fortran
(27 files, 3364 lines)
[root]/CCA/Components/Arches/Radiation
fortran
(27 files, 3364 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 92 (100.0%) | 2500 (100.0%) | 27.1 |
| derekhar | 43 (46.7%) | 1701 (68.0%) | 39.5 |
| jthornoc | 24 (26.1%) | 695 (27.8%) | 28.9 |
| dav | 9 (9.8%) | 86 (3.4%) | 9.5 |
| jas | 16 (17.4%) | 18 (0.7%) | 1.1 |
Recommitting Arches changes that were reverted by Dav's commit, r52897.
0 lines of code changed in 10 files:
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.
60 lines of code changed in 5 files:
Added an additional particle model for radiation. The constant complex-index-refraction model. Decoupled the particle temperature from the gas temperature for radiation.
441 lines of code changed in 4 files:
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.
4 lines of code changed in 1 file:
Made the 2 regression test work, and dqmom_test_1. Modified radiation
files so that they are compatible with new coal data base, and new
labels.
7 lines of code changed in 1 file:
Added bullet-proofing for several of the labels used radiation coefficient model.
Fixed some radiation related screen-output. General housekeeping changes.
5 lines of code changed in 1 file:
Minor housekeeping commit. Changed spacing and coding-order to be easier to read.
5 lines of code changed in 1 file:
This commit, moves all computations of abskp to radPropertyCalculator.cc. It also makes improvements to DO-radiation scattering, and radprops.
A new class was created in this commit, which contains the machinery for computing particle absorption coefficients.
This commit changes the answers to two arches tests, coal_channel and coal_RadPropsPlanck.
612 lines of code changed in 4 files:
Fix Regression tests. Should have exact comparison.
3 lines of code changed in 1 file:
Moved initialization of source term so that the sum is properly initialized to zero for radiation scattering.
6 lines of code changed in 1 file:
Added Scattering in discrete ordinates radiation using the radProps property model. Also made some changes to reflections in discrete ordinates radiation. In this version, the complex index of refraction is a constant for all particles.
280 lines of code changed in 6 files:
Fixed compile time warnings, as well as a compile time error.
2 lines of code changed in 3 files:
This is Stage 1 of a commit which adds reflections for DO-Radiation. The RT-Tests are expected to fail, due to a new VarLabel in the checkpoints. The uda files are expected to remain unchanged.
116 lines of code changed in 11 files:
This commit has added a regression test and is expected to cause failure in the nightly RT on coal_RadPropsPlanck.ups!
Fixed the interface for computation of absorption coefficients using the RadProps library.
The RadProps library can use one of two methods to compute the particle absorption coefficients (Planck or Rossland).
The new R-Test is similar to the coal-channel case called coal_RadPropsPlanck.
This commit also removed a work-around (or hack) due to a boundary condition bug, which was fixed by Tony Saad.
35 lines of code changed in 2 files:
A number of clean ups for Vulcan (LLNL - BGQ machine). Most
importantly, fixed memory usage reporting (see ProcessInfo.cc).
M CCA/Components/SimulationController/AMRSimulationController.h
M CCA/Components/SimulationController/AMRSimulationController.cc
- Added white space, removed tabs, line up params, etc.
M CCA/Components/SimulationController/SimulationController.cc
- Moved toHumanUnits() to ProcessInfo so it can be used by others.
- Line up variables, add white space.
- Consistent (correct) capitalization/punctuation of some comments.
M CCA/Components/LoadBalancers/SingleProcessorLoadBalancer.h
M CCA/Components/LoadBalancers/SingleProcessorLoadBalancer.cc
- inNeighborhood() did not have the same declaration as its parent
(superclass)... removed "const MaterialSubset*" to fix this... not
sure how this worked before.
- White space.
M CCA/Components/LoadBalancers/LoadBalancerCommon.h
- Add "d_" to several class variables to be consistent and conform to coding standard.
- Removed extra (unnecessary) level of indentation.
- White space, line up variables.
M CCA/Components/LoadBalancers/LoadBalancerCommon.cc
- Add "d_" to several class variables to be consistent and conform to coding standard.
- White space.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Alphabetize #includes to more easily determine what is included.
- White space, line up variables.
M CCA/Components/Schedulers/UnifiedScheduler.cc
- Minor white space, coding standard update.
M CCA/Components/Schedulers/MPIScheduler.cc
- Minor white space fix.
M CCA/Components/Schedulers/SchedulerCommon.cc
- ProcessInfo GetMemoryResident() renamed with lowercase 'g' to match coding standard.
- Added processor rank to commented out memory usage print statement.
M CCA/Components/Arches/Radiation/RadPropertyCalculator.h
- Alphabetize #includes, remove superfluous ;s, remove tabs, line up functions/variables.
M Core/OS/ProcessInfo.h
M Core/OS/ProcessInfo.cc
- Fixed (added) BGQ memory usage querying code. Previously, it was
calling the generic linux version, and trying to open
/proc/<pid>/status to get memory info. On BGQ machines, this file
does not exist (except on the I/O node - where, while it exists,
it does not have valid information in it). In the generic linux
version, if the file fails to open, then an error is NOT thrown,
and 0 is returned... most likely we should fix this so that it
throws an error...
