May 2014 Commit Log

Number of Commits:
100
Number of Active Developers:
12
harman 2014-05-30 16:48 Rev.: 51906

Pulled weeds, removed the variable _label_sched_init. It's no longer needed.

22 lines of code changed in 38 files:

awabboud 2014-05-30 10:38 Rev.: 51904

Fix the indexing of this variable

1 lines of code changed in 1 file:

harman 2014-05-30 09:35 Rev.: 51903

- added ups validation spec for new regridder.

- added comments
removed debugging code
minor simplifications.

29 lines of code changed in 3 files:

jsutherland 2014-05-30 08:12 Rev.: 51902

Revert "- modify interface for get_memory_window_for_uintah_field"

This reverts commit a37efda43a440a272ecaff236298d60b15b8870f.

195 lines of code changed in 2 files:

jsutherland 2014-05-30 06:50 Rev.: 51901

- modify interface for get_memory_window_for_uintah_field
- move some template specializations & implementations to the .cc file rather than the header and addi appropriate explicit instantiations.

252 lines of code changed in 2 files:

jsutherland 2014-05-30 06:20 Rev.: 51900

Get Warches compiling again.

7 lines of code changed in 1 file:

jsutherland 2014-05-30 05:59 Rev.: 51899

Remove another superfluous "typename"

1 lines of code changed in 1 file:

jsutherland 2014-05-29 19:07 Rev.: 51898

Fix a missing template.

1 lines of code changed in 1 file:

jsutherland 2014-05-29 18:59 Rev.: 51897

remove a few more superfluous "typename" declarations.

4 lines of code changed in 1 file:

jsutherland 2014-05-29 18:43 Rev.: 51896

- Remove an extra "typename" that makes some compilers barf.
- Use consistent inferred type in particle field wrapper.

5 lines of code changed in 1 file:

harman 2014-05-29 16:12 Rev.: 51895

Initial commit of a new regridder that allows
the user to change the patch layout on a single level. This is needed
if you want to increase the number of procs used on a restart

Status: 75% complete. It works on a small Arches simulation. More testing
and polish is needed.

289 lines of code changed in 4 files:

jsutherland 2014-05-29 15:24 Rev.: 51893

Preliminary work to get support for particles in ExprLib and SpatialOps working with Wasatch.

148 lines of code changed in 8 files:

jsutherland 2014-05-29 11:08 Rev.: 51891

Revert "silence hundreds of warnings."

This reverts commit 60418b8c811e6b9dc6dbb0f4249b6acc799db645.

0 lines of code changed in 2 files:

jsutherland 2014-05-29 10:13 Rev.: 51890

remove an argument supplied to variable creation that was a bit confusing and unnecessary.

13 lines of code changed in 6 files:

jsutherland 2014-05-29 10:13 Rev.: 51889

minor formatting changes

71 lines of code changed in 2 files:

jsutherland 2014-05-29 10:13 Rev.: 51888

silence hundreds of warnings.

22 lines of code changed in 1 file:

harman 2014-05-29 07:50 Rev.: 51887

Added the ability to regrid only once. This mechanism will be used
to regrid on a single level restart.

RegridderCommon.cc
problemSetup_Bulletproofing()
- removed maxLevel > 1 test

SchedulersCommon.cc
scheduleAndDoDataCopy()
- verify that when reduction variables are copied to the new_dw they are actually reduction vars.
Previously, SoleVariables were included in this copy.

AMRSimulationController.cc
run()
- added code to regrid once if specified.

Usage:
<AMR>
<Regridder type="Tiled">
<regrid_once> true </regrid_once>
</Regridder>
</AMR>

50 lines of code changed in 3 files:

dav 2014-05-28 16:03 Rev.: 51886

IO depends on Exceptions now, so for static builds IO must be listed before Exceptions.

1 lines of code changed in 1 file:

dav 2014-05-28 15:34 Rev.: 51885

The following commits are mostly cosmetic in nature and should not
change any answers.

Lots of white space and indentation fixes. It is so much easier to
read code when variables are lined up, and values assigned to them
are also lined up.

M CCA/Components/Parent/Switcher.cc

- Variable "no_solver_specified" was misleading. It meant "no command
line solver specified". However, this is the default case and thus
this variable is not needed.

