particle splitting. Specialize for diffusion calcs.
This will likely still evolve a bit, but it is a start.

58 lines of code changed in 5 files:

guilkey 2016-02-25 13:32 Rev.: 54909

Put the area value in the vector component to which it is normal.

2 lines of code changed in 1 file:

tsaad 2016-02-25 11:54 Rev.: 54907

revert sci_algorithm to get GPU building again.

36 lines of code changed in 1 file:

u0407585 2016-02-24 17:41 Rev.: 54905

Made root function in char oxidation model a little faster.

19 lines of code changed in 2 files:

derekhar 2016-02-24 17:31 Rev.: 54904

Fixed kokkos box iteration range, in construction of the A_matrix for radiation.

4 lines of code changed in 1 file:

jas 2016-02-24 17:19 Rev.: 54903

Turn off c++-11 temporarily

3 lines of code changed in 1 file:

jas 2016-02-24 16:56 Rev.: 54900

Set the nvcc compiler flag to use c++-11

3 lines of code changed in 1 file:

bpeterson 2016-02-24 15:58 Rev.: 54898

Extensive changes to support concurrency of data coming into and out of the GPU data warehouse

3504 lines of code changed in 15 files:

jas 2016-02-24 15:37 Rev.: 54895

Enable a c++-11 macro that will turn on c++-11 support automatically. Resolve casting issues from int to long for UMATTR.cc file. Eliminate old is_sorted definition that is no longer needed with c++-11.

1 lines of code changed in 3 files:

u0407585 2016-02-24 12:25 Rev.: 54894

Removed redundant cell loop.

3 lines of code changed in 1 file:

u0407585 2016-02-24 12:08 Rev.: 54893

Moved varlable creation into problem setup. This won't effect regression tests.

23 lines of code changed in 1 file:

derekhar 2016-02-23 17:18 Rev.: 54888

DORadiation can now construct the Amatrix in radiation using kokkos.

51 lines of code changed in 1 file:

tsaad 2016-02-23 14:45 Rev.: 54885

cleanup a bunch of header inclusions and move some code around to simplify operator usage

24 lines of code changed in 22 files:

jas 2016-02-23 14:15 Rev.: 54884

Initialization of mutex required for static builds.

6 lines of code changed in 1 file:

u0407585 2016-02-22 16:25 Rev.: 54881

Time-step initilize the copy of wall temperature in cells where the wall heat transfer model isn't active. This will break coal problems with the wall heat trasnfer model activated.

1 lines of code changed in 1 file:

jthornoc 2016-02-19 18:40 Rev.: 54867

Enable handoff files with heat loss.

2 lines of code changed in 1 file:

guilkey 2016-02-19 17:52 Rev.: 54865

Fix a bug in particle area calculation. Fix a comment as well.

2 lines of code changed in 1 file:

jas 2016-02-19 16:51 Rev.: 54864

Increase the precision to 17 digits to match the DOM version for floating point numbers.

3 lines of code changed in 1 file:

tsaad 2016-02-19 10:28 Rev.: 54861

remove an annoying cout statement

0 lines of code changed in 1 file:

harman 2016-02-18 17:27 Rev.: 54858

DataArchiver.cc saveLabels_PIDX()
- updated ToDo list
- removed t_buffer, it's not needed.
- updated call to printBuffer()

PIDXOutput
- created a wrapper for printBuffer to take into account CCVariable<int>.
- changed the form of the hard wired equation used for debugging buffer.


69 lines of code changed in 4 files:

jas 2016-02-18 15:36 Rev.: 54857

Turn off the generation of grid.xml to get visit working again.

1 lines of code changed in 1 file:

guilkey 2016-02-18 13:56 Rev.: 54856

Add a new option for particle splitting based on dividing a particle across the
direction of greatest stretch, thereby reducing the particle aspect ratio.

151 lines of code changed in 1 file:

jas 2016-02-17 21:38 Rev.: 54854

Check if grid_file exists before attempting to close it.