Note, the code for using the "mallinfo" (for BGQ) version of memory
checking was also added to this file, but is commented out and not
used because it uses an integer as the return variable and thus
does not correctly handle systems with more than 2 GB of memory.
- Coding standard updates.
- Moved toHumanUnits() here.
- Use lowercase letter for first letter in function names to be consistent and follow standard.
M Core/Parallel/Parallel.cc
M Core/Thread/Thread_pthreads.cc
- Minor white space, capitalization/punctuation.
M StandAlone/sub.mk
- For static builds, need Wasatch 3P libs to link.
M StandAlone/sus.cc
- Alphabetize #includes.
12 lines of code changed in 1 file:
Pushing in Arches Task interface updates.
2 lines of code changed in 1 file:
Added a 3rd party library under regression testing within arches. The thrid party library reads a 1-D table for radiation properties of gray gases including chemical species CO2 H2O CO OH and NO.
Also added linear initialization of transported variables (in the x-direction only) which can be invoked using TransportEqn->Eqn->initialization(linear-x).
3 lines of code changed in 1 file:
Fixed error in RadProps-Arches interface. A label intended for abskp was using the label used by abskg.
1 lines of code changed in 1 file:
Cleaning up some more bugs associated with an earlier commit.
1 lines of code changed in 1 file:
** THIS COMMIT CHANGES THE ANSWERS **
Moving the radiation properties into the property model. Currently, the
properties are being computed every timestep on every RK stage. This
fact changes the answers from previous results. Also, the ERSCG term was
moved into the fortran for DORadiation which also caused some numerical
fuzzzzzzzzzz.
With this commit, the radiation properties are completely independent
from the radiation model allowing for use of multiple radiation models
at once (ie, DORadiation + RMCRT virtual radiaometer).
261 lines of code changed in 2 files:
Complete divorce of the radiation properties from the radiation models
themselves. This simplified the radiation models considerably. The
properties are now being computed upstream and only accessed by the
models themselves.
For the RadProps models with particles, the particle interface needs to
added back in. It should be done in a generic way so as not to preclude
any CQMOM interface.
350 lines of code changed in 3 files:
Cleaning up the abskg/abskp stuff for the DO radiation model.
Also pulled some weeds and spruced the place up.
69 lines of code changed in 3 files:
Changed how Arches.cc interfaces with radproperty_Calculator.
Changed default name of abskp to abskp_HS.
Removed redundant and unneeded line in DORadiation.cc.
4 lines of code changed in 1 file:
Removed bug in Arches.cc relating to variable abskp of the radiation property calculator.
3 lines of code changed in 1 file:
--Changed the default name of abskp so regression testing passes.
--Added Coal case to the nightly RT.
1 lines of code changed in 1 file:
This patch changes the interface used to invoke radiation property models: hottel-sarofim, Burns-christian, and constant.
///---IMPORTANT!! OLD INPUT FILES WILL NO LONGER PARSE CORRECTLY AND MUST INVOKE THE DESIRED PROPERTY MODEL USING "property_calculator" WITHIN THE RADIATION MODEL --//
The property models are now called using property_calculator. The regression test input files show the correct syntax to invoke the property models.
This was done to improve the modularity of the code.
A coal regression test has also been added.
Other notes:
--The OPL for hottel-sarofim can no longer be passed through the radiation model and must also be passed through the property_calculator.
--The label for the absorption coefficient must be set through the property_calculator.
--For coal cases, the label of abskp must be set to "Julien_abskp" in both the PropertyModel and property_calculator. The user will be given more freedom in future patches. This was done to prevent a multiple-computes error.
--For coal cases, computation of the abskp values is less than ideal. Currently, abskp is computed for every time step, however it is only needed when then the radiation solve is executed. This will be removed in future patches.
--For coal cases, a bug was removed where abskp was summed to be 3x its correct value when using second order Runge-Kutta. Fortunately, first order Runge-Kutta computed the correct value for abskp.
181 lines of code changed in 3 files:
Changed the DOM16 regression test to use the new interface for radiation. Also fixed a bug associated with the new interface.
3 lines of code changed in 1 file:
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.
5 lines of code changed in 3 files:
Update includes to eliminate C linkage with Petsc 3.4 version includes.
6 lines of code changed in 1 file:
Fixed a number of warnings. ICC compiler pointed out a number of
times where functions where returning "const int" (or some such), and
that it does not make any sense to return a const number, as the
caller can do what they want with the result. (This removes 1000s of
warning messages during compilation.)
(I assume that the author did not mean to put the "const" after the
function name? It didn't appear that this was what was desired, but
perhaps he/she could take a look?)
Also, removed a lot of stray ';'s (semi-colons). Seems like someone
just randomly through them in without knowing what lines require them
and what lines do not. I only removed the ones near the locations of
the "const" return values, but there are probably many more that
should be cleaned up.
M TransportEqns/EqnBase.h
Removed const from return value of get_stage().
M Radiation/RadPropertyCalculator.h
M Radiation/RadPropertyCalculator.cc
Removed const from return value of does_scattering().
M SourceTerms/SourceTermBase.h
Removed const from return value of stage_compute().
10 lines of code changed in 2 files:
Updated copyright information.
12 lines of code changed in 15 files: