July 2011 Commit Log

Number of Commits:
58
Number of Active Developers:
11
qymeng 2011-07-31 00:26 Rev.: 47394

output PAPI flops counter after each timestep.
cleanup prefix flops counter code from scheduler.

28 lines of code changed in 9 files:

qymeng 2011-07-30 16:32 Rev.: 47393

Reduce the frequency to acquire write lock
1. Disable variable scrubbing for multi-thread scheduler, unused variable still will be cleaned at the end of each timestep
2. Separate current running task lock from data warehouse lock

21 lines of code changed in 3 files:

ahumphrey 2011-07-29 15:06 Rev.: 47392

Added support for the following PAPI hardware counters:
PAPI_FP_OPS - Floating point operations

This replaces the older, unused PERFEX code used on the LANL SGI machines years ago.

PAPI support is incorporated into Uintah's build system and available by using:
--with-papi=DIR

New configure script was generated with autoconf v2.68 per spec, and diffs are minimal.

474 lines of code changed in 10 files:

jthornoc 2011-07-29 03:59 Rev.: 47391

RT challenged....

Fixed missing comma.

1 lines of code changed in 1 file:

jthornoc 2011-07-29 02:37 Rev.: 47390

fixed a vim typo.

1 lines of code changed in 1 file:

jthornoc 2011-07-28 18:00 Rev.: 47389

Pulled some weeds.
Added new prefill stuff...about %80 done.
Clip scalar then apply boundary conditions.

192 lines of code changed in 9 files:

harman 2011-07-28 12:42 Rev.: 47387

added missing #include

1 lines of code changed in 1 file:

harman 2011-07-28 11:38 Rev.: 47386

cosmetics: vertical & horizontal spaces

Instrumented by adding debugStream to main tasks.

112 lines of code changed in 1 file:

harman 2011-07-27 16:32 Rev.: 47385

added try/catch block in main() so the exception messages are displayed
Thanks Dav!

279 lines of code changed in 1 file:

jsutherland 2011-07-27 15:55 Rev.: 47384

Updating some documentation
Minor formatting changes in a few places.

367 lines of code changed in 49 files:

ahumphrey 2011-07-27 15:45 Rev.: 47383

Deleted unnecessary/empty aclocal.m4 file from trunk/src/build_scripts. Looks like this file was abandoned in 1999.

0 lines of code changed in 1 file:

harman 2011-07-27 15:36 Rev.: 47382

added support for little or big endianness bytes in the raw input files

Usage: rawToUniqueGrains [options] <ups file>
options:
-b, -binary: binary output
-l, -littleEndian: input file contains little endian bytes [default]
-B, -bigEndian: input file contains big endian bytes



58 lines of code changed in 1 file:

jsutherland 2011-07-27 10:34 Rev.: 47380

Merge branch 'ExtraCells'

26 lines of code changed in 3 files:

guilkey 2011-07-24 16:36 Rev.: 47377

Use proc0cout in place of cerr to reduce spew.

13 lines of code changed in 3 files:

jsutherland 2011-07-21 17:23 Rev.: 47371

Merge branch 'ExtraCells'

Conflicts:
src/CCA/Components/Wasatch/FieldAdaptor.h

1 lines of code changed in 1 file:

jsutherland 2011-07-21 17:00 Rev.: 47370

rework field wrapping a bit - preparing for extra cells

150 lines of code changed in 8 files:

jsutherland 2011-07-21 11:45 Rev.: 47368

remove some dead code that I forgot to remove earlier.

0 lines of code changed in 1 file:

jsutherland 2011-07-20 17:10 Rev.: 47364

quiet some warnings

2 lines of code changed in 2 files:

jpeterson 2011-07-20 17:00 Rev.: 47362

Added a Birch-Muranaghan EOS to ICE. The temperature dependent form is only partially implemented.

484 lines of code changed in 4 files:

jsutherland 2011-07-20 16:29 Rev.: 47361

oops - fix a typo.

1 lines of code changed in 1 file:

jsutherland 2011-07-20 16:26 Rev.: 47360

Move some stuff from ExprLib into Wasatch.
Use SpatialOps-style operators rather than Uintah iterators on a few field ops in the time integrator.

39 lines of code changed in 2 files:

jthornoc 2011-07-20 10:20 Rev.: 47357

Fix an indexing problem with local labels.

1 lines of code changed in 1 file:

jeff788 2011-07-20 09:48 Rev.: 47356

some enhancements were added for the simplifiedGeomodel.cc

55 lines of code changed in 2 files:

jthornoc 2011-07-20 09:19 Rev.: 47355

Cleaning up westbrook/dryer model for new table abstraction. Should also
allow for easier operator splitting for the chemistry.

Cleaned up and updated spec.

73 lines of code changed in 2 files:

jpeterson 2011-07-19 15:31 Rev.: 47354

Fixed an artificial threshold accidentally added in the last commit. Updated to the model used in the validation study.