2 lines of code changed in 1 file:

jthornoc 2016-02-17 17:38 Rev.: 54850

pow() -> std::pow()

22 lines of code changed in 5 files:

harman 2016-02-17 17:18 Rev.: 54849


Removed PIDX debugging code and added method to hardwire the buffer values if needed for
sanity checks and debugging.

hardWireBufferValues(t_buffer, patchExts, arraySize, sample_per_variable );

This method supports all uintah types and subtypes.


65 lines of code changed in 3 files:

jas 2016-02-17 16:00 Rev.: 54848

Use xmlTextWriter to write out <Grid> and <Data> section to grid.xml.

418 lines of code changed in 3 files:

harman 2016-02-17 15:27 Rev.: 54847


- consolidated code for setting the level extents to PIDXOutputContext.

59 lines of code changed in 4 files:

derekhar 2016-02-17 14:43 Rev.: 54846

Using std::pow( double , int ) causes answers to change when using c++11, changed to pow(double, double)

15 lines of code changed in 6 files:

jholmen 2016-02-17 12:55 Rev.: 54844

* Fixed OpenMP reductions for Intel compilers

8 lines of code changed in 1 file:

harman 2016-02-17 12:26 Rev.: 54843

code consolidation:
- moved code to check the PIDX return codes to PIDXOutputContext.cc
- moved code to compute the Patch extents to PIDXOutputContext -- setPatchExtents()
- created struct to hold the patchExtents.

171 lines of code changed in 6 files:

harman 2016-02-16 16:18 Rev.: 54840

PIDXOutputContext:
Add function printBuffer() that prints out the PIDX buffer in a human readable format.
Thanks Dav for the needed push

DataArchive.cc & dataArchiver.cc
- cleaned out gross debugging code and replaced with printBuffer(). Debugging output is wrapped with
SCI_DEBUG calls.


152 lines of code changed in 4 files:

harman 2016-02-16 14:54 Rev.: 54839

query()
- Feplaced getenv call with a new function to determine if PIDX is enabled.

9 lines of code changed in 2 files:

harman 2016-02-11 19:25 Rev.: 54825

Bulletproofing:
Throw an exception if the user tries to read a PIDX uda using stock code.

12 lines of code changed in 1 file:

harman 2016-02-11 17:57 Rev.: 54824

Added a filename to the VarData struct. With PIDX each variable has a different filename.

query() PIDX section
- open the file defined in the VarData struct.
- Wrapped debugging code with conditional statements controlled with SCI_DEBUG vars.

48 lines of code changed in 2 files:

harman 2016-02-11 16:48 Rev.: 54823

fixed annoying compiler warning

1 lines of code changed in 1 file:

tsaad 2016-02-11 14:57 Rev.: 54822

Enable GPU for a few more expressions for fully compressible simulations on the GPU!

60 lines of code changed in 8 files:

harman 2016-02-11 14:15 Rev.: 54821

Level.h - pullled a weed.

Variable.cc/h
- added readPIDX() method which passes an pidxBuffer into an Array3
- commented emitPIDX()

DataArchive.cc
query() PIDX section
-Now pushing pidxBuffer into an Array3 via readPIDX()

With this commit the user can output:PIDX and read:PIDX. Also:

compare_uda -exact PIDX.uda stock.uda

compares exactly. Only 1 variable in index.xml works. There's a bug with multiple variables.


62 lines of code changed in 4 files:

u0407585 2016-02-11 12:57 Rev.: 54820

Added additional check for clipping coal temperature. This may break arches coal regression tests but it is needed to ensure physical temperatures in the case of an unconverged solution.

2 lines of code changed in 1 file:

u0407585 2016-02-11 12:55 Rev.: 54819

Initialized temporary variable AreaSum.

2 lines of code changed in 1 file:

derekhar 2016-02-11 12:29 Rev.: 54818

Made scattering consistent with previous radiation changes.

0 lines of code changed in 2 files:

harman 2016-02-11 10:56 Rev.: 54817

level
- added computeVariableExtents() which returns the low and high cell index for that
variable type (CCVariable, SFC(*)Variable, NCVariable)

DataArchiver.cc saveLabels_PIDX()
- using level->computeVariableExtents() to set the PIDX globalExtents.
- cleanup debugging array output. Now writing cell indicies to easy sanity checks.

