May 2017 Commit Log

Number of Commits:
76
Number of Active Developers:
14
allen 2017-05-31 18:17 Rev.: 56588

moved intialization out of the Visit ifdef

1 lines of code changed in 1 file:

allen 2017-05-31 17:20 Rev.: 56587

another rework for sim interface

20 lines of code changed in 2 files:

allen 2017-05-31 16:54 Rev.: 56586

slight rework for sim interface

4 lines of code changed in 1 file:

allen 2017-05-31 16:02 Rev.: 56585

slight rework for wasatch

27 lines of code changed in 3 files:

allen 2017-05-31 14:29 Rev.: 56584

to to record vars changes with the insitu I added an output and restart problem spec restart to the archiver. As a side affect I compartmentalized the setup in the sim controller

235 lines of code changed in 11 files:

jthornoc 2017-05-30 13:45 Rev.: 56583

Ensure that enthalpy is updated at the correct location when heat loss
is a parameter in the table.

Add some warnings to help guide the user.

100 lines of code changed in 8 files:

derekhar 2017-05-26 17:49 Rev.: 56582

Added Sweeps with partial spatial scheduling. Multi-box friendly implementation. Scattering physics are integrated. Reflections are not natively supported. No temporal scheduling supported.

2061 lines of code changed in 6 files:

bisaac 2017-05-26 11:59 Rev.: 56581

Removed clipping bug in FOWY, and gas-integration bugs that were making it so we couldn't run second-order. This commit will break pcoal_drag (second order), coal_RadPropsPlanck (second order), and partMassFlow (clipping).

6 lines of code changed in 10 files:

guilkey 2017-05-24 14:50 Rev.: 56578

Cleaning up some unused declarations.

1 lines of code changed in 1 file:

guilkey 2017-05-24 14:50 Rev.: 56577

Added a deviatoric elastic-perfectly plastic response to increase the stability
of the model in MPM. Deviatoric response is optional.

84 lines of code changed in 2 files:

guilkey 2017-05-24 13:34 Rev.: 56576

Whitespace

1 lines of code changed in 1 file:

jthornoc 2017-05-24 12:32 Rev.: 56573

For the variable_stats model: allow the single_variable or flux_variable
to specify if the current variable is a table lookup variable. This
alleviates the need of specifying the variable in the dataArchiver.

Also add a SCI_DEBUG in the TaskVariableTools class.

31 lines of code changed in 4 files:

ahumphrey 2017-05-24 11:39 Rev.: 56571

TaskLevel SCI_DEBUG flag is now dialed in.
Including OncePerProc tasks in printTaskLevels() method.

10 lines of code changed in 2 files:

ahumphrey 2017-05-24 11:16 Rev.: 56570

* Fix TaskDBG DebugStream (now a Dout object). The reporting is also safe for multi-rank and multi-thread output without locks
* Updated environmentalFlags.txt
* Added speciallized printTask() and printTaskLevels() back into DbgOutput.h/cc
* Converted a few more DebugStreams to Dout while under the hood
* Use C++11 auto keyword for type inference in a few places to clean things up

203 lines of code changed in 7 files:

harman 2017-05-24 10:43 Rev.: 56569

Minor correction.

1 lines of code changed in 1 file:

allen 2017-05-24 07:46 Rev.: 56568

fixed data ownership

51 lines of code changed in 3 files:

allen 2017-05-24 07:41 Rev.: 56567

removed the colon and active bit to where it is really needed

5 lines of code changed in 2 files:

jthornoc 2017-05-23 17:03 Rev.: 56566

Enable the addition of sources from the TurbulenceModelFactory to the
momentum solver.

Fix a bug in the KMomentum initialize (Oscar).

109 lines of code changed in 4 files:

bisaac 2017-05-23 14:53 Rev.: 56565

Now the thermal conductivity of the respecitve ash layers will be computed at the layers central average temperature. This commit also evaluates the t.c. upfront like the emissivity. This commit will change the answers for the 1GW_RT and 1GW_em_tc RT tests.

66 lines of code changed in 3 files:

harman 2017-05-22 17:10 Rev.: 56562

For RT machine added --with-mpi=/usr/ to configure command.

7 lines of code changed in 1 file:

dav 2017-05-22 16:32 Rev.: 56561

M configure
M configure.ac

- Check to make sure the user has specified the use of MPI. When configuring, the user must now
explicitly either specify --with-mpi=dir (or --with-mpi-include/lib), or use --with-mpi=built-in.
- Add in compiler spam reduction flag for Intel compiler remarks.

