May 2011 Commit Log

Number of Commits:
81
Number of Active Developers:
11
jas 2011-05-25 18:42 Rev.: 47229

Add mpich_threadm and mpl to the mpich search patch needed for Qingyu's
threaded/mpi work on kraken and jaguar.

1038 lines of code changed in 2 files:

ihunsaker 2011-05-25 17:05 Rev.: 47228

20 lines of code changed in 1 file:

ihunsaker 2011-05-25 13:35 Rev.: 47226

23 lines of code changed in 1 file:

harman 2011-05-25 10:21 Rev.: 47225

corrected checkpoint path

3 lines of code changed in 1 file:

jpeterson 2011-05-24 15:28 Rev.: 47224

Fixed a bug in last commit. Initialize variable to false.

1 lines of code changed in 1 file:

harman 2011-05-24 15:20 Rev.: 47223

Parallel copy script based off of pscp2. This script works with one node

274 lines of code changed in 2 files:

jthornoc 2011-05-24 07:25 Rev.: 47222

Updated the transformation. This is the better way to handle this for
restart reasons.

1 lines of code changed in 1 file:

harman 2011-05-23 09:40 Rev.: 47221

replaced >&/dev/null with >/dev/null

This should fix the dashism error:
Bad fd number

1 lines of code changed in 1 file:

jthornoc 2011-05-23 08:45 Rev.: 47220

Turned off memory testing for these two tests for now until this is
sorted out.

2 lines of code changed in 1 file:

jthornoc 2011-05-20 19:11 Rev.: 47219

Added input interface to slow/fast transform.

7 lines of code changed in 1 file:

jthornoc 2011-05-20 17:31 Rev.: 47218

Added slowfast chemistry mixture fraction transformation.

52 lines of code changed in 1 file:

jthornoc 2011-05-20 17:17 Rev.: 47217

Turning off memory tests for these two tests until this issue is sorted
out.

2 lines of code changed in 1 file:

jpedel 2011-05-20 16:12 Rev.: 47216

Reverting previous changes, for some reason Charles' method doesn't seem to work

84 lines of code changed in 3 files:

jpedel 2011-05-20 15:11 Rev.: 47215

Adopting method from Charles' Branch to build b faster

126 lines of code changed in 2 files:

qymeng 2011-05-19 12:11 Rev.: 47214

add a ALL_CELLS value for requesting all cells in a level

2 lines of code changed in 1 file:

harman 2011-05-19 10:32 Rev.: 47213

rayTrace()
- require abskg and sigmaT4 with an semi-infinite number of ghost cells

Only output the efficiency of the calculation on patch 0 to cut down on
the chatter.

14 lines of code changed in 1 file:

jas 2011-05-19 10:25 Rev.: 47212

Ignore if already present.

2 lines of code changed in 1 file:

jas 2011-05-19 09:59 Rev.: 47211

Link to the testdata.

9 lines of code changed in 1 file:

jas 2011-05-18 17:51 Rev.: 47210

Fix posix problems.

15 lines of code changed in 27 files:

harman 2011-05-18 17:30 Rev.: 47209

ignore blank lines in the tst files.

Now able to do run replace_XML_value on the global file. This
will let you change multiple levels box dimensions.

0 lines of code changed in 4 files:

qymeng 2011-05-18 15:41 Rev.: 47208

Support more than 2 ghost cells.
This will allow a task to request any number of ghost cells up to the whole grid.

18 lines of code changed in 6 files:

tsaad 2011-05-18 15:37 Rev.: 47207

Add specific information to the error thrown by Hypre when used with periodic boundary conditions. Conforming to this restriction allows running hypre with periodic conditions on multiple processorss.

1 lines of code changed in 1 file:

harman 2011-05-18 15:02 Rev.: 47206

deleted empty first line. Shell scripts need to declare what shell interperter
to use on the first line.

0 lines of code changed in 1 file:

harman 2011-05-18 10:37 Rev.: 47204

roundNearest()
- added cast (int).

0 lines of code changed in 2 files:

harman 2011-05-18 10:32 Rev.: 47203

Pass in the environmental variable "SCI_MALLOC_ENABLED" through to the
component tests.

5 lines of code changed in 1 file:

jthornoc 2011-05-17 18:15 Rev.: 47202

Updated westbrook dryer model to work with modifications to the new
tables interface. Updated spec accordingly.