67 lines of code changed in 3 files:

tsaad 2016-02-11 10:26 Rev.: 54816

Make all Wasatch fields persistent on the initial condition tree. This is needed for initial conditions that are "derived" from other variables and that ExprLib sees as non-persistent.
We can, in the future, only track those fields that are transported and mark them as persistent. But that requires passing information around across Wasatch.
This is a more elegant solution and does not affect the time advance graphs.

6 lines of code changed in 1 file:

allen 2016-02-10 19:14 Rev.: 54815

added strip charting and clean up

489 lines of code changed in 9 files:

guilkey 2016-02-10 18:29 Rev.: 54814

Fix the failing RT for the Collide problem. The logic for refining particles
and/or grid is painful.

58 lines of code changed in 1 file:

harman 2016-02-10 17:24 Rev.: 54813

query() pidx section
- simpilified testing return codes.
- added debugging code to output the array read in.

87 lines of code changed in 2 files:

tsaad 2016-02-10 14:47 Rev.: 54812

Make sure we get GPU versions of the pressure and density IC for compressible flows.

150 lines of code changed in 2 files:

tsaad 2016-02-10 12:41 Rev.: 54811

add a readme file to the R_Tester directory to remind users how to set environmental flags that control which component and which tests to run. This is useful for automated bash scripting.

12 lines of code changed in 1 file:

harman 2016-02-10 11:41 Rev.: 54810

saveLabels_PIDX()
- now checking the return codes on all PIDX calls. Throw an exception if
there is a problem.
- added sanity check code (disabled) to display the array values before and after a PIDX write.

91 lines of code changed in 2 files:

u0407585 2016-02-10 11:12 Rev.: 54809

Fixed another sign error in new char oxidation model.

8 lines of code changed in 1 file:

derekhar 2016-02-09 16:12 Rev.: 54808

Fixed a virtual class to be consistent with its parent class. Building arches without petsc remains possible.

0 lines of code changed in 2 files:

u0407585 2016-02-09 15:33 Rev.: 54807

fixed onother sign error in blowing parameter for new char oxidation model.

6 lines of code changed in 1 file:

tsaad 2016-02-09 15:33 Rev.: 54806

Particle contributions to the gas phase are not GPU runnable yet.

1 lines of code changed in 1 file:

allen 2016-02-09 14:37 Rev.: 54805

changed var name and added stop features

140 lines of code changed in 10 files:

u0407585 2016-02-09 01:40 Rev.: 54804

Fixed mass transfer coefficient correction factor, and sign errors in the new char oxidation model.

51 lines of code changed in 2 files:

jthornoc 2016-02-08 18:05 Rev.: 54803

Fix a bug with DQMOM + handoff files.
For variable_stats, add some more documentation in the spec file + throw an error if velocities are being averaged. One should use the flux_variable instead for velocities.
Add task name to the throw in TaskInterface.
Remove a premature create_local_labels in utility factory.

263 lines of code changed in 4 files:

harman 2016-02-08 17:59 Rev.: 54802

Added ability to outputDoublesAsFloats in PIDX. Not Verified.

DataArchiver.cc
- saveLabels_PIDX() - top of the stack for writing PIDX
set pc.setOutputDoubleAsFloat()

Variable.cc
- added dividers
- emitPIDX()
pass in expected bufferSize and check against it.
Pass into emitNormal() outputDoubleAsFloat argument

PIDXOutputContext.*
- added methods setOutputDoubleAsFloat() and isOutputDoubleAsFloat()

DataWarehouse.h OnDemandDataWarehouse.h
- updated parameters for emitPIDX()

OnDemandDataWarehouse::emitPIDX()
- added {}
- passing expect buffer size through to var->emitPIDX()



150 lines of code changed in 9 files:

derekhar 2016-02-08 17:44 Rev.: 54801

Changed Arches-hypre interface to take advantage of 4-point stencil data management.
Added construction of A-matrix using a c++ functor.

This commit is expected to change the solutions to all arches-radiation Regression tests.

285 lines of code changed in 11 files:

harman 2016-02-08 10:00 Rev.: 54800

Reverted back to including the uda path,

./advectPIDX.uda.000/t00009/l0/CCVars

in the idx filename. If you don't then the idx directories are placed outside of the uda.