M StandAlone/sus.cc

- Cosmetic: Add in a code comment.

1 lines of code changed in 1 file:

bisaac 2017-05-22 15:35 Rev.: 56560

Added ash fusion temperatures to ParticleProperties. This shouldn't impact regression tests.

58 lines of code changed in 4 files:

dav 2017-05-22 15:33 Rev.: 56559


M CCA/Components/FVM/GaussSolve.cc

- Only real change: Fix Mac compilation by changing "0" to "nullptr".
- Cosmetics: line up variables, coding standards.

36 lines of code changed in 1 file:

dav 2017-05-22 15:20 Rev.: 56558

Remove the unused (and unnecessary/confusing) copy constructor that had propagated via cut and paste for Todd and Jim.

M CCA/Components/MPM/ConstitutiveModel/ArenaSoilBanerjeeBrannon/ArenaPartiallySaturated.cc
M CCA/Components/MPM/ConstitutiveModel/ArenaSoilBanerjeeBrannon/ArenaPartiallySaturated.h
M CCA/Components/MPM/ConstitutiveModel/Arenisca.cc
M CCA/Components/MPM/ConstitutiveModel/Arenisca.h
M CCA/Components/MPM/ConstitutiveModel/Arenisca3.cc
M CCA/Components/MPM/ConstitutiveModel/Arenisca3.h
M CCA/Components/MPM/ConstitutiveModel/Arenisca4.cc
M CCA/Components/MPM/ConstitutiveModel/Arenisca4.h
M CCA/Components/MPM/ConstitutiveModel/CNH_MMS.cc
M CCA/Components/MPM/ConstitutiveModel/CNH_MMS.h
M CCA/Components/MPM/ConstitutiveModel/CompMooneyRivlin.cc
M CCA/Components/MPM/ConstitutiveModel/CompMooneyRivlin.h
M CCA/Components/MPM/ConstitutiveModel/ConstitutiveModel.cc
M CCA/Components/MPM/ConstitutiveModel/ConstitutiveModel.h
M CCA/Components/MPM/ConstitutiveModel/Diamm.cc
M CCA/Components/MPM/ConstitutiveModel/Diamm.h
M CCA/Components/MPM/ConstitutiveModel/ElasticPlasticHP.cc
M CCA/Components/MPM/ConstitutiveModel/ElasticPlasticHP.h
M CCA/Components/MPM/ConstitutiveModel/HypoElastic.cc
M CCA/Components/MPM/ConstitutiveModel/HypoElastic.h
M CCA/Components/MPM/ConstitutiveModel/HypoElasticFortran.cc
M CCA/Components/MPM/ConstitutiveModel/HypoElasticFortran.h
M CCA/Components/MPM/ConstitutiveModel/HypoElasticImplicit.cc
M CCA/Components/MPM/ConstitutiveModel/HypoElasticImplicit.h
M CCA/Components/MPM/ConstitutiveModel/IdealGasMP.cc
M CCA/Components/MPM/ConstitutiveModel/IdealGasMP.h
M CCA/Components/MPM/ConstitutiveModel/JWLppMPM.cc
M CCA/Components/MPM/ConstitutiveModel/JWLppMPM.h
M CCA/Components/MPM/ConstitutiveModel/Kayenta.cc
M CCA/Components/MPM/ConstitutiveModel/Kayenta.h
M CCA/Components/MPM/ConstitutiveModel/MWViscoElastic.cc
M CCA/Components/MPM/ConstitutiveModel/MWViscoElastic.h
M CCA/Components/MPM/ConstitutiveModel/MurnaghanMPM.cc
M CCA/Components/MPM/ConstitutiveModel/MurnaghanMPM.h
M CCA/Components/MPM/ConstitutiveModel/NonLocalDruckerPrager.cc
M CCA/Components/MPM/ConstitutiveModel/NonLocalDruckerPrager.h
M CCA/Components/MPM/ConstitutiveModel/P_Alpha.cc
M CCA/Components/MPM/ConstitutiveModel/P_Alpha.h
M CCA/Components/MPM/ConstitutiveModel/PortableTongeRamesh/TongeRameshPTR.cc
M CCA/Components/MPM/ConstitutiveModel/PortableTongeRamesh/TongeRameshPTR.h
M CCA/Components/MPM/ConstitutiveModel/ProgramBurn.cc
M CCA/Components/MPM/ConstitutiveModel/ProgramBurn.h
M CCA/Components/MPM/ConstitutiveModel/RFElasticPlastic.cc
M CCA/Components/MPM/ConstitutiveModel/RFElasticPlastic.h
M CCA/Components/MPM/ConstitutiveModel/RigidMaterial.cc
M CCA/Components/MPM/ConstitutiveModel/RigidMaterial.h
M CCA/Components/MPM/ConstitutiveModel/ShellMaterial.cc
M CCA/Components/MPM/ConstitutiveModel/ShellMaterial.h
M CCA/Components/MPM/ConstitutiveModel/SoilFoam.cc
M CCA/Components/MPM/ConstitutiveModel/SoilFoam.h
M CCA/Components/MPM/ConstitutiveModel/TH_Water.cc
M CCA/Components/MPM/ConstitutiveModel/TH_Water.h
M CCA/Components/MPM/ConstitutiveModel/TransIsoHyper.cc
M CCA/Components/MPM/ConstitutiveModel/TransIsoHyper.h
M CCA/Components/MPM/ConstitutiveModel/TransIsoHyperImplicit.cc
M CCA/Components/MPM/ConstitutiveModel/TransIsoHyperImplicit.h
M CCA/Components/MPM/ConstitutiveModel/UCNH.h
M CCA/Components/MPM/ConstitutiveModel/ViscoPlastic.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoPlastic.h
M CCA/Components/MPM/ConstitutiveModel/ViscoSCRAMHotSpot.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoSCRAMHotSpot.h
M CCA/Components/MPM/ConstitutiveModel/ViscoScram.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoScram.h
M CCA/Components/MPM/ConstitutiveModel/ViscoScramImplicit.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoScramImplicit.h
M CCA/Components/MPM/ConstitutiveModel/ViscoTransIsoHyper.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoTransIsoHyper.h
M CCA/Components/MPM/ConstitutiveModel/ViscoTransIsoHyperImplicit.cc
M CCA/Components/MPM/ConstitutiveModel/ViscoTransIsoHyperImplicit.h
M CCA/Components/MPM/ConstitutiveModel/Water.cc
M CCA/Components/MPM/ConstitutiveModel/Water.h

