BoundaryConditions
(29 files, 5595 lines)
PatchBVH
(9 files, 821 lines)
Variables
(91 files, 12763 lines)
[root]/Core/Grid
BoundaryConditions
(29 files, 5595 lines)
PatchBVH
(9 files, 821 lines)
Variables
(91 files, 12763 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 205 (100.0%) | 6286 (100.0%) | 30.6 |
| tsaad | 14 (6.8%) | 2343 (37.3%) | 167.3 |
| dav | 37 (18.0%) | 1517 (24.1%) | 41.0 |
| leavy | 7 (3.4%) | 1104 (17.6%) | 157.7 |
| harman | 21 (10.2%) | 784 (12.5%) | 37.3 |
| ahumphrey | 9 (4.4%) | 256 (4.1%) | 28.4 |
| guilkey | 4 (2.0%) | 165 (2.6%) | 41.2 |
| jas | 108 (52.7%) | 76 (1.2%) | 0.7 |
| qymeng | 4 (2.0%) | 39 (0.6%) | 9.7 |
| jthornoc | 1 (0.5%) | 2 (0.0%) | 2.0 |
Reverting code to r52880 before my memory use fix commit. While most tests passed, the ones using AMR and the dynamic load balancer were not passing and the weeds are too deep within them to quickly figure out what is causing the problems. Next week I will attempt to figure out what is going on with them. My guess is that it will take quite a bit of effort to understand the inner workings of the dynamic loadbalancer in order to get everything to work, so it may be quite a while before this fix may go in.
476 lines of code changed in 20 files:
Finishing cleaning up the memory reduction commit... Main fix
was to add "delete d_archive" back to SimulationController.cc.
M CCA/Components/SimulationController/SimulationController.cc
- Add back in "delete d_archive"... This still needs to be investigated.
M CCA/Components/LoadBalancers/CostProfiler.cc
M CCA/Components/LoadBalancers/DynamicLoadBalancer.cc
- Remove warning: numLevels is unsigned now.
- Cosmetics: coding standard, white space, {}s, etc
M Core/Grid/Patch.cc
M CCA/Components/Schedulers/DWDatabase.h
M CCA/Components/Schedulers/MPIScheduler.cc
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Cosmetics: line up variables, untabify, coding standard, white space, {}s, etc
M CCA/Components/Schedulers/SchedulerCommon.cc
- Remove warning: numLevels is unsigned now.
27 lines of code changed in 1 file:
Hopefully this fixes errors from the previous larege memory use reduction commit.
M CCA/Components/SimulationController/SimulationController.cc
- I need to investigate the delete of the temporary data archive... Commenting it out for now.
M CCA/Components/DataArchiver/DataArchiver.cc
- White space clean up.
- Removed a releaseDocument() that should not have been there. (The release happens
automatically when the var goes out of scope.)
M Core/Grid/Grid.cc
- Handle periodic boundaries in the input xml file.
16 lines of code changed in 1 file:
This is the first commit (of what may be several over the next month or so) dealing with Uintah's excessive use
of memory with respect to its XML data structures (that are used for I/O) when running on thousands of patches.
This commit specificly addresses the excessive use of memory when restarting a simulation. Before this commit,
Uintah would read in a timestep.xml file (from the checkpoints/t00000/) directory and create an huge DOM
structure in memory. (On 8K patches on Vulcan (BGQ - LLNL) memory per process would increase by 100% (by
20 MB per process on the advect sample problem). On 30K patches, memory use of 200 MB or more has been observed.)
To solve this problem, instead of reading the XML into memory, we parse it on the fly and extract the data we need,
but do not save it. Note, there are two parts of the timestep.xml file that cause the memory issue: the 1000s of
<Grid> and <DataItem> tags. Small XML nodes are not a problem, and thus we still use them for some things (for
example, the component section read from the timestep.xml file. A full DOM of this node is created (during the
streaming read of the rest of the file) and this node is passed down to the component as before.
