July 2012 Commit Log

Number of Commits:
81
Number of Active Developers:
12
harman 2012-07-31 13:28 Rev.: 49006

Added matl index 0 to the global matl set. This is the index for fileInfo variable.

added d_zero_matl to the requires(fileVarStructlabel) statement

3 lines of code changed in 1 file:

dav 2012-07-31 09:59 Rev.: 49005

Remove extra PATH stuff... user should have their PATH set correctly suck that the script doesn't need to add to it... Specifically we need to remove /usr/lib as this is causing Wasatch3P CMake to find the wrong libs for boost.

1 lines of code changed in 1 file:

guilkey 2012-07-30 17:32 Rev.: 49004

Get the explode2D_amr case going again.

1 lines of code changed in 1 file:

dav 2012-07-30 17:29 Rev.: 49003

debugging...

7 lines of code changed in 1 file:

harman 2012-07-30 17:06 Rev.: 49002

turning Wasatch back on. This is testing.

4 lines of code changed in 1 file:

harman 2012-07-30 15:56 Rev.: 49001

File pointers are now stored in the dataWarehouse. These are put in a PerPatch struct
(fileInfo) that is required and computed in the taskgraph. When regridding
or loadbalancing changes which processor own which file the files are closed and
then opened by the new owner (processor). The file pointers remain open
until regridding or loadbalancing occurs.


98 lines of code changed in 3 files:

harman 2012-07-30 14:34 Rev.: 49000

SchedulerCommon & Scheduler:
- added containeers for variables that a component does not want to checkpoint
or copied to a new AMR grid, notCopyData_ & notCheckpointVars. The components
can access these via

scheduler::overrideVariableBehavior()

DataArchiver:
- do not checkpoint any variable in the notCheckpointVars container

Other files:
- updated calls to overrideVariableBehavior()


This is commit is ground work for updating how I/O is handled with
OnTheFly data analysis tasks.

*This commit should not change the answers.

98 lines of code changed in 8 files:

harman 2012-07-30 11:34 Rev.: 48999

echo to the screen which cmake is being used.

3 lines of code changed in 1 file:

jsutherland 2012-07-30 10:40 Rev.: 48998

Force ExprAlgebra builder to take an enum rather than string. String->enum conversion is now done during parse.

79 lines of code changed in 4 files:

jsutherland 2012-07-30 10:40 Rev.: 48997

Fix a compiler warning.

2 lines of code changed in 1 file:

banerjee 2012-07-29 15:58 Rev.: 48996

1) Fixed UCNH restart problem.
2) Replaced RK-4 with Backward Euler in burn fraction calculation.

39 lines of code changed in 2 files:

dav 2012-07-29 15:01 Rev.: 48995

Fix use of MKL for blas/lapack with respect to PETSc.

4 lines of code changed in 2 files:

banerjee 2012-07-27 20:43 Rev.: 48994

Correct wrong type for vel gradient.

5 lines of code changed in 1 file:

jthornoc 2012-07-27 15:15 Rev.: 48993

Add missing rho in the molecular diffusivity term for scalars.

43 lines of code changed in 3 files:

harman 2012-07-27 11:54 Rev.: 48992

added default matl index

1 lines of code changed in 1 file:

banerjee 2012-07-26 22:41 Rev.: 48991

Add controls for the algorithm used to control deformation gradient
calculations.

105 lines of code changed in 2 files:

harman 2012-07-26 16:11 Rev.: 48989

Turn off wasatch component.

4 lines of code changed in 1 file:

banerjee 2012-07-26 14:46 Rev.: 48988

Corrected exponential and logarithm sums.

22 lines of code changed in 1 file:

tsaad 2012-07-26 12:05 Rev.: 48987

Allow the InterpolateExpression to interpolate from all-fields to all-fields. It was originally designed to interpolate to SVolFields only. This is useful for example when trying to add a source term to the momentum equations (i.e. YVolField) based on an SVolField scalar. The interpolate expression makes this possible.