63 lines of code changed in 73 files:

milo 2017-05-22 12:13 Rev.: 56557

Modified regression coefficients for Illinois No6. This shouldn't impact regression tests

9 lines of code changed in 1 file:

harman 2017-05-19 17:12 Rev.: 56556

Wrap timer code with #ifdef USE_TIMER so wasatch test will pass. Stop gap measure.

23 lines of code changed in 1 file:

dav 2017-05-19 14:47 Rev.: 56555


M build_scripts/so_epilogue.mk
M configVars.mk.in

Revert previous commit.


7 lines of code changed in 3 files:

dav 2017-05-19 14:20 Rev.: 56554


The SOFLAGS make variable was redundant with the LDFLAGS make var. It also
was not used everywhere that it was needed. So put the SOFLAGS info into
the LDFLAGS var. This should fix Todd's build on microslip.

M build_scripts/so_epilogue.mk
M configVars.mk.in

6 lines of code changed in 2 files:

cam 2017-05-19 13:57 Rev.: 56553

update pidx build to be more efficient

0 lines of code changed in 2 files:

dav 2017-05-19 13:49 Rev.: 56552

Few minor mostly cosmetic fixes. Should not effect Rt.


M AMRSimulationController.cc

- Removed unused variable.

M SimulationController.h
M SimulationController.cc

- Renamed 'd_archive' to 'd_restart_archive' as that is what it is and is only used for restarting.

142 lines of code changed in 3 files:

milo 2017-05-18 18:25 Rev.: 56551

Added Illinois No 6 to the coal-ash database. This shouldn't impact regression tests

18 lines of code changed in 1 file:

dav 2017-05-18 17:55 Rev.: 56550

Add in the --enable-pidx flag which will automatically build the PIDX I/O library for you.

M configure

- Place the bullet proofing (enable_option_checking=fatal) back at the top of the configure script.

M configure.ac

- Added --enable-pidx
- Validates that only --enable-pidx or --wiht-pidx=DIR is used.
- Enable PIDX needs CMake so validate CMake in this case.
- Use Cameron's script to build PIDX locally.

AM build_scripts/build_pidx.sh

- Initial commit of script for auto-downloading/building PIDX for Uintah (original draft provided by Cameron).

84 lines of code changed in 1 file:

harman 2017-05-18 17:27 Rev.: 56549

rayTrace()
- added computes/modifies for PPTimerLabel.


