| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 158 (100.0%) | 3270 (100.0%) | 20.6 |
| Core/DataArchive/ | 3 (1.9%) | 957 (29.3%) | 319.0 |
| CCA/Components/DataArchiver/ | 12 (7.6%) | 784 (24.0%) | 65.3 |
| Core/Grid/Variables/ | 23 (14.6%) | 291 (8.9%) | 12.6 |
| CCA/Ports/ | 12 (7.6%) | 272 (8.3%) | 22.6 |
| StandAlone/tools/puda/ | 30 (19.0%) | 246 (7.5%) | 8.2 |
| StandAlone/ | 5 (3.2%) | 149 (4.6%) | 29.8 |
| Core/Geometry/ | 1 (0.6%) | 68 (2.1%) | 68.0 |
| CCA/Components/Schedulers/ | 5 (3.2%) | 65 (2.0%) | 13.0 |
| CCA/Components/Arches/Task/ | 1 (0.6%) | 58 (1.8%) | 58.0 |
| Core/ProblemSpec/ | 5 (3.2%) | 53 (1.6%) | 10.6 |
| / | 2 (1.3%) | 41 (1.3%) | 20.5 |
| CCA/Components/LoadBalancers/ | 3 (1.9%) | 40 (1.2%) | 13.3 |
| R_Tester/helpers/ | 3 (1.9%) | 37 (1.1%) | 12.3 |
| StandAlone/tools/extractors/ | 16 (10.1%) | 31 (0.9%) | 1.9 |
| Core/OS/ | 7 (4.4%) | 29 (0.9%) | 4.1 |
| Core/Grid/ | 5 (3.2%) | 26 (0.8%) | 5.2 |
| CCA/Components/Arches/SourceTerms/ | 1 (0.6%) | 23 (0.7%) | 23.0 |
| CCA/Components/SimulationController/ | 3 (1.9%) | 20 (0.6%) | 6.6 |
| VisIt/interfaces/ | 1 (0.6%) | 15 (0.5%) | 15.0 |
| Core/Util/ | 4 (2.5%) | 13 (0.4%) | 3.2 |
| Core/Parallel/ | 1 (0.6%) | 9 (0.3%) | 9.0 |
| CCA/Components/Examples/ | 1 (0.6%) | 7 (0.2%) | 7.0 |
| CCA/Components/Arches/ | 2 (1.3%) | 7 (0.2%) | 3.5 |
| StandAlone/tools/ | 2 (1.3%) | 6 (0.2%) | 3.0 |
| CCA/Components/Application/ | 1 (0.6%) | 6 (0.2%) | 6.0 |
| CCA/Components/Arches/TurbulenceModels/ | 1 (0.6%) | 5 (0.2%) | 5.0 |
| StandAlone/tools/dumpfields/ | 2 (1.3%) | 4 (0.1%) | 2.0 |
| StandAlone/tools/pfs/ | 1 (0.6%) | 2 (0.1%) | 2.0 |
| StandAlone/Benchmarks/ | 1 (0.6%) | 2 (0.1%) | 2.0 |
| CCA/Components/PostProcessUda/ | 1 (0.6%) | 2 (0.1%) | 2.0 |
| build_scripts/ | 1 (0.6%) | 1 (0.0%) | 1.0 |
| CCA/Components/Models/Radiation/RMCRT/ | 2 (1.3%) | 1 (0.0%) | 0.5 |
Fix (this time for sure...?) earlier fix for deleting directories on certain file systems. Note, this routine is only used when 'boost' is not enabled (via configure)... otherwise the boost 'remove' is called (and does not suffer from this issue). This is why only a small subset of users were seeing the issue of some checkpoint dirs not being deleted.
0 lines of code changed in 2 files:
This fixes an issue with (older/non-compliant?) file systems with respect to deleting directories.
For many years We had a 'hack' in place for AIX file systems to use 'stat' instead of the cheaper
"file->d_type" check. It turns out that we should (have been) use the hack anytime that file->d_type
is DT_UNKNOWN, not just under AIX. This should fix the problem that some people were seeing on some
file systems where (checkpoint) diretories were not being deleted when they should have been.