A number of changes in this commit are cosmetic, dealing with white space and coding standards, and were made
while I was digging through the code to understand where the memory issue was and how to fix it. To better
see real changes in the code, I highly suggest that you use a diff that ignores generic white space changes,
such as:
svn diff --diff-cmd diff --extensions -w <file_name>
Note,asIgetolderInolongercanreadtextlikethis,soIamaddingspacesintothecodetomakeit easier to see. :)
M CCA/Components/SimulationController/AMRSimulationController.cc
- Number of levels in a Grid (grid->numLevels()) cannot be negative and thus should be an unsigned int... it is now.
- Costmetic: English sentences start with capital letters and end with punctuation... yeah yeah I know.
M CCA/Components/SimulationController/SimulationController.cc
- queryGrid: pass through a pointer, don't create a new copy.
- Unsigned int for grid level number.
- Cosmetic white space/coding standards/English updates. Fixed some strange indentation. Untabify.
M CCA/Components/Parent/Switcher.cc
- Unsigned int for grid level number.
- Cosmetic: Swatted some evil endl's. :) (Why write 8 more characters of code, when 2 will do? And makes it easier to add to strings later...)
M CCA/Components/LoadBalancers/ParticleLoadBalancer.cc
M CCA/Components/LoadBalancers/ParticleLoadBalancer.h
- Updates to consolidate code in load balancers... Still needs some direct attention as opposed to this
first pass while working on something else.
M CCA/Components/LoadBalancers/SingleProcessorLoadBalancer.h
- Add 'do-nothing' implementation of restartInitialize() to this class.
M CCA/Components/LoadBalancers/CostModelForecaster.cc
- Cosmetic: Untabbify, white space, {} around one line ifs, English.
M CCA/Components/LoadBalancers/DynamicLoadBalancer.h
M CCA/Components/LoadBalancers/DynamicLoadBalancer.cc
- Moved restartInitialize() (and a number of supporting class d_ variables) into LoadBalancerCommon.
- Cosmetic: Line up variables, untabbify, white space, {} around one line ifs, English.
M CCA/Components/LoadBalancers/ProfileDriver.cc
M CCA/Components/LoadBalancers/CostModeler.h
- grid->numLevels() is now unsigned updates.
- Coding standard cleanups / English / white space.
M CCA/Components/LoadBalancers/LoadBalancerCommon.cc
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
- Make global DebugStream variables be less global (made static to file).
- Unsigned int for grid level number.
- Move restartInitialize() from DynamicLoadBalancer and ParticleLoadBalancer (code was exact duplicate in both files) here.
M CCA/Components/Solvers/AMR/AMRSolver.cc
- Cosmetic: White space, line up variables, English.
- Unsigned int for grid level number.
M CCA/Components/DataArchiver/DataArchiver.cc
M CCA/Components/DataArchiver/DataArchiver.h
- Comment added for where next XML memory fix should take place.
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
M CCA/Ports/ProblemSpecInterface.h
M CCA/Components/ProblemSpecification/ProblemSpecReader.h
M CCA/Components/ProblemSpecification/ProblemSpecReader.cc
- Created new version of readInputFile() which takes a list of patches that are specific to this processor. However,
I don't think anyone (me?) is using it yet, and I'm actually not convinced that it is the right function to fix
(see comments in code). I'm committing it just in case it turns out that we need it as we fix the rest of the
XML memory bloat issues. However, at that point if it turns out not to be useful, it should be removed.
M CCA/Components/Schedulers/TaskGraph.h
M CCA/Components/Schedulers/TaskGraph.cc
- Add some consistency to the member variable naming in this file. Half the variables use d_, and the other half
have a trailing _, and the third half ;) didn't do either one... sigh. Some examples.
lb -> d_lb
dts_ -> d_dts
- A few cosmetic fixes - variable line up, white space, etc.
- Removed var/matl from lb->getOldProcessorAssignment()... need to verify that this is correct... see above.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Removed unused parameters to lb->getOldProcessorAssignment(). However, the DynamicLoadBalancer still uses the
version with parameters (though it doesn't really need them either). It is unclear why getOldProcessorAssignment()
is not declared in LoadBalancerCommon common or several of the other Load Balancers, and also unclear which function
is actually being called. This is defined in the LoadBalancer.h in CCA/Ports/. This needs more investigation.