49 lines of code changed in 2 files:

tsaad 2012-07-26 10:36 Rev.: 48986

add Arches density to initialization graph to resolve error for variable density warches.

7 lines of code changed in 1 file:

banerjee 2012-07-25 20:54 Rev.: 48984

Reverted back to Jim's version of defgrad calculation.

21 lines of code changed in 1 file:

banerjee 2012-07-25 20:16 Rev.: 48983

Improved (?) the deformation gradient calculation and generalized
the subcycling algorithm for burn fraction calculation.

65 lines of code changed in 2 files:

banerjee 2012-07-25 20:13 Rev.: 48982

Added first cuts of methods for computing exponentials and logarithms.
Needs to be checked for accuracy.

33 lines of code changed in 2 files:

jthornoc 2012-07-25 16:54 Rev.: 48981

Tony/Jeremy: Added a placeholder expression for density. This is
currently a hack.

Jeremy: Added molecular diffusivity for Arches scalar transport.

75 lines of code changed in 5 files:

harman 2012-07-25 09:37 Rev.: 48980

Turned Wasatch back on in the regression tester.

3 lines of code changed in 1 file:

banerjee 2012-07-24 21:55 Rev.: 48979

Change input variable names, stabilized reaction rate calculation,
added correct deformation gradient for initial stress.

233 lines of code changed in 2 files:

qymeng 2012-07-23 15:46 Rev.: 48977

Add a new variable type for OnTheFlyAnalysis to save file pointers as PerPatch

58 lines of code changed in 2 files:

tsaad 2012-07-23 12:45 Rev.: 48976

allow creation of SpatialOps interior memory windows. This will be used for the upcoming boundary conditions improvements.

14 lines of code changed in 2 files:

tsaad 2012-07-23 12:23 Rev.: 48975

allow Wasatch to turn on the usage of extra-cells without having to comment certain code. this is done at compile time and the extra-cells flag is passed in the configure script using --enable-wasatch-in-arches.

10 lines of code changed in 2 files:

jsutherland 2012-07-20 13:44 Rev.: 48974

Update boost location information as it is passed down to the Wasatch3P libraries.

2 lines of code changed in 1 file:

jthornoc 2012-07-20 10:35 Rev.: 48973

BIG CODE CHANGE:
Turning OFF the dummy solve. This is being done with a logical at the moment. Once things settle down, we should tear the whole thing out. Please note, this will cause answers to change for MPMArches, wide spread chaos, and lots of spam. GS will need an update.

25 lines of code changed in 2 files:

harman 2012-07-20 10:05 Rev.: 48972

removed the troubled restart test until the RT is fully functional.

4 lines of code changed in 1 file:

harman 2012-07-19 16:17 Rev.: 48971

added \\

1 lines of code changed in 1 file:

harman 2012-07-19 16:06 Rev.: 48970

Turn off compiling wasatch until the libboost issue is resolved.

4 lines of code changed in 1 file:

jsutherland 2012-07-19 16:05 Rev.: 48969

Eliminate a few warnings and clean up a bit.

8 lines of code changed in 1 file:

tsaad 2012-07-19 13:53 Rev.: 48968

Add ability to clip any field from the input file.

200 lines of code changed in 3 files:

dav 2012-07-19 13:04 Rev.: 48967

Fix compilation error on Updraft (etc) as pow(int,int) is ambiguous, so need to make it pow(float,int).

1 lines of code changed in 1 file:

sadeghirad 2012-07-19 12:41 Rev.: 48966

modified cpdiInterpolator.cc based on Dr. Guilkey's comments

24 lines of code changed in 1 file:

sadeghirad 2012-07-19 12:05 Rev.: 48965

changed cpdiInterpolator.cc to be consistent with the conforming CPDI formulation

98 lines of code changed in 1 file:

guilkey 2012-07-18 15:49 Rev.: 48964

Turning the explode2D_amr case back on.