M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/DataArchiver/DataArchiver.cc
- Const'ify a number of method params that are not changed in the functions (and thus should be declared const).
- Add some white space for readability.
- Actually print out warning messages when old checkpoint directories fail to be deleted.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
M CCA/Components/SimulationController/SimulationController.cc
- Purely cosmetic: Add some white space for readability.
M CCA/Ports/Output.h
- Match updated interface (ie, use of const) for DataArchiver.
- Add some white space for readability.
M Core/OS/Dir.h
M Core/OS/Dir.cc
- Add 'const' due to addition of const above.
- Add some white space for readability.
- Fix the check that we use to determine if a 'file' is a directory (see above).
M Core/OS/Dir_boost.cc
- Add const, white space, and {} for if statement.
113 lines of code changed in 10 files:
Updates toward getting particle data to work with PIDX. This commit is not the complete fix,
but particles aren't being used with PIDX anyway, so it won't affect anything.
M CCA/Components/DataArchiver/DataArchiver.cc
- Add PIDX support for IntVector.
- Fix the long64_type params.
- Initial setting of particle position index, though this will change soon with the updating of PIDX to use multiple particles at some point.
M CCA/Ports/PIDXOutputContext.cc
- Fix name from UPS spec, just use "CHUNKING_ZFP" instead of "PIDX_CHUNKING_ZFP".
- Fix name of ParticleVars and NCVars output files.
M Core/DataArchive/DataArchive.cc
- Fixes for handling particle data in PIDX. Not a complete fix, but a step in the right direction.
Particle RT tests do NOT pass at this point.
143 lines of code changed in 4 files:
Fix bad var name from sed
2 lines of code changed in 1 file:
Updates to support PIDX particle output (based on work last week with
Sid and Steve). The PIDX code is passing most local (non-particle)
tests, and the particle data is being saved to some extent at this
point - but the numbers do not compare exactly and there are a few other
strange things going on. I'm committing this so that Steve and Sid
can take a look.
(Note, there are a number of debug prints in the PIDX sections that
need to be removed when the other issues are resolved.)
Updated files:
M Components/DataArchiver/DataArchiver.cc
M Ports/PIDXOutputContext.cc
M Ports/PIDXOutputContext.h
60 lines of code changed in 4 files:
This commit updates the code to support a newer version of PIDX, including the beginnings
of particle support. This update passes all of the local RT using UDA output, but
fails on a number of (previously passing) PIDX tests. I am committing so that Sid/Steve
can take a look and fix the issue.
Sid, here is the output from (one of) the failing test:
Running test ---methane_fire_8patch--- (mpi 8 proc) at 01:04:31
Command Line: /usr/bin/time -p /usr/installed/mpich/mpich-3.2-gcc4.9.2-install/bin/mpirun -genvlist MALLOC_STATS -np 8 sus -svnStat -svnDiff methane_fire_8patch.ups
Successfully ran to completion
Comparing udas
*** ERROR, test (methane_fire_8patch) failed uda comparison, tolerances exceeded (256)
See /ssd2/home/dav/SVN/Uintah_Baseline/opt-mpich/local_RT/ARCHES-results/methane_fire_8patch/compare_sus_runs.log.txt for more comparison information.
Changes:
--------
M CCA/Components/DataArchiver/DataArchiver.cc
M CCA/Ports/PIDXOutputContext.h
M CCA/Ports/PIDXOutputContext.cc
- Updates for newer version of PIDX with (I think) the beginnings of particle support.
- Allow for better (finer grained) specification of PIDX flags in .ups input file.
M Core/Util/XMLUtils.h
M Core/Util/XMLUtils.cc
M Core/ProblemSpec/ProblemSpec.h
M Core/ProblemSpec/ProblemSpec.cc
- Added ability to check for unsigned ints.
M StandAlone/tools/extractors/particle2tiff.cc
- Fix compiler warning. White space. Use {} on one line 'if' statements.
M StandAlone/tools/pfs/sub.mk
M StandAlone/Benchmarks/sub.mk
- Link in PIDX.