M CCA/Components/Schedulers/DetailedTasks.h
M CCA/Components/Schedulers/DetailedTasks.cc
- Almost all cosmetic, white space, untabbify, lining up vars, English, etc changes.
- Add trailing _ to numPendingInternalDependencies to denote member var.
M CCA/Components/Schedulers/MPIScheduler.cc
- Few cosmetic cleanups.
M CCA/Components/Schedulers/SchedulerCommon.cc
M StandAlone/tools/pfs/rawToUniqueGrains.cc
M StandAlone/tools/puda/PIC.cc
M StandAlone/tools/extractors/extractV.cc
M StandAlone/tools/extractors/extractF.cc
M StandAlone/tools/extractors/partextract.cc
M StandAlone/partvarRange.cc
M StandAlone/tools/puda/jim1.cc
M StandAlone/tools/puda/jim3.cc
M StandAlone/tools/puda/varsummary.cc
M StandAlone/tools/puda/puda.cc
M StandAlone/tools/puda/POL.cc
M StandAlone/slb.cc
- Cosmetic white space fixes.
- numLevels() casts to avoid warnings.
M CCA/Components/Arches/Radiation/RadHypreSolver.cc
- Few cosmetic changes.
M CCA/Components/Regridder/RegridderCommon.cc
M CCA/Components/Regridder/SingleLevelRegridder.cc
M CCA/Components/Regridder/TiledRegridder.cc
- Cosmetic white space fixes.
- numLevels() casts to avoid warnings.
M CCA/Ports/Output.h
- Use const vars when possible.
- White space, English.
M CCA/Ports/LoadBalancer.h
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
M Core/OS/Dir.h
M Core/OS/Dir.cc
M Core/OS/Dir_boost.cc
- Use 'const' when variables don't change.
- Cosmetic: line up variables, untabbify, white space, {} around one line ifs, English.
- Don't use "std::" in half the file and not in the other half.
M Core/Grid/Patch.h
M Core/Grid/Patch.cc
- Cosmetic: Line up variables, untabbify, white space, {} around one line ifs, English.
M Core/Grid/Grid.h
M Core/Grid/Grid.cc
- Added readLevelsFromFile(), parseLevelFromFile(), and parseGridFromFile() to parse XML without creating a full DOM.
This provides a 50% memory decrease (per process) on Vulcan (LLNL-BGQ) for 8K processors when restarting the
advect problem. At some point in the future it might be nice to replace my (brute force - straightfoward -
assumes that the input xml file is very well behaved) approach with the streaming reader functions from the
lib xml library. This is not done at this point as it is unclear how well that library will fit into our use
case, how much time it will take to convert to, and the fact that we want to get this pushed out to the users asap.
- Cosmetic: Line up variables, untabbify, white space, {} around one line ifs, English, coding standards.
- numLevels is now an unsigned int.
M Core/Grid/Task.cc
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
M Core/Grid/SimulationState.h
M Core/Grid/SimulationState.cc
- Cosmetic: Alphabetize/sort #includes.
M Core/Grid/Level.h
M Core/Grid/Level.cc
- Returned patch from addPatch() is not used anywhere so remove the return type.
- Cosmetic: line up variables, untabbify, white space, {} around one line ifs, English.
M Core/Geometry/Vector.h
M Core/Geometry/Vector.cc
- Added the fromString() function.
- Cosmetic: Alphabetize/sort #includes.
M Core/Geometry/IntVector.h
M Core/Geometry/IntVector.cc
- Added the fromString() function.
M Core/Containers/HashTable.h
- Moved the call to first() into the constructor... Not quite sure what the reason for this is,
but everywhere a HashTable is created, "first()" is immediately called, so it makes sense
to just do it in once place instead of having to do it each time it is used.
D Core/Containers/StringUtil.cc
D Core/Containers/StringUtil.h
A + Core/Util/StringUtil.h
A + Core/Util/StringUtil.cc
M Core/Grid/SimulationTime.cc
M Core/Tracker/TrackerServer.cc
M Core/Persistent/Pstreams.cc
M Core/Persistent/Persistent.cc
M Core/Util/FileUtils.cc
- Moved StringUtil.* to Core/Util/ to all its use in other locations (higher up the build tree).