81 lines of code changed in 4 files:

harman 2011-05-17 17:24 Rev.: 47201

Hack so Malloc_strict and Malloc_Stats will work on Lenny machines --Dav

30 lines of code changed in 6 files:

jthornoc 2011-05-17 11:50 Rev.: 47200

Last leak...

3 lines of code changed in 1 file:

jthornoc 2011-05-17 11:49 Rev.: 47199

Delete needed for cold flow mixing model.

2 lines of code changed in 1 file:

dav 2011-05-17 11:24 Rev.: 47198

Updates to allow for Memory checking in the local regression tester.

M configure
M configure.ac

- Added in "SCI_MALLOC_ON" variable that will tell the system if --enable-sci-malloc was used during configure.

M configVars.mk.in

- Add in the new SCI_MALLOC_ON var. Removed the MALLOC_TRACE_ON var as it wasn't set or used.

M Makefile.in

- Updated make RT targets to pass in SCI_MALLOC_ON.

M R_Tester/toplevel/startLocalTest

- Memory test update based on whether SCI_MALLOC is ON. Also now passing in whether this is (or is not) a debug build.

M R_Tester/toplevel/generateGoldStandards.py

- Now takes in whether we are using a debug build, and whether SCI_MALLOC is enabled.
- Better catching/reporting of error if component name is mis-spelled/wrong.

M R_Tester/helpers/runSusTests.py

- Turn off env var MALLOC_STATS if --enable-sci-malloc was not used (otherwise sus will throw an error and quit).
- Put SVN_OPTIONS into own variable so they can more easily be turned off while debugging.

M Core/Malloc/sub.mk

- Removed Trace.cc build statement as Trace.cc isn't actually in the code base, and MALLOC_TRACE_ON is never set.

111 lines of code changed in 10 files:

jthornoc 2011-05-17 11:17 Rev.: 47197

Plugging a few little leaks.

8 lines of code changed in 4 files:

jthornoc 2011-05-17 11:16 Rev.: 47196

Consolidating common code into parent class.

48 lines of code changed in 5 files:

jpedel 2011-05-16 16:44 Rev.: 47195

Comminting print out statements

5 lines of code changed in 1 file:

harman 2011-05-16 15:57 Rev.: 47194

output the number of particles on a per level basis.
only compute the L2norm if the number of particles > 0.

14 lines of code changed in 1 file:

jpedel 2011-05-16 15:54 Rev.: 47193

Fixing a sign error

5 lines of code changed in 1 file:

qymeng 2011-05-16 11:52 Rev.: 47192

Removed some debug output.

2 lines of code changed in 1 file:

harman 2011-05-16 10:31 Rev.: 47191


IntVector.h
- added roundNearest(). This will round the Vector v to the nearest integer

Level.cc
findNodeIndexRange(), findCellIndexRange(), findInteriorCellIndexRange()
findInteriorNodeIndexRange()

using roundNearest() on the lowIndex and highIndex.


This change fixes the following bug.
----------------------------------------------------------------
WORKS
<Box label="1">
<lower> [0.00,-0.0, 0.0] </lower>
<upper> [2.4, 0.1, 0.004] </upper>
<extraCells> [1,1,1] </extraCells>
<patches> [8,1,1] </patches>
<resolution> [160,12,1] </resolution>
</Box>

Debugging output:

findCellIndexRange: l [-1.0000000000000000e+00 -1.0000000000000000e+00 -1.0000000000000000e+00]
h [1.6100000000000000e+02 1.3000000000000000e+01 2.0000000000000000e+00]
lowIndex [int -1, -1, -1] highIndex [int 161, 13, 2]

----------------------------------------------------------------
NOWORK!
<Box label="1">
<lower> [0.00,-0.001, 0.0] </lower>
^^^^^^ <ONLY DIFFERENCE> <<<<<<<<<<<<<<<<<<<<<<<<,
<upper> [2.4, 0.1, 0.004] </upper>
<extraCells> [1,1,1] </extraCells>
<patches> [8,1,1] </patches>
<resolution> [160,12,1] </resolution>
</Box>


findCellIndexRange: l [-1.0000000000000000e+00 -9.9999999999999978e-01 -1.0000000000000000e+00]
^^^^^^^^^^^^^^^^^^^^^^^???????

h [1.6100000000000000e+02 1.3000000000000000e+01 2.0000000000000000e+00]
lowIndex [int -1, 0, -1] highIndex [int 161, 13, 2]
^^ <<<<<<<<<<<<<This cause all sorts of problems downstream.
----------------------------------------------------------------


**** This should not change the answers *****

22 lines of code changed in 2 files:

harman 2011-05-16 10:18 Rev.: 47190

added 3Level axis aligned mms test to the order of accuracy tests.