M CCA/Components/Wasatch/Expressions/EmbeddedGeometry/EmbeddedGeometryHelper.h

- InvalidState exception moved to Uintah namespace.

M CCA/Components/Solvers/AMR/AMRSolver.h

- Parent scheduleInitialize() is purely virtual so must be implemented
in each solver. This allows the user to more easily see whether the
scheduleInitialize() step actually does anything or not.

M CCA/Components/Solvers/HypreSolver.cc

- 'firstPassThrough_' is a class variable so needs the '_' suffix to
meet coding standard.

M CCA/Components/Solvers/SolverFactory.cc
M CCA/Components/Solvers/DirectSolve.cc
M CCA/Components/Solvers/HypreSolver.h
M CCA/Components/Solvers/SolverFactory.h
M CCA/Components/Solvers/DirectSolve.h
M CCA/Components/Solvers/CGSolver.h

- Indentation.
- Added (empty) scheduleInitialize() to Solvers that
require it to be implemented but do not actually use it.

M CCA/Ports/SolverInterface.h

- Moved destructor/constructor empty implementations into .h file for
easier viewing.
- Indentation / white space.

M CCA/Ports/SolverInterface.cc

- This file is empty now so should most likely be removed soon.

M CCA/Components/Arches/ChemMix/ClassicTableInterface.cc

- Throw exception if gzipInflate fails (previously it tried to just
kept going and the error was thus hard to find).

M CCA/Ports/sub.mk

- Don't need to compile empty file SolverInterface.cc now.

M Core/Exceptions/ErrnoException.h
M Core/Exceptions/ErrnoException.cc

- Change var name from errno_ to err_ as it might be easy to confuse "errno_" with "errno".

M Core/Exceptions/sub.mk

- Alphabetize list of libraries.

M Core/Exceptions/InvalidValue.cc

- Don't need superfluous "using std::cout".

M Core/Exceptions/InvalidState.cc
M Core/Exceptions/InvalidState.h

- Moved from SCIRun namespace to Uintah for two reasons:
1) SCIRun namespace will eventually go away.
2) InvalidState exception is already in Uintah namespace and these should be consistent.

M Core/IO/sub.mk

- IO now relies on Exception as the UintahZlibUtil now throws an exception if an error occurs.

M Core/IO/UintahZlibUtil.h

- White space / indentation.
- Add comment about what gzipInflate returns.

M Core/IO/UintahZlibUtil.cc

- Throw an exception when an error occurs instead of just return 0, as
the 0 is never checked and causes debugging to be more difficult.

M StandAlone/sus.cc

- Indent / white space.
- Print out which solver is being used.

395 lines of code changed in 42 files:

harman 2014-05-28 14:31 Rev.: 51883

Dusting off old comparison scripts

0 lines of code changed in 4 files:

awabboud 2014-05-28 08:58 Rev.: 51881

Disabling CQMOM tests for now. Run fine on OSX but not Linux. Re-enable after this is fixed.

4 lines of code changed in 1 file:

harman 2014-05-27 17:03 Rev.: 51880

helper functions that will be needed to regrid level 0

14 lines of code changed in 3 files:

harman 2014-05-27 16:24 Rev.: 51879

Prep work for a much bigger commit comming.

Added stub functions to utilize AMR regridder to reconfigure the coarse level
patches on a restart.


14 lines of code changed in 2 files:

awabboud 2014-05-27 15:34 Rev.: 51878

Change the capatilization of the RT

4 lines of code changed in 1 file:

awabboud 2014-05-27 14:52 Rev.: 51877

Actually add the CQMOM input files to the regression tests.

4 lines of code changed in 1 file:

jthornoc 2014-05-27 10:11 Rev.: 51874

Revert "Choose the correct sign for the presure head based on which way is up."

This reverts commit f51638c8fdb1a01199e1fdd0ec9c079f9970716d.

0 lines of code changed in 24 files:

kamojjala 2014-05-26 11:49 Rev.: 51873

Updated the Uintah wrappers to be consistent with the latest F90 Kayenta Code

0 lines of code changed in 6 files:

harman 2014-05-23 16:51 Rev.: 51872

dust off. Also copy non-timestep directories.

0 lines of code changed in 2 files:

derekhar 2014-05-23 12:00 Rev.: 51871

This commit adds a regresssion test for the radiation model DOM16. This test simply evaulates radiative fluxes within a stagnant rectangular domain with one hot surface. The gas absorption coefficients are all set to zero.

2 lines of code changed in 1 file:

ahumphrey 2014-05-22 22:54 Rev.: 51870

Revert commit 51850 until Mira DDT problem is debugged.

101 lines of code changed in 4 files:

jthornoc 2014-05-22 20:57 Rev.: 51869

Choose the correct sign for the presure head based on which way is up.

48 lines of code changed in 12 files:

harman 2014-05-22 16:34 Rev.: 51868

added sqrt() to variance calc. -Arash

0 lines of code changed in 2 files:

tsaad 2014-05-22 14:16 Rev.: 51867

forgot to commit this

1 lines of code changed in 1 file:

tsaad 2014-05-22 14:15 Rev.: 51866

more documentation and cleanup

12 lines of code changed in 5 files:

tsaad 2014-05-22 13:09 Rev.: 51865

remove the scalar performance test for now. Will turn it back on when the new RT machine is in.

1 lines of code changed in 1 file:

qymeng 2014-05-22 13:01 Rev.: 51864

When a reduction variable being computed by multiple tasks,
schedule the reduction task after the very last task that computes this variable.

27 lines of code changed in 5 files:

tsaad 2014-05-22 12:45 Rev.: 51863

minor cleanup

2 lines of code changed in 1 file:

tsaad 2014-05-22 12:15 Rev.: 51862

remove obsolete map from BCHelper. Document BoundaryConditionBase

78 lines of code changed in 2 files:

derekhar 2014-05-21 16:48 Rev.: 51860

Added functionality for DOM radiation model to handel up to 16 ordinates. The current number of ordinates supported are now 2, 4, 6, 8, and 16. The code will also throw and error if ordinates outside of these discrete values is called.

0 lines of code changed in 2 files:

dav 2014-05-21 16:42 Rev.: 51859


Finish fix/cleanup of code to use the correct underscore version of
some Fortran routines.

M CCA/Components/MPM/ConstitutiveModel/fortran/MIGUtils.cc
M CCA/Components/Arches/CQMOMInversion.h

- FIX_NAME macro (in previous commit) was moved to include/sci_defs/uintah_defs.h.

M CCA/Components/Arches/TransportEqns/EqnBase.h
M CCA/Components/Arches/Arches.cc

- Use proc0cout instead of cout to minimize spew.

M Core/Math/sci_lapack.cc

- Removed tabs.
- FIX_NAME macro (in previous commit) was moved to include/sci_defs/uintah_defs.h.

28 lines of code changed in 7 files:

dav 2014-05-21 16:19 Rev.: 51858

Need to make sure the dsyev routine uses the appropriate underscore convention...

28 lines of code changed in 3 files:

awabboud 2014-05-21 13:01 Rev.: 51857

Change the input file to CQMOM to get ready for velocity internal coordinates.

40 lines of code changed in 4 files:

tsaad 2014-05-20 19:48 Rev.: 51856

update a few incorrect comments

10 lines of code changed in 1 file:

guilkey 2014-05-20 14:23 Rev.: 51855

Set pLocalized_new to -999 if you want to have the particle deleted.

1 lines of code changed in 1 file:

jsutherland 2014-05-20 08:06 Rev.: 51854

minor formatting changes.

20 lines of code changed in 2 files:

awabboud 2014-05-19 10:11 Rev.: 51853

Add in the preliminary code for CQMOM particles in Arches. Currently this only works for 2 or 3 internal coordinates which are passive scalars. Todo: addition of soruce terms, convective flux for kinetic equations, expansion to N number of internal coordinates, regression tests.

2390 lines of code changed in 16 files:

ahumphrey 2014-05-16 23:44 Rev.: 51852

Finish stripping out Windows support.
Also update UPS_Spec from previous commit.

41 lines of code changed in 29 files:

ahumphrey 2014-05-16 23:02 Rev.: 51851

Remove some obsolete GPU-related input files, etc.

0 lines of code changed in 1 file:

ahumphrey 2014-05-16 22:04 Rev.: 51850

Add per level suppport for maxGhostCells and maxLevelOffset. These are the horizontal and vertical ranges considered by the loadbalancer when creating a neighborhood.

68 lines of code changed in 4 files:

jsutherland 2014-05-16 16:31 Rev.: 51849

Just some minor formatting changes.

58 lines of code changed in 4 files:

dav 2014-05-16 14:20 Rev.: 51848


M configure
M configure.ac

Added '--with-math=' to allow specificiation of math library.
Currently this is only used on Vulcan. (Without this configure flag,
-lm will be used.) This replaces the hard coded path to the math
library for BGQ machines that was previously in configure.

74 lines of code changed in 2 files:

tsaad 2014-05-16 13:01 Rev.: 51847

Add more clarification for an error related to boundary conditions specification in Uintah.

1 lines of code changed in 1 file:

qymeng 2014-05-16 10:16 Rev.: 51845

remove reduction task map

0 lines of code changed in 3 files:

ahumphrey 2014-05-15 15:03 Rev.: 51844

Excise last bits of Windows support from src/testprograms

7 lines of code changed in 19 files:

dav 2014-05-15 14:47 Rev.: 51843

Fix typo from previous commit in removal of WIN stuff...

1 lines of code changed in 1 file:

dav 2014-05-15 14:29 Rev.: 51842

Fix check for boost filesystem v3 namespace (displayed on Vulcan).

6 lines of code changed in 2 files:

ahumphrey 2014-05-15 14:28 Rev.: 51841

Excise last bits of Windows support from:
* src/Teem
* src/Visit
* src/StandAlone

3 lines of code changed in 14 files:

ahumphrey 2014-05-15 14:21 Rev.: 51840

Excise last bits of Windows support from src/CCA

31 lines of code changed in 15 files:

jthornoc 2014-05-14 21:29 Rev.: 51838

Missed a function re-def.

0 lines of code changed in 2 files:

jthornoc 2014-05-14 20:48 Rev.: 51837

Getting rid of the density reference reduction variable in favor of the
density reference array. Since the reference density is being computed
once at startup, there was no need to carry around the extra label
anymore.

167 lines of code changed in 19 files:

qymeng 2014-05-14 12:36 Rev.: 51836

restrict to use only one thread for the first timestep
We should treat restart and init timestep separately in the future,
so that init timestep can use multi-thread while restart timestep use only one thread.

6 lines of code changed in 2 files:

jsutherland 2014-05-14 07:13 Rev.: 51835

Fix an improper header inclusion guard

0 lines of code changed in 2 files:

ahumphrey 2014-05-12 11:38 Rev.: 51833

Excise Windows support from build system.
Also delete MS Visual Studio related files.
Generate new configure script.

29 lines of code changed in 8 files:

wyxpuma 2014-05-12 09:16 Rev.: 51832

to fix the drag force balance

3 lines of code changed in 3 files:

ahumphrey 2014-05-12 08:39 Rev.: 51831

Excise Windows support in Core/Thread and sus.cc
Some formattig and { }

593 lines of code changed in 38 files:

ahumphrey 2014-05-11 22:01 Rev.: 51830

Excise Windows support in Core/Util
Some formattig and { }

266 lines of code changed in 39 files:

tsaad 2014-05-11 07:41 Rev.: 51829

Update the ReadFromFile expression to use a more robust test based on dx/2 to check if a point (x,y,z) is in the current patch or not.

37 lines of code changed in 1 file:

jsutherland 2014-05-10 19:44 Rev.: 51828

Revert "Make SetCurrentTime expression GPU runnable since it uses nebo syntax."

This reverts commit 28e319bc9e5a6a383579955cc703377f77ce8ae5.

0 lines of code changed in 1 file:

jsutherland 2014-05-10 13:05 Rev.: 51827

Make SetCurrentTime expression GPU runnable since it uses nebo syntax.

2 lines of code changed in 1 file:

tsaad 2014-05-09 14:21 Rev.: 51826

disallow adding auxiliary boundary conditions with functors. this is to avoid the issue of common dependencies across all patches.

1 lines of code changed in 2 files:

tsaad 2014-05-09 12:45 Rev.: 51825

Add a new interface to the TimeAdvance expression that allows us to use it with estimators (i.e. specify phi_old instead of inferring it directly). Cleanup the TimeStepper by removing some obsolete sets. Rename a function.

62 lines of code changed in 7 files:

harman 2014-05-09 09:02 Rev.: 51824

Removed unnecessary calls to:

sched->overrideVariableBehavior(hypre_solver_label.....)

You only need to overide the behavior once in the solver component, unless
you're using a subscheduler. In ICE, which uses a subscheduler, you have to override
using the parent scheduler.

* should not change the answers.


5 lines of code changed in 7 files:

harman 2014-05-08 16:52 Rev.: 51823

Turned off in-flight compression. This bumped up the transter rate by 50% on 16 threads

0 lines of code changed in 2 files:

harman 2014-05-08 16:35 Rev.: 51822

formatting for readability
-added {}
-added divider lines
-added vertical spaces.

287 lines of code changed in 1 file:

harman 2014-05-08 13:40 Rev.: 51821

Added chgrp to top directory.

0 lines of code changed in 2 files:

tsaad 2014-05-08 12:43 Rev.: 51820

repair Warches in light of recent changes in Wasatch

6 lines of code changed in 2 files:

tsaad 2014-05-08 10:14 Rev.: 51819

disallow specification of BCs on velocity estimates. Those are automatically inferred from the velocity field

14 lines of code changed in 2 files:

harman 2014-05-08 09:43 Rev.: 51818

removed scripts that are not being maintained.

pscp2: change the group on the transferred uda to the remote parent directory's group

One less step in the post processing routine.

23 lines of code changed in 5 files:

tsaad 2014-05-08 08:51 Rev.: 51817

Reduce the required specification for velocity and momentum boundary conditions on Velocity boundaries: only specify non-zero velocity and momentum components. if a velocity/momentum component is not specified in the input file, then set it to zero. This will reduce input file clutter by up to 66%. Also add a python script that will process input files for you to remove zero velocity and momentum BCs from your input files.

10 lines of code changed in 1 file:

tsaad 2014-05-08 06:58 Rev.: 51816

Forgot to commit these files. This should fix all the failing builds.

346 lines of code changed in 3 files:

tsaad 2014-05-08 06:40 Rev.: 51815

This is a significant refactor in Wasatch which introduces an Expression-based approach for time integration. This results in a cleaner implementation of our timeadvance task by placing it as a node on our DAG graphs. This also results in less Uintah tasks and will make it easy to apply complex boundary conditions on conserved variables based on primitive variables. For those who are using Wasatch, you will need to modify your input files. A new expression state has been introduced: STATE_DYNAMIC. The distinction is now as follows: STATE_N always points to the old datawarehouse, STATE_NONE always points to the new dw, and STATE_DYNAMIC will switch between old and new based on the Runge-Kutta stage. Please update your input files: all initial conditions should now be STATE_DYNAMIC. All source terms that depend on a transported scalar should also use STATE_DYNAMIC for that scalar.

185 lines of code changed in 18 files:

wyxpuma 2014-05-07 08:02 Rev.: 51813

to update the drag force

212 lines of code changed in 7 files:

dav 2014-05-07 01:41 Rev.: 51812

Fix the case where the user adds a superfluous trailing / to "/usr/" when
specifying the location of boost. This should fix the problem with
the nightly RT.

M configure.ac
M configure

- Strip trailing / from --with-boost DIR (if there is one.
- Remove invalid , from print statement.

M configVars.mk.in

- In some strange cases (usually on a Mac but could be anywhere),
the XML2_LIBRARY flag includes -lz which points to a different
libz then Uintah finds. If we place the Z_LIBRARY flag at the
beginning of the XML2_LIBRARY flag, this fixes the problems
(and thus we don't get half of Uintah linked vs line libz, and
the other half linked vs a different one.) Note, even without
this fix, the make system detects this problem and prints out
an error message.

M aclocal.m4

- Strip traling / as necessary from include directories.


114 lines of code changed in 4 files:

dav 2014-05-06 17:04 Rev.: 51811

Need to generate boost_defs.h regardless of whether boost is found.

4 lines of code changed in 2 files:

harman 2014-05-06 17:03 Rev.: 51810

Tweaking for boost configure check. Turns out that the mt lib version
check, if told to look in a non-standard place, in the mt libs do not
exist in the non-standard place, can find the mt libraries in the
standard location. Need to check for this and stop it from happening if
necessary.