M Core/Containers/sub.mk
- Untabbify.
M Core/DataArchive/DataArchive.h
M Core/DataArchive/DataArchive.cc
- Rename variables so they are readable, eg: d_tsurl becomes d_ts_path_and_filename, d_tstimes becomes d_ts_times, etc.
- Change a few more functions to parse xml file data on the fly (instead of parsing DOMs), eg: queryEndiannessAndBits()
- Use NULL instead of 0.
- Pass strings as 'const &' instead of copying them every time.
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
M Core/ProblemSpec/ProblemSpec.h
M Core/ProblemSpec/ProblemSpec.cc
- Added constructor to take in a string buffer to create a new DOM from. (Use: stream parse an xml file and put the
needed pieces into a string, then turn only that information into a DOM.)
- Added routines to help in the stream parsing of an XML file: findBlock()
- checkForInputError() replaced.
- parseIntVector replaced with fromString() in respective files.
M Core/Util/DynamicLoader.cc
- Alphabetize #includes.
M Core/Util/sub.mk
- Alphabetize
A Core/Util/XMLUtils.h
A Core/Util/XMLUtils.cc
- Added new helper functions for parsing xml files on the fly.
M StandAlone/compare_uda.cc
- Cosmetic: Alphabetize/sort #includes, line up variables, untabbify, white space, {} around one line ifs, English.
- numLevels() is unsigned now.
- Bulletproofing - verify input args are actually directories.
M StandAlone/restart_merger.cc
- Minor cosmetic fixes.
M StandAlone/sus.cc
- Bulletproofing - catch case when user accidentally runs sus with a UDA and not a UPS.
970 lines of code changed in 10 files:
Added patch IDs to dbg.
0 lines of code changed in 2 files:
Initial Convected Particle Tetrahedral domain Interpolation (CPTI) method implementation. Input files are used to import tetrahedral mesh geometries to better fit complex shapes. The axisymmetric version is just a placeholder for now. CPTI uses a similar technique to the one used in CPDI.
1104 lines of code changed in 6 files:
test commit for cpti changes
0 lines of code changed in 1 file:
Formatting:
- Added {} and method dividers.
120 lines of code changed in 1 file:
* Cleanup CUDA stream creation flow (we should only need 1 stream per GPU task with aggregated H2D & D2H copies).
* Report more & better info for GPUStats DebugStream.
* Add temporary fix for Wasatch case where a field exists on the GPU, but requires a ghost update.
* This should allow James to put some more GPU regression testing in place.
* Some minor cleanup in a few spots
1 lines of code changed in 2 files:
- Cleanups from Vulcan@LLNL. Mostly cosmetic, though a few real fixes
found while porting to BGQ machine.
- Replaced proc0thread0cerr with proc0cerr as proc0cerr is (now
specifically) defined to only print out from thread 0 of process 0.
M CCA/Components/SimulationController/AMRSimulationController.cc
- Cosmetic
- Alphabetize the #includes for better readability and to remove duplicates.
- Put the #ifdef USE_GPERFTOOLS around entire block, instead of having
it multiple times and leaving dead if statements around it.
M CCA/Components/SimulationController/SimulationController.cc
- Cosmetic: Fix indentation (use diff -b to better see differences.)
M CCA/Components/DataArchiver/DataArchiver.cc
- Added the ability to specify checkpoint time via hours (in addition to seconds).
- Cleaned up the code to make it more readable for parsing this
information from input file - ie, use variable names that correspond
to the data they hold.
- Commented out a few lines of code that didn't do anything.
- Indented for readability, lined up some variable assignments.
M CCA/Components/Arches/CompDynamicProcedure.cc
- Alphabetize the #includes for better readability and to remove duplicates.
- Replaced proc0thread0cerr with proc0cerr.
M CCA/Components/Arches/DQMOM.cc
M CCA/Components/Arches/PropertyModels/PropertyModelBase.h
M CCA/Components/Arches/IncDynamicProcedure.cc
M CCA/Components/Arches/Arches.cc
- Replaced proc0thread0cerr with proc0cerr.
M CCA/Components/Arches/ChemMix/ClassicTableInterface.cc
- Throw a ProblemSetupException as that is what the error is.