225 lines of code changed in 3 files:

harman 2011-05-13 15:42 Rev.: 47189

changed

A = A * normalization
to
A = A0 * normalization

for multilevel problems

2 lines of code changed in 1 file:

harman 2011-05-13 15:07 Rev.: 47188

Added replace_XML_value to the tools that a user can select from when
replacing values in a ups file For example, use:

<replace_values>
/Uintah_specification/Grid/Level/Box[@label=1]/resolution:[8,8,1]
</replace_values>

to replace

<Grid>
<Level>
<Box label="1">
<resolution>[16,16,1]</resolution>
</Box>
</Level>


Put a muzzle on some of the system commands.

142 lines of code changed in 5 files:

harman 2011-05-13 15:01 Rev.: 47187

This script is a wrapper around the command xmlstarlet to replace elements of complex
xml documents. This was designed for editing ups files that have
multiple elements with the same name or when an xml tag spans more than one line.

Usage: replace_XML_value <xml path to element> <replacement value> <xmlfile>

To find the xml path run the command:

xmlstarlet el -v <xmlFile>

97 lines of code changed in 1 file:

harman 2011-05-13 13:32 Rev.: 47186

updated prototype

2 lines of code changed in 1 file:

jeff788 2011-05-13 10:11 Rev.: 47184

updated the simplifiedGeoModel

261 lines of code changed in 2 files:

harman 2011-05-12 11:27 Rev.: 47183

output the cell index of the worst particle.

13 lines of code changed in 1 file:

qymeng 2011-05-12 10:37 Rev.: 47182

Fixed a problem which caused task phases are not synced when using threaded MPI scheduler.

1 lines of code changed in 1 file:

jthornoc 2011-05-11 17:47 Rev.: 47181

Turned off restart for a few tests. Will fix this later.

8 lines of code changed in 2 files:

harman 2011-05-11 15:05 Rev.: 47180

RMCRT_test.cc
- comment out scheduling of sigmaT4. It's computed in initProperties

Ray.cc/.h
-modified rayTrace task to work on multiple patches.

* This should not change the answers

41 lines of code changed in 3 files:

jthornoc 2011-05-11 12:29 Rev.: 47178

Added new test. Updated old tests to do a compare.
Todd will add gold standards to the RT.

6 lines of code changed in 2 files:

harman 2011-05-11 10:44 Rev.: 47177

Removed flat arrays.

Moved declaration of variables to within the scope that they're being used.

elminated several intermediate variable arrays.

*This should not change the answers.


22 lines of code changed in 1 file:

harman 2011-05-11 08:44 Rev.: 47175

explode2D_amr: no longer doing exact comparison. Results are not repeatable.

1 lines of code changed in 1 file:

harman 2011-05-10 17:06 Rev.: 47174

Removed all #ifdef RAYVIZ code
- general cleanup
- formatting
- using Vector shorthand instead of explicitly manipulating individual components
- simplified conditional blocks.

- Removed Jeremy's to do list.

*This should not change the answers

174 lines of code changed in 1 file:

harman 2011-05-10 09:14 Rev.: 47170

initial commit of new pressure solver. This will eventually replace
PressureSolver

1140 lines of code changed in 2 files:

jthornoc 2011-05-10 09:06 Rev.: 47169

Fixed some compiler warnings in PetscSolver.cc
Updated spec for radiation solver options.

3 lines of code changed in 1 file:

harman 2011-05-10 09:02 Rev.: 47168

PetscLinearSolve()
Added ability to output RHS, B & the matrix A to a file, currently turned off.
To do it right we need to pass in the timestep number & iteration number and
include that info in the file name.

24 lines of code changed in 1 file:

tsaad 2011-05-07 13:14 Rev.: 47166

Fix bug in momentum right hand side calculation. As of this fix, the pressure projection is now fully functional for periodic problems in Wasatch.

2 lines of code changed in 1 file:

harman 2011-05-06 12:54 Rev.: 47164

corrected label in curve fit equation

3 lines of code changed in 1 file:

harman 2011-05-06 12:32 Rev.: 47163

RMCRT.m: turn on plotting.

RMCRT_wrapper: dump out which direction is being tested

test_config_files: Added order-of-accuracy test for RMCRT benchmark test.