M src/configure.ac
M src/configure

- Make sure the boost library is found in the requested location.

M src/StandAlone/tools/sub.mk
M src/StandAlone/tools/compare_mms/sub.mk

- A number of utility programs need to link vs Boost...


37 lines of code changed in 4 files:

harman 2014-05-06 16:27 Rev.: 51809


Fix for inconsistencies with the namespace boost uses for its
filesystem utilities. I had originally seen this on Vulcan, but have
duplicated it on Todd's Debian system Fin. On Fin there are two
versions of boost installed. While the both claim to be using the
boost filesystem version 3, only one of them actually uses the
namespace boost::filesystem3... The other, and the default on many
machines, is boost::filesystem.

I have added a test in configure to determine which namespace to use
and then updated the code to make the correct choice. I have tested
this on Fin, and will verify that it works on other systems after
this commit (in addition to letting the RT take a swing at it too).

- Dav


M src/configure.ac
M src/configure

- Remove the include dir with_boost/include/boost as the '/boost'
comes from the #include line.
- Added check for namespace boost::filesystem3.

M src/build_scripts/build_wasatch_3p.sh

- If boost in in the default /usr location, then don't use CMAKE boost
flags.

M src/include/sci_defs/boost_testdefs.h.in

- Add "#define UINTAH_BOOST_FILESYSTEM_NAMESPACE_V3 1" as necessary to this file.

M src/Core/OS/Dir_boost.cc

- #include sci_defs/boost_defs.h to determine which boost filesystem namespace to use.

494 lines of code changed in 6 files:

jsutherland 2014-05-06 12:56 Rev.: 51808

Pass boost location to ExprLib build system.

3 lines of code changed in 1 file:

jthornoc 2014-05-05 13:20 Rev.: 51807

Update to Arches Task Interface including:
* a task factory for automatic task creation and storage
* tasks now are required to have an initialization method
* creating an operator database/patch
* properly destroying local labels for tasks
* added a problemSetup interface for tasks

637 lines of code changed in 16 files:

jthornoc 2014-05-05 13:20 Rev.: 51806

Remove some more "using namespace" in header files.
Polish off the SpatialOps field interface. Should now work for CC and
Face doubles.
Also add a templated example task.

127 lines of code changed in 9 files:

jthornoc 2014-05-05 13:20 Rev.: 51805

Removing "using namespace SCIRun" in various Arches headers.

91 lines of code changed in 16 files:

jthornoc 2014-05-05 13:20 Rev.: 51804

Adding spatial fields as a capability.

227 lines of code changed in 7 files:

dav 2014-05-05 11:13 Rev.: 51803

Add missing test to validate --with-mkl directory.

16 lines of code changed in 2 files:

harman 2014-05-05 10:51 Rev.: 51802

Keep a copy of the sus output when updating performance tests.

Changed obnoxious all caps variables to lower case.


81 lines of code changed in 5 files:

tsaad 2014-05-01 22:03 Rev.: 51801

forgot to commit two files

119 lines of code changed in 2 files:

tsaad 2014-05-01 21:45 Rev.: 51800

change the scope of the TurbulenceModelsNames for more enum safety.

46 lines of code changed in 8 files:

tsaad 2014-05-01 17:26 Rev.: 51799

allow specification of the variable density model for drhodt through the input file. This will prevent errors when running the MMS cases where one may forget changing the model for alpha in the source terms. This also sets the stage for automated verification and convergence of the analytical and MMS solutions.

193 lines of code changed in 12 files:

awabboud 2014-05-01 13:43 Rev.: 51798

Add in the synthetic eddy tubrulent inlet method in the same standalone executable as the digital filter method.

0 lines of code changed in 2 files:

qymeng 2014-05-01 10:39 Rev.: 51796

fix hash map namspace issue

6 lines of code changed in 3 files:

qymeng 2014-05-01 10:08 Rev.: 51795

Removed many of datawarehouse locks by using atomic operations

401 lines of code changed in 19 files:

tsaad 2014-05-01 09:23 Rev.: 51794

rip out obsolete variable density code related to the 2D MMS

0 lines of code changed in 1 file:

April 2014 »

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