1 lines of code changed in 1 file:

tsaad 2012-07-18 15:40 Rev.: 48963

Add a random number generator expression. This currently generates uniformly distributed random numbers using a mersenne twister. the expression can be easily extended to other types of distributions by templating on the boost random library tools. for the moment uniform distributions are sufficient.

136 lines of code changed in 3 files:

jsutherland 2012-07-18 12:23 Rev.: 48962

Update boost library dependencies to ensure functionality with boost 1.50.

2 lines of code changed in 2 files:

tsaad 2012-07-18 12:11 Rev.: 48961

update wasatch RT to reflect recent input file changes and additions.

4 lines of code changed in 1 file:

harman 2012-07-18 09:08 Rev.: 48959

removed a duplicate tool

1 lines of code changed in 4 files:

harman 2012-07-17 16:52 Rev.: 48958

Do not remove the base output directory.
Remove timestep files and directories when over writing.

30 lines of code changed in 1 file:

guilkey 2012-07-17 14:27 Rev.: 48956

Improve, slightly, the useInitialStress feature by adjusting the deformation
gradient to be consistent with the prescribed stress.

4 lines of code changed in 1 file:

harman 2012-07-17 12:02 Rev.: 48955

Fixed equation for determing the scale:

scale = pow( 2, nBits ) - 1.0;

2 lines of code changed in 1 file:

jthornoc 2012-07-16 16:48 Rev.: 48954

Superfluous print statement.

0 lines of code changed in 1 file:

harman 2012-07-13 16:09 Rev.: 48951

readParameters()
Added documentation about the various knobs from the Hypre manual

14 lines of code changed in 1 file:

tsaad 2012-07-13 15:53 Rev.: 48950

Add stepfunction for initialization among other things.

139 lines of code changed in 2 files:

jthornoc 2012-07-12 16:39 Rev.: 48948

Making the gaussian spec more intuitive.

3 lines of code changed in 1 file:

harman 2012-07-12 16:18 Rev.: 48946

A script that summarizes a series of exectimes files.
--The Ghost of Justin

29 lines of code changed in 2 files:

jthornoc 2012-07-12 15:47 Rev.: 48945

Bug fix in the cold flow model. Wasn't taking the inverse of the
MPMArches micro-density. This will affect the answers.

Also adding a gaussian initialization function for scalars.

42 lines of code changed in 3 files:

guilkey 2012-07-12 12:17 Rev.: 48944

Fix syntax problem introduced in last commit.

1 lines of code changed in 1 file:

guilkey 2012-07-12 10:15 Rev.: 48943

Turn BurnRate test back on. Fingers crossed...

1 lines of code changed in 1 file:

harman 2012-07-12 09:20 Rev.: 48942

gnuplot script for plotting scaling results

40 lines of code changed in 1 file:

guilkey 2012-07-11 21:21 Rev.: 48941

Move the location of the res tag to a kind of non-standard place for the
PressureBC in order to get restarts working.

1 lines of code changed in 1 file:

guilkey 2012-07-11 21:04 Rev.: 48940

Add use_load_curves to the outputProblemSpec

1 lines of code changed in 1 file:

harman 2012-07-11 15:48 Rev.: 48939

small bug

0 lines of code changed in 2 files:

harman 2012-07-11 15:39 Rev.: 48938

script that computes the average time spent in the solver and the average
mean time per timestep. This is used for scaling plots.

usage:
extractSolverScalingData <sus_output.1, sus_output_2, sus_output_3 ....>


81 lines of code changed in 1 file:

harman 2012-07-11 14:43 Rev.: 48937

slightly more general purpose.
updated

0 lines of code changed in 2 files:

harman 2012-07-11 12:23 Rev.: 48936

added comment on how to view top 10 tasks with ExecTimes

3 lines of code changed in 1 file:

guilkey 2012-07-10 21:43 Rev.: 48935

In the interest of putting my money where my mouth is, commenting out the two
cases that restart from checkpoint until new checkpoints can be generated. One
will be easy, the other will take some time.