M Core/Exceptions/InvalidState.cc
- Propagate (user supplied) error message.
M Core/Grid/Patch.cc
- Whitespace cleanup for readability.
M Core/Grid/Grid.h
- Whitespace cleanup for readability.
- Parameter to setExtraCells() is now (explicitly) const.
M Core/Grid/Level.cc
M Core/Grid/Grid.cc
- Coding standard and whitespace cleanup.
M Core/Parallel/Parallel.h
- Updated proc0cout to handle threaded versions of Uintah. If in MPI
only mode, then only prints for proc 0. If in threaded mode, only
prints for proc 0 thread 0.
- Removed proc0thread0cout as now only proc0cout is needed.
M Core/Thread/ThreadPool.h
- Remove tabs, line up code.
M Core/Thread/Thread.h
M Core/Thread/Parallel.h
M testprograms/Thread/parallel.cc
- Added the ThreadNS namespace because there are two classes named
'Parallel' in Uintah, and the one in the new ThreadNS is only used
in a few locations and thus is easier to move into its own NS.
M StandAlone/inputs/UPS_SPEC/ups_spec.xml
- Added 'walltimeStartHours' and 'walltimeIntervalHours' (to augment the
version that uses just seconds).
- Lined up for better readability.
M tools/StackTrace/StackTrace.cc
- Fixes for the stack trace tool for machines that only provide symbol
numbers in their stack traces. However, unfortunately, this still
doesn't seem to provide a valid stack trace on Vulcan.
27 lines of code changed in 4 files:
* Fix another leak in the recently added interior boundaries
* Allow PostProcessing graphs to be used through the input file
4 lines of code changed in 1 file:
memory leak cleanup
5 lines of code changed in 1 file:
Add support for specifying interior boundaries through the Uintah interface. A great use of this is to attach surface boundaries to intrusions.
usage:
* To specify an interior boundary through the input file, use the <InteriorFace> xml block. This is identical to the <Face> specification used for domain boundaries. Example:
<InteriorFace ellipse="x-" origin="0.2 0.5 0.5" major_radius="0.2" minor_radius="0.05" angle="270" name="my boundary">
<BCType var="Dirichlet" label="f" value="10.0"/>
</InteriorFace>
* The minus/plus face spec will determine which cell iterator is returned. For a minus spec, the iterator will return the cells that are to the minus side of the interior boundary. The opposite is true for a plus spec
* TO access the cell iterator, use: Patch::getInteriorBndBCDataArray(Patch::FaceType face). All other access methods used domain boundaries remain the same. See Wasatch::BCHelper.cc for a great example of how to access the BC data associated with an interior boundary
* Interior boundaries currently support all boundaries supported by the existing interface (except for a side boundary - use rectangle instead): rectangle, circle, annulus, ellipse.
Limitations:
* Does NOT handle unions/differences. While support for those can be added later, there is no clear way on how to combine boundaries with different boundary conditions. Note that this limitation also applies to the current domain boundary conditions.
* Interior boundaries MUST be parallel to domain boundaries. For example, you cannot specify an inclined interior boundary.
Algorithmic details:
For a given grid resolution, the interior boundary is moved to the closest face (or layer of nodes parallel to that boundary). If the interior
boundary coincides with a cell center, then it is moved to the face side (minus/plus) that is
specified through the input file. The face side (minus/plus) determines which cell iterator is
returned. For a minus boundary, the cells on the minus side are returned. For a plus boundary,
the cells on the plus side are returned.
2263 lines of code changed in 4 files:
Further minor optimization for cpdi when particle size is being scaled back.
0 lines of code changed in 2 files:
* Add support for handling "Spatially scheduled" tasks in the taskgraph checksum ( MPIScheduler::verifyChecksum() ).
An example would be the radiometer task, which is not scheduled on all patches (only a smalll subset).
* This commit begins to address making this checksum more sophisticated.
24 lines of code changed in 2 files:
Fixing an error in yesterday's commit. The RT will still fail, but now the differences are
round off, not factors of 2.
45 lines of code changed in 1 file:
This belongs with previous commit. Added d_ to all_patches and each_patch.