44 lines of code changed in 1 file:

harman 2011-07-18 18:08 Rev.: 47352

made the tool more general. The user can now map material indices to threshold
ranges. The uniqueGrains tag is now optional. Usage:


<PreprocessTools>
<rawToUniqueGrains>
<image> unique_grains.raw </image>
<ppc> [1,1,1] </ppc>
<res> [154,252,1] </res>
<outputBasename> points/16bit_grains </outputBasename>

<matl index="0">
<threshold> [0,0] </threshold>
</matl>

<matl index="2">
<threshold> [67,69] </threshold>
</matl>

<uniqueGrains>
<matlIndex> [1,2,3,4,5] </matlIndex>
<threshold> [1,80] </threshold>
</uniqueGrains>

</rawToUniqueGrains>
</PreprocessTools>




126 lines of code changed in 1 file:

tsaad 2011-07-18 15:53 Rev.: 47351

Modify Dirichlet BC implementation for staggered fields by setting values directly on appropriate cells.

64 lines of code changed in 4 files:

jthornoc 2011-07-18 07:46 Rev.: 47349

Undoing Julien's commit.

Fixing a problem with two of the vectors -- resize needed to keep the
vectors from growning beyond the length of the # of indep. vars. This
was affecting the property values in the boundary.

10 lines of code changed in 1 file:

jthornoc 2011-07-18 07:46 Rev.: 47348

Adding method for operator splitting the chemistry.

170 lines of code changed in 3 files:

jthornoc 2011-07-18 07:00 Rev.: 47347

Passing labels into source. Checking rate vs. dt and local concentration.

35 lines of code changed in 3 files:

jpedel 2011-07-16 15:01 Rev.: 47346

Fixing boundary condition for density

6 lines of code changed in 1 file:

jpeterson 2011-07-15 16:06 Rev.: 47345

Changed the computation of the pressure, specifically, reused some values that were computed already. Got rid of a few pow() calls in density computation.

7 lines of code changed in 1 file:

jsutherland 2011-07-15 14:15 Rev.: 47343

clean up some compiler warnings

4 lines of code changed in 3 files:

guilkey 2011-07-14 19:17 Rev.: 47341

Use timestepinc in the -partvar option.

6 lines of code changed in 1 file:

jsutherland 2011-07-13 17:21 Rev.: 47338

rip out the obselete "SpatialOps" component.

4 lines of code changed in 27 files:

dav 2011-07-13 16:35 Rev.: 47337

Previous commit fixed this... don't need 'using std::abs'.

0 lines of code changed in 2 files:

jsutherland 2011-07-13 16:24 Rev.: 47336

more cleanup and chasing the Arches test failures.

82 lines of code changed in 9 files:

dav 2011-07-13 16:18 Rev.: 47335

fabs() for doubles, not abs().

6 lines of code changed in 2 files:

dav 2011-07-13 16:12 Rev.: 47334

Fix namespace issue for VisIt plugin.

3 lines of code changed in 1 file:

dav 2011-07-13 16:01 Rev.: 47333


Fix for an issue that arose when 'using namespace std' was removed from
header files.

M CCA/Components/Arches/CoalModels/PartVel.cc

abs() only works on int's. Need 'fabs()' for floating point numbers.

M R_Tester/toplevel/generateGoldStandards.py
M R_Tester/helpers/runSusTests.py

Added a (commented out) line that makes debugging faster...

M Core/Parallel/BufferInfo.h

Don't need 'using namespace std' any more as the above update to
PartVel fixes the problem.

16 lines of code changed in 4 files:

jsutherland 2011-07-13 13:49 Rev.: 47332

This should fix the failing Arches test, but really opens up the std namespace to a wide spectrum of the code base.

I suspect that this is hiding a name clash or something that is causing failures in the Arches DQMOM tests.

2 lines of code changed in 1 file:

jsutherland 2011-07-13 13:49 Rev.: 47331

a bit more cleanup.

12 lines of code changed in 4 files:

jsutherland 2011-07-13 13:49 Rev.: 47330

tighten up a few things here.

15 lines of code changed in 7 files:

jsutherland 2011-07-13 13:49 Rev.: 47329

fix in Arches/Filter.h

1 lines of code changed in 1 file:

dav 2011-07-13 13:02 Rev.: 47328


Update to fix issues arising from removing 'using namespace std' from header files.

M StandAlone/tools/uda2nrrd/wrap_nrrd.cc
M StandAlone/tools/uda2nrrd/handleVariable.cc
M StandAlone/tools/uda2nrrd/particles.cc

- namespace std fixes.

M Core/Datatypes/NrrdData.cc

- Removed evil 'endl's and replaced with nicer "\n". :)

M StandAlone/tools/uda2nrrd/sub.mk

- On some systems, uda2nrrd needs to link vs the thread_library...