4 lines of code changed in 1 file:

jpeterson 2012-07-10 14:27 Rev.: 48934

Corrected the Birch-Murnaghan implementation in VS. Add P0 offset to pressure function and corrected dP/drho calculation to give correct soundspeed.

20 lines of code changed in 1 file:

dav 2012-07-09 16:37 Rev.: 48933

Update MKL check. Check both blas/lapack at same time. Handle newer MKL where there is no libguide.

91 lines of code changed in 2 files:

jthornoc 2012-07-09 13:47 Rev.: 48932

Reverting a portion of the last commit re: diffusion at Dirichlet
BCs and adding some clarifying comments.

Seems to make most sense to assume piecewise constant at boundaries
and live with it. Interpolating back from the bc_value and
interior nodes (last commit) doesn't make sense because it potentially violates
realizability for bounded scalars.

13 lines of code changed in 1 file:

sadeghirad 2012-07-08 17:25 Rev.: 48931

committes all the changes required to make possible to describe particle domains by (Matrix3 psize). Old implementations described particle domains by (Vector psize)

284 lines of code changed in 84 files:

ahumphrey 2012-07-06 17:21 Rev.: 48930

Initial implementation of the Unified multi-threaded CPU/GPU scheduler.

TODO:
1.) make GPU related data structures thread-safe
2.) weave in GPU task queue logic

2024 lines of code changed in 4 files:

dav 2012-07-06 14:18 Rev.: 48929

Fix configure check for when PETSc does not exist on system.

58 lines of code changed in 2 files:

ahumphrey 2012-07-06 13:01 Rev.: 48928

Simplify check for PTX generation when configuring with CUDA support.

2 lines of code changed in 2 files:

tsaad 2012-07-06 12:10 Rev.: 48926

remove patch dependency from the expression that reads data from an input file.

77 lines of code changed in 3 files:

guilkey 2012-07-06 10:53 Rev.: 48925

Formatting

4 lines of code changed in 1 file:

tsaad 2012-07-06 08:04 Rev.: 48924

add an expression that reads from an input file. current usage is for initializing fields with experimental or DNS filtered data. impelementation is currently for SVOL data although the expression can handle all types of fields.

169 lines of code changed in 3 files:

ahumphrey 2012-07-05 17:13 Rev.: 48923

Parameterize vars used in AC_MSG_CHECKING([for NVCC compilation to PTX])

2 lines of code changed in 2 files:

ahumphrey 2012-07-04 15:14 Rev.: 48922

Fix PETSc related IMPM seg fault.

9 lines of code changed in 1 file:

ahumphrey 2012-07-03 17:58 Rev.: 48921

MPM PETSc interface now supports PETSc v3.1, 3.2, 3.3
Jim - This doesn't break IMPM...

98 lines of code changed in 1 file:

ahumphrey 2012-07-03 17:07 Rev.: 48920

ARCHES PETSc interface now supports PETSc v3.1, 3.2 and 3.3
API changes present in PETSc v3.1-->3.2 and v3.2-->3.3

27 lines of code changed in 4 files:

ahumphrey 2012-07-03 15:32 Rev.: 48919

Conditionally create PTX/CUBIN directory when configuring with CUDA.

12 lines of code changed in 1 file:

guilkey 2012-07-02 22:41 Rev.: 48918

Remove the endl's from the << operator. Introduce a prettyPrint function which
prints out the data in the same manner that the << operator used to.

12 lines of code changed in 2 files:

guilkey 2012-07-02 20:54 Rev.: 48917

Allow extraction of Matrix3 data.

5 lines of code changed in 1 file:

awabboud 2012-07-02 09:54 Rev.: 48916

Made reaction source term consistent with multi-environment model and cleaned up iterators

35 lines of code changed in 3 files:

June 2012 »

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