255 lines of code changed in 7 files:

harman 2011-05-06 11:52 Rev.: 47162

octaveWrap: Silly wrapper around the octave command.
For some reason /usr/bin/env octave -qf doesn't work.

RMCRT_wrapper: This calls RMCRT.m in the X,Y,Z directions.
RMCRT.m: calling octaveWrap instead of /usr/local/bin/octave

42 lines of code changed in 3 files:

harman 2011-05-06 11:49 Rev.: 47161

Made symbolic links to replace_XML_line & findReplace

Throw errors if any replace_XML_line or findReplace command fail

Improved OS portability.

278 lines of code changed in 5 files:

guilkey 2011-05-05 10:41 Rev.: 47159

Add the declarations/gets/requires for pColor to go along with Comer's stuff.

10 lines of code changed in 1 file:

harman 2011-05-05 09:49 Rev.: 47158

Fixed memory leak

5 lines of code changed in 1 file:

harman 2011-05-05 09:08 Rev.: 47157

harden the script

0 lines of code changed in 2 files:

harman 2011-05-05 08:41 Rev.: 47156

moved my XML find & replace scripts to a better spot

119 lines of code changed in 4 files:

jthornoc 2011-05-05 03:05 Rev.: 47155

Fixed memory leak for the case where A is constructed only once for the
pressure solver.

19 lines of code changed in 6 files:

jas 2011-05-04 18:22 Rev.: 47154

Remove the explode2D_amr from testing.

0 lines of code changed in 2 files:

jthornoc 2011-05-04 18:21 Rev.: 47153

Fixed a couple of leaks.
Code still leaks for cases where A is only constructed once. That fix
to come soon....

1 lines of code changed in 1 file:

harman 2011-05-04 17:18 Rev.: 47152

Changed filename EXAMPLES.py -> Examples.py so it would run in the local_RT

Added single level RMCRT regression test.

RMCRT_test_1L.ups: run for 10 timesteps dump a checkpoint
and reduced the number of rays to 25


50 lines of code changed in 2 files:

harman 2011-05-04 16:34 Rev.: 47150

octave script that computes the L2norm of a benchmark test

218 lines of code changed in 1 file:

jeff788 2011-05-04 16:20 Rev.: 47149

added the simplifiedGeoModel constitutive model

899 lines of code changed in 4 files:

harman 2011-05-04 12:05 Rev.: 47148

sub.mk: cleanup

Utils.cc/h
areAllValuesPositive() is now templated and works for SFC(*)<double> and CCVariable<double>

-Dav

50 lines of code changed in 4 files:

harman 2011-05-04 11:07 Rev.: 47147

Moved function is areAllValuesPositive upstream to core/Grid/Variables/Utils.h,
so other components can use it.

126 lines of code changed in 7 files:

guilkey 2011-05-04 08:17 Rev.: 47145

Put ifdef Comer back into UCNH.

10 lines of code changed in 2 files:

jthornoc 2011-05-04 07:05 Rev.: 47144

Initializing second mixture fraction and heat loss in boundary object
setup.

30 lines of code changed in 1 file:

jas 2011-05-03 15:48 Rev.: 47143

Add advect_3L_3D test.

6 lines of code changed in 1 file:

jas 2011-05-03 12:17 Rev.: 47142

Check if the DataWarehouse has been allocated for memory logging.

2 lines of code changed in 1 file:

jthornoc 2011-05-03 08:28 Rev.: 47140

Cleared up some warning messages and squashed a bug in the table
interpolator.

15 lines of code changed in 3 files:

jpeterson 2011-05-02 14:34 Rev.: 47139

Added an option to PUDA that prints out the max pressure each timestep as well as the max pressure achieved during the simulation.

165 lines of code changed in 5 files:

guilkey 2011-05-02 13:23 Rev.: 47138

Make the nightly tests use "exact_comparison" to be consistent with the RT.

0 lines of code changed in 2 files:

harman 2011-05-02 09:42 Rev.: 47137

In wasatch configure command set

--without-hypre
--without-petsc


This should catch when FakePetsc.cc won't compile.


0 lines of code changed in 2 files:

harman 2011-05-02 09:36 Rev.: 47136

Updated parameter lists

9 lines of code changed in 1 file:

jpeterson 2011-05-01 13:42 Rev.: 47135

Fixed a lost criteria in the last few commits. Prevents surface burning in a cell that will be consumed by detonation in the next timestep.

10 lines of code changed in 1 file:

April 2011 »

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