14 lines of code changed in 6 files:

jsutherland 2011-07-13 07:31 Rev.: 47327

another try - still compiles fine on my machine

2 lines of code changed in 1 file:

jsutherland 2011-07-13 06:34 Rev.: 47326

another try - this compiles fine on my machine

3 lines of code changed in 1 file:

jsutherland 2011-07-13 06:14 Rev.: 47325

Fix one file that I missed last time

2 lines of code changed in 1 file:

jsutherland 2011-07-12 23:04 Rev.: 47324

Eliminate "using namespace std" and similar from header files. That is a big no-no!

650 lines of code changed in 207 files:

jsutherland 2011-07-12 16:42 Rev.: 47323

get rid of another namespace opening in a header file.

1 lines of code changed in 1 file:

jsutherland 2011-07-12 16:31 Rev.: 47322

replace std::cout with proc0cout

74 lines of code changed in 8 files:

dav 2011-07-11 17:27 Rev.: 47320


M configure
M configure.ac

- If Uintah is built in debug mode, then build the Wasatch 3P in debug
mode too (assuming it is requested).

- Updated configure to require autoconf version 2.68 as the last
commit was made using it and this will help reduce the 2+ MB diffs
that happen when people switch between versions. If you don't have
2.68 on your machine, it takes less then 2 minutes to download it,
and build it.

M build_scripts/build_wasatch_3p.sh

- If Uintah is being built as a debug build, then build these libs in
debug mode too.

- Use the named variable BASE_BUILD_DIR instead of '$1' throughout the
script. Added a tiny bit of indentation.

44 lines of code changed in 4 files:

harman 2011-07-11 14:52 Rev.: 47319

This prepocessing tool is used to create a separate pts file for each material and patch
after analyzing an image raw file. This was designed for raw images that contain granular
materials with binder (0) and individual grains. To avoid issues with the contact algorithm
(grains sticking together) the individual grains will be assigned to separate matls.
Below is a raw image slice with 4 regions or grains. This tool indentifies all
intensities > 0 and maps that intensity to a mpm matl.

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 50 50
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 50
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 63 63 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 63 63 63 63 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 63 63 63 63 63 63 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 63 63 63 63 63 63 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 63 63 63 63 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 64 64 0 0 0 0 0 0 0 0 0 0 0 63 63 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 64 64 64 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
- - - - - - - - - - - - - - - - | 64 64 64 64 - - - - - - - - - - - - - - - - - - - -
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 64 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 65 65 65 0 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 65 65 65 65 65 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 0 0 66 66 66 66 0 0 0 0 0 0 0
0 0 0 65 65 65 65 65 0 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 0 0 66 66 66 66 66 66 66 66 0 0 0 0 0
0 0 0 65 65 65 65 65 65 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 0 0 0
0 0 0 65 65 65 65 65 65 0 0 0 0 0 0 0 | 0 0 0 0 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 0
0 0 0 65 65 65 65 65 65 65 0 0 0 0 0 0 | 0 0 0 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66
0 0 0 0 65 65 65 65 65 65 0 0 0 0 0 0 | 0 0 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66
0 0 0 0 65 65 65 65 65 65 0 0 0 0 0 0 | 0 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66
0 0 0 0 0 0 65 65 65 0 0 0 0 0 0 0 | 0 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 | 0 0 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66 66


ups file specification:

<PreprocessTools>
<rawToUniqueGrains>
<numGrainMatls> 3 </numGrainMatls>
<image> simple_sugar_mock_blob3d_unique_grains.raw </image>
<ppc> [1,1,1] </ppc>
<res> [154,252,1] </res>
<threshold> [1,80] </threshold>
<outputBasename> points/16bit_grains </outputBasename>
</rawToUniqueGrains>
</PreprocessTools>

Mapping of intensity to matl:

Intensity Levels: 79 min: 1 max: 79
Intensity level to mpm matl mapping
Intensity: 0 = matl 0
Intensity: 1 = matl 1
Intensity: 2 = matl 2
Intensity: 3 = matl 3
Intensity: 4 = matl 1
Intensity: 5 = matl 2
Intensity: 6 = matl 3
Intensity: 7 = matl 1
Intensity: 8 = matl 2
Intensity: 9 = matl 3
Intensity: 10 = matl 1


Assumptions:
- All pixels with an intensity of 0 belong to matl 0.
- The particle per cell (ppc) is a constant for all matls.


487 lines of code changed in 2 files:

harman 2011-07-08 16:20 Rev.: 47317

added 16 bit image support.
- You need to recompile the code to use it. This should be fixed.

28 lines of code changed in 1 file:

jthornoc 2011-07-08 13:54 Rev.: 47316

Updated the westbrook/dryer model to be consistent with the two mixture
fraction approach.

40 lines of code changed in 2 files:

jeff788 2011-07-07 11:51 Rev.: 47312

modifications to NonLocalDruckerPrager model

147 lines of code changed in 2 files:

harman 2011-07-07 10:52 Rev.: 47311

formatting:
- added vertical spaces
- tabs
- added comments
- added {} around conditionals

95 lines of code changed in 1 file:

guilkey 2011-07-05 11:14 Rev.: 47309

Comment out some extra output

1 lines of code changed in 1 file:

June 2011 »

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