2 lines of code changed in 1 file:
formatting
- add d_ to global variables eachPatch and allPatches.
- added vertical and white spaces everywhere.
- added {} to conditional and loops
- added method/function dividers
- no longer line wrapping at 80 columns, our screens are bigger than a dec terminal.
- 2 space indentation, not 3!
470 lines of code changed in 2 files:
Only carry out re-calculations of dsize and relative_node_location if a particle actually
needs to be rescaled.
120 lines of code changed in 1 file:
SimulationState:
- added bool d_recompileTaskGraph, getRecompileTaskGraph(), setRecompileTaskgraph().
This is used by code deep inside a component with no easy access to the existing
simComp->needRecompile().
AMRSimulationController
needRecompile()
- check the sharedState if a taskgraph recompile has been requested.
11 lines of code changed in 2 files:
Code cleanup.
added {}, horizontal and vertical spaces.
174 lines of code changed in 1 file:
Removed function faceTypeToString(). It's redundant with getFaceName()
2 lines of code changed in 1 file:
here's another shot at fixing the boundary condition geometry objects. This is supposed to fix the leak. Note that the MPMICE burners may still fail.
4 lines of code changed in 1 file:
Revert "delete BCGeom objects from patches that they don't belong to. This gives us an extra level of security against using empty boundary iterators."
This reverts commit dbd3c523046bcc8ac5adf4d626b0aacab7fb838d.
3 lines of code changed in 1 file:
delete BCGeom objects from patches that they don't belong to. This gives us an extra level of security against using empty boundary iterators.
4 lines of code changed in 1 file:
This is a very minor commit.
M Core/Grid/Level.h
M Core/Parallel/Parallel.h
- Fix indentation.
M Core/Grid/BoundaryConditions/BCGeomBase.h
M Core/Grid/BoundaryConditions/BCGeomBase.cc
- Fix white space, line up variables.
- Remove 'const' from several return values as it doesn't make sense and icc gives a warning.
- All arguments for determineIteratorLimits() should be const (as none of them change or return anything).
- Remove superfluous ;s after some function definitions.
- Plase "template<>" on the preceding line from "class" per standard and consistency.
1 lines of code changed in 1 file:
allow BCGeomBase to store, compute, and return its surface area on the current patch. No reductions yet to compute total surface area across patches.
39 lines of code changed in 2 files:
Allow underlying, raw Task to know it's deviceID when GPU-enabled. This commit is on behalf of Abhishek Bagusetty with modifications by Alan Humphrey.
218 lines of code changed in 2 files:
Cleaning up memory errors.
2 lines of code changed in 1 file:
Cleanup some stale Scheduler/Task code while waiting on the debug queue.
13 lines of code changed in 1 file:
add a method to Uintah::Patch that computes and returns cell volume. The method is called cellVolume() to be consistent with other methods in the patch class. Also, this method will throw an internal error if the mesh is stretched. This function should now replace traditional ways of computing cell volumes, i.e.
Vector dx = patch->dCell();
double vol = dx.x()*dx.y()*dx.z();
Now you can use:
const double vol = patch->cellVolume();
20 lines of code changed in 2 files:
added mutex lock to << operator. Striving for warning free thread sanitizer output.
3 lines of code changed in 1 file:
Added float instantiations of coarsenDriver(), fineToCoarseOperator(), compute_mag_gradient()
Cleaned up the alignment of parameter lists.
0 lines of code changed in 6 files:
Comment out all SCI_DEBUG.setActive() calls. This
will reduce the amount of output then using the thread sanitizer.
1 lines of code changed in 1 file:
Add pidx to sub.mk files.
6 lines of code changed in 1 file:
Finish stripping out Windows support.
Also update UPS_Spec from previous commit.
0 lines of code changed in 2 files:
Add more clarification for an error related to boundary conditions specification in Uintah.
1 lines of code changed in 1 file:
Removed many of datawarehouse locks by using atomic operations
2 lines of code changed in 2 files:
spring cleaning.
- removed WIN32 code. Much more to come.....
0 lines of code changed in 2 files:
Eliminate warnings as turned up by clang.
8 lines of code changed in 3 files:
(3 more)