11 lines of code changed in 2 files:

leavy 2016-02-08 06:53 Rev.: 54799

modfied p.scalefactor for compatibility with cpdi and cpti particle domain visualization

3 lines of code changed in 1 file:

harman 2016-02-07 17:25 Rev.: 54798

restartInitialize()
- indices -> ts_indices ts == timestep

query() PIDX section
- removed hardwired timestep. Now using the global variable d_ts_indices

9 lines of code changed in 2 files:

harman 2016-02-07 16:46 Rev.: 54797

DataArchiver::output PIDX
- removed the path for the idxfilename. Pass that string around.

DataArchive::query()
- added enum to help if a variable is a patch based or a reduction.
- open reduction variables using the standard used plumbing.
- only open pidx files with patch based variables.
- removed hard coding for the pidx filename.

14 lines of code changed in 4 files:

guilkey 2016-02-06 11:12 Rev.: 54796

Removed hardwired refinement criteria.

2 lines of code changed in 1 file:

allen 2016-02-05 19:13 Rev.: 54794

moved one time init calls

10 lines of code changed in 2 files:

harman 2016-02-05 18:47 Rev.: 54793

DataArchiver::saveLabels_PIDX()
- output pXXXX.xml files. Use the same format as a stock uda. We can use
the existing data Structures inside of DataArchieve so we/I don't have to do a complete overhaul.

DataArchive::query()
- read from the pXXXX.xml files, which have been parsed upstream, the variable index
Use that index when pulling variables from the pidx file.
- use the time index in the pidx query.

The 1Level, 1matl, checkpoint variables can be read into a local buffer. Heavy construction zone.

56 lines of code changed in 4 files:

allen 2016-02-05 18:40 Rev.: 54792

removed warnings

5 lines of code changed in 2 files:

allen 2016-02-05 18:37 Rev.: 54791

aded time ranging

91 lines of code changed in 6 files:

harman 2016-02-05 15:23 Rev.: 54790

DataArchiver::saveLabels_PIDX
- added exception if allocating memory for the buffers failed.

DataArchive::query()
- added machinery to read a variable from a PIDX file. This is a heavy construction
zone with hardwired variables. It will read in a single variable.

151 lines of code changed in 2 files:

derekhar 2016-02-05 14:46 Rev.: 54789

Uncommented all of the commented local tests in ARCHES.py.

64 lines of code changed in 1 file:

harman 2016-02-05 13:28 Rev.: 54788

Added plumbing back to identify if an uda is using stock or PIDX file format.

Thanks valgrind for the clue.


87 lines of code changed in 2 files:

allen 2016-02-05 10:36 Rev.: 54787

var name change

6 lines of code changed in 4 files:

harman 2016-02-04 18:46 Rev.: 54786

Fixed one memory issue kicked up by DDT.....there are others.
- removed d_lb, it's not used.

2 lines of code changed in 2 files:

allen 2016-02-04 18:32 Rev.: 54785

added the ability to save images

353 lines of code changed in 8 files:

tsaad 2016-02-04 15:09 Rev.: 54784

remove a couple of annoying couts.

0 lines of code changed in 1 file:

harman 2016-02-04 11:16 Rev.: 54783

revert to 54770. This should fix the compare_uda crashing.

private:
friend class DataArchive::TimeData;
DataArchive( const DataArchive& );
DataArchive& operator=( const DataArchive& );

enum outputFileFormat {UDA, PIDX};
outputFileFormat d_outputFileFormat; <<<<< this was causing a problem.

31 lines of code changed in 2 files:

u0407585 2016-02-03 18:08 Rev.: 54782

Finishing touches to new CharOxidation model. Added effective diffusivity calculation and cleaned up a few bugs.