9 lines of code changed in 1 file:

allen 2017-05-18 16:53 Rev.: 56548

update the in-situ for per patch data and the new strip chart interface

483 lines of code changed in 8 files:

allen 2017-05-18 12:16 Rev.: 56546

removed testing comments for per patch timing and added in var and dbg to the in-situ

46 lines of code changed in 2 files:

allen 2017-05-17 18:13 Rev.: 56544

added test code for per patch timing and updated the timers

113 lines of code changed in 2 files:

dav 2017-05-17 16:08 Rev.: 56543


M Makefile.in

Fix type for removing dependency (.d) files. Needed ".d" and not just "d".


1 lines of code changed in 1 file:

jthornoc 2017-05-17 16:04 Rev.: 56542

Adding a separate Re limit for wall_upwind vs hybrid scheme for
momentum to avoid confusion. Updated documentation in the
arches_spec.xml.

24 lines of code changed in 4 files:

dav 2017-05-16 17:21 Rev.: 56541



Previously we used a VarHashMap to keep track on our variables and
where they were located in the DataArchive (UDA) files on
disk. However, as it was a hash map, there was no prescribed order to
how the variables were stored in that map. When using PIDX, the
variables must be read and written in exactly the same order. To
solve this problem, instead of hashing, I have just created a vector
to hold this data. The change is fairly straightforward, and Todd and
Sid have tested this, and my own local RT over ICE works, so I am
fairly certaint that this will not break the RT.

However, I have not analyzed how often this code is actually called
during a simulation and there could be some performance issues.
Though I don't think this should be the case, I am leaving this note
in the commit log in case someone sees an issue in the future
hopefully it will make it easier to track down. The performance issue
would come from the fact that instead of pulling a variable directly
out of the hash map [O(1)], we now have to search the vector [O(n)]
for it. If this is shown to be an issue, we will need to rethink how
to solve the two issues (savinging in a defined order - while not
having to linearly search the vector). -Dav


39 lines of code changed in 2 files:

harman 2017-05-16 13:25 Rev.: 56540

Use the version of python in the user's environment, not /usr/bin/python.

2 lines of code changed in 3 files:

jsutherland 2017-05-16 11:12 Rev.: 56539

Update NSCBC again.

1 lines of code changed in 1 file:

jthornoc 2017-05-16 10:21 Rev.: 56537

Fix the grid coordinates for cases when the domain does not start at
zero.

27 lines of code changed in 1 file:

jsutherland 2017-05-16 10:13 Rev.: 56536

1. Update git hash for NSCBC. This allows all NSCBC expressions to be run on GPU.
2. A few minor modifications to get past error trapping on new Mac compilers.

9 lines of code changed in 8 files:

allen 2017-05-15 17:07 Rev.: 56534

remove passing the tiemstep

5 lines of code changed in 1 file:

allen 2017-05-15 17:01 Rev.: 56533

added check for when one has pidx but not using it

2 lines of code changed in 1 file:

allen 2017-05-15 16:42 Rev.: 56532

added the ability to see PerPatch vars in-situ

149 lines of code changed in 3 files:

allen 2017-05-15 16:38 Rev.: 56531

added finer grained timing for IO and addded Dout to the in-situ

552 lines of code changed in 11 files:

allen 2017-05-15 16:37 Rev.: 56530

type change tounsigned

4 lines of code changed in 1 file:

jthornoc 2017-05-15 16:27 Rev.: 56529

Buffer the intrusion/patch deletion by one cell so as not to clip out
intrusion inlets that are on the face of patches.

4 lines of code changed in 1 file:

allen 2017-05-15 16:20 Rev.: 56527

added get/set methods for the active state

2 lines of code changed in 1 file:

cgritton 2017-05-15 16:19 Rev.: 56526

Skeleton code for the modified poisson nerst-planck finite volume solver

272 lines of code changed in 4 files:

guilkey 2017-05-15 16:10 Rev.: 56525

Removing debugging spew.

0 lines of code changed in 1 file:

guilkey 2017-05-15 16:06 Rev.: 56524

Remove spew from GeometryObject.h.

Stop created d_planes in the TriGeometryPiece by default. This code can be
re-enabled using an ifdef, but it doesn't seem to be getting used and adds
significantly to the memory overhead.

19 lines of code changed in 3 files:

bisaac 2017-05-15 15:17 Rev.: 56523

Added Proc0 statement when using in-situ vis. This shouldn't impact regression tests.