236 lines of code changed in 2 files:

allen 2016-02-03 15:16 Rev.: 54781

remove the memory spefic code as it now paret of the runtime

17 lines of code changed in 1 file:

allen 2016-02-03 15:15 Rev.: 54780

changed the print stats to be at the end ofthe timestep

59 lines of code changed in 1 file:

allen 2016-02-03 15:14 Rev.: 54779

redid the interface and added checks

24 lines of code changed in 2 files:

allen 2016-02-03 15:01 Rev.: 54778

split the Uintah UI

531 lines of code changed in 1 file:

dsunder 2016-02-03 08:56 Rev.: 54777

remove c++11 header from example to fix build

0 lines of code changed in 1 file:

allen 2016-02-02 20:09 Rev.: 54776

changed the mpi stat to a reduction model

130 lines of code changed in 7 files:

allen 2016-02-02 19:25 Rev.: 54775

removed cerr

0 lines of code changed in 1 file:

allen 2016-02-02 19:22 Rev.: 54774

rewroke the stats collection

529 lines of code changed in 12 files:

dsunder 2016-02-02 18:27 Rev.: 54773

Implement parallel_for and parallel_reduce over 3D ranges

93 lines of code changed in 2 files:

harman 2016-02-02 16:44 Rev.: 54772

Adding plumbing to identify the output file format (uda/pidx) in the index.xml files.

97 lines of code changed in 3 files:

dsunder 2016-02-02 14:44 Rev.: 54771

Remove spurious ouput from poisson1 example

0 lines of code changed in 1 file:

harman 2016-02-02 12:54 Rev.: 54770

write_xml_files()
- added comments, spaces, dividers, and aligned code


111 lines of code changed in 1 file:

dav 2016-02-02 11:57 Rev.: 54769

Fix linking issue when using MPI rank in output... Needed to link in Uintah/Parallel lib.

4 lines of code changed in 3 files:

ahumphrey 2016-02-02 10:39 Rev.: 54768

Disambiguate isnan calls in MPM constitutive model (for C++11 compliance).
Silence warning (signed - unsigned comparison) in SimulationController

3 lines of code changed in 2 files:

allen 2016-02-01 20:35 Rev.: 54767

fixed commented out code

1 lines of code changed in 1 file:

allen 2016-02-01 20:04 Rev.: 54766

added performance stats

102 lines of code changed in 4 files:

allen 2016-02-01 20:03 Rev.: 54765

moved the global reduction stats to be a member variable and white space clean up

41 lines of code changed in 2 files:

harman 2016-02-01 18:27 Rev.: 54764

modified some logic so gobal.xml and global.data files are output when using the PIDX format.

8 lines of code changed in 1 file:

harman 2016-02-01 18:26 Rev.: 54763

formatting.
- added dividers.
- added {}

88 lines of code changed in 2 files:

harman 2016-02-01 18:25 Rev.: 54762

added MIT license

23 lines of code changed in 1 file:

allen 2016-02-01 17:17 Rev.: 54761

added a grod stat table

132 lines of code changed in 4 files:

allen 2016-02-01 15:34 Rev.: 54760

clean up and comments on timing stats

47 lines of code changed in 3 files:

cgritton 2016-02-01 15:30 Rev.: 54759

Finished moving ReactiveDiffusion components from arl_dev

2396 lines of code changed in 17 files:

harman 2016-02-01 14:10 Rev.: 54758

DataArchiver: outputVariables()
- now saving to the runTimeStats the number of bytes saved during file IO. Both stock and PIDX formats

OnDemandDataWarehouse, DataWarehouse, Variables:
- emit() now returns the number of bytes written.

Simulation State:
- changed units from bytes/sec -> MBytes/sec.

We can now monitor the IO rates per MPI rank.


49 lines of code changed in 8 files:

tsaad 2016-02-01 12:06 Rev.: 54757

support Lagrangian particle transport with compressible flows.

52 lines of code changed in 7 files:

ahumphrey 2016-02-01 11:15 Rev.: 54756

1.) Consolidate pendingMPIRecvs() into MPIScheduler.

2.) Silence compiler warnings (signed-unsigned comparisons), cleanup and formatting.

26 lines of code changed in 5 files:

harman 2016-02-01 10:39 Rev.: 54754

SimulationState:
- Added new runtimeStat to measure the file IO rate per MPI rank.
- change outputTime -> outputFileIO

Schedulers:
- code consolidation. Moved the calculation of the net runTimeStats into a single method
computeNetRunTimeStats()
There's no need to do the same thing in each scheduler.

DataArchiver:
- Now setting the FileIO_rate to a bogus number that needs to be implemented.

42 lines of code changed in 9 files:

January 2016 »

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