1 lines of code changed in 1 file:

allen 2017-05-15 15:12 Rev.: 56522

changed defaults to be zero so then ignored

52 lines of code changed in 2 files:

bisaac 2017-05-15 14:42 Rev.: 56521

Finished fixing syntax for sharedState when called with getVisIt. Shouldn't impact regression tests.

2 lines of code changed in 1 file:

cgritton 2017-05-15 14:04 Rev.: 56520

Added variables to compute gradients for both positively and negatively charged concentrations.

91 lines of code changed in 7 files:

ahumphrey 2017-05-15 13:16 Rev.: 56519

Fix segfault in GPU-builds.
Previous changes to UnifiedScheduler::myRankThread() did not consider master thread, which was a case when called from the GPUDW.

1 lines of code changed in 1 file:

ahumphrey 2017-05-15 11:23 Rev.: 56518

Add a skeleton KokkosOpenMPScheduler. Need to plug in the OMP 4.0 paritioning management handled by Kokkos, though it curretnly works in single-thread mode. This sched is turned on by explicit request in input file combined with "-do_not_validate". Will make this scheduler option part of the UPS spec once things are working completely.

Cleaned up some unused thread-related args in postMPISends(), and runTask(), no longer necessary.

605 lines of code changed in 9 files:

guilkey 2017-05-15 09:45 Rev.: 56517

Spew in the GeometryObject destructor.
Clear the vectors in the TriGeometryPiece destructor.

10 lines of code changed in 2 files:

guilkey 2017-05-15 09:43 Rev.: 56516

Debugging spew in in geometry object deletion.

2 lines of code changed in 1 file:

allen 2017-05-12 16:17 Rev.: 56515

added changes for in-situ Visit to have state access

5 lines of code changed in 3 files:

derekhar 2017-05-12 14:46 Rev.: 56514

Repair regression tests from over stripping code in commit #56509.

2 lines of code changed in 1 file:

bisaac 2017-05-12 14:27 Rev.: 56513

Added the ability to change the Re_limit when using insitu vis. This will not impact regression tests.

23 lines of code changed in 1 file:

dav 2017-05-11 17:12 Rev.: 56512


- Fixes by Sid (with some help from Dav)

* Update to create individual MPI_Comms for use by PIDX.
* Update to newest PIDX API.

* Minor formatting, variable alignment for readability. Remove tabs.
* Pass strings as const references (&) to avoid copy.

M CCA/Components/DataArchiver/DataArchiver.cc
M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/SimulationController/AMRSimulationController.cc
M CCA/Ports/PIDXOutputContext.cc
M CCA/Ports/PIDXOutputContext.h
M Core/DataArchive/DataArchive.cc
M Core/DataArchive/sub.mk

167 lines of code changed in 10 files:

guilkey 2017-05-11 14:18 Rev.: 56511

Add a missing requires for the new computeNormals code.

1 lines of code changed in 1 file:

guilkey 2017-05-11 13:29 Rev.: 56510

Create the ability to delete geometry objects after particle creation. Helpful
when geometry objects are enormous triangulated surfaces.

54 lines of code changed in 7 files:

derekhar 2017-05-10 17:04 Rev.: 56509

Clean-up of early functor/kokkos work that was reformulated.

0 lines of code changed in 2 files:

jas 2017-05-09 09:21 Rev.: 56508

Update to Uintah 2.0. Remove --sysroot for MacOSX when trying to detect if boost is available.

374 lines of code changed in 4 files:

guilkey 2017-05-08 14:25 Rev.: 56506

Get ghost particles for use in computing surface normals.

2 lines of code changed in 1 file:

jthornoc 2017-05-08 11:45 Rev.: 56505

Bug fix.

2 lines of code changed in 1 file:

jthornoc 2017-05-08 11:14 Rev.: 56504

Fix an indexing error.

1 lines of code changed in 1 file:

guilkey 2017-05-05 22:38 Rev.: 56499

Add scheduling of computeNormals to MPMICE.

3 lines of code changed in 1 file:

guilkey 2017-05-05 22:31 Rev.: 56498

Adding a ocuple of deletes to address the memory failures.

4 lines of code changed in 1 file:

guilkey 2017-05-04 20:08 Rev.: 56494

Pull calculation of normal, used in several contact models, out of the
contact models into a common place. This will enable more flexibility
going forward, like using different friction coefficients between matl 1 and 2 than between 1 and 3, etc.

263 lines of code changed in 14 files:

bpeterson 2017-05-03 23:12 Rev.: 56493

Just fixing a misspelling
wq!

2 lines of code changed in 1 file:

April 2017 »

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