M configure.ac
M configure
- Newest PIDX requires the zfp library.
282 lines of code changed in 15 files:
Fix VarLabel memory leak. (Note, the use of the VarLabel to synchronize the tasks is a hack and hopefully will be addressed at some point.)
11 lines of code changed in 2 files:
This commit brings the PIDX data I/O branch (named: pidx_xml) back into the trunk.
All PIDX data I/O is, by default, turned off. To use PIDX you have to configure
against the PIDX library (either installing manually and pointing at it, or using
the --with-pidx flag (not 100% certain that this works at the moment)), and you must
set <DataArchiver type="PIDX"> (as opposed to the default which is type="UDA") in
the .ups input file.
Other caveats:
- Particles are not (currently?) supported in PIDX so any simulation that has a
particle data type will fail (most will print an error that PIDX does not
support them, but it seems some just die).
- Simulations that have overlapping patches (this may just be AMR type
sims) (eg: multibox_rmcrt_coal_1L) can save (slightly different) results.
In the multibox_rmcrt_coal_1L, we saw (only) a handful of differences like this:
((A 1 vs a 0 in a couple of locations) Also note that the UDA itself compared
successfully, but the checkpoint underneath it did not...)
DIFFERENCE [int 36, 5, 0] Time: 0.0003106658 Level: 0 Patch1: 0 Patch2: 0 Material: 0 Variable: areaFractionFX
multibox_RMCRT_coal_1L.uda/checkpoints goldStandard/.../multibox_RMCRT_coal_1L.uda/checkpoints
1 0
- "#if HAVE_PIDX" is used inconsistently through a number of files. Some PIDX stuff is #if'd out, while other code
is left in and compiles, it is just not used.
- There are a lot of cleanups that can and should take place wrt the PIDX integration.
While the code passes all the local RT tests (with the exception of particle tests),
I don't believe it has been run at large scale (though it should work) on a BGQ or Quartz@llnl.
Summary of changes: (Note, see pidx_xml branch commits if you want more information.)
M CCA/Ports/ApplicationInterface.h
M CCA/Components/Application/ApplicationCommon.h
- Added the ability to record (and retrieve) the number for the last regrid time step.
M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/DataArchiver/DataArchiver.cc
- When saving as PIDX, only create/output timestep.xml on the initial (I/O) time step that occurs after the regrid.
- Fixes that allow PIDX to save correctly (and efficiently) in parallel. If you are ever trying
to trace this back, read the comments from the commit logs for the "pidx_xml" branch.
- Remove createPIDX_dirs() as it was commented out and Sid tells me that PIDX creats its own dirs and we don't need this.
- Lot of white space fixes.
M CCA/Components/Examples/RMCRT_Test.cc
M CCA/Components/PostProcessUda/PostProcess.cc
- The DataArchive (DA) queryVariables() function now also returns the number of materials for each variable.
- "else" and "else if" should be on a separate line to make it easier to read.
M CCA/Components/Models/Radiation/RMCRT/RayGPU.cc
- Differentiate the output between the GPU and non-GPU reports so the viewer knows explicitly whether the GPU code was run.
M CCA/Components/Schedulers/OnDemandDataWarehouse.h
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Cosmetics: Line up variables, use more than 80 chars per line, white space.
Add in comments denoting default param values.
M CCA/Components/Schedulers/SchedulerCommon.cc
- Cosmetics.
M CCA/Components/SimulationController/AMRSimulationController.cc
- Cosmetics: Use more white space, 80+ chars per line for better readability, etc.
M CCA/Ports/PIDXOutputContext.h
- const'ify some params.
- checkReturnCode() is a static function so mark it so.
M CCA/Ports/PIDXOutputContext.cc
- White spacee. Code alignment for readability.
M Core/DataArchive/DataArchive.h
M Core/DataArchive/DataArchive.cc
- Add in PIDX functions. Note, queryPIDXSerial() is used (currently) by standalone codes (eg: puda).
Its purpose is to wrap the setupQueryPIDX()/queryPIDX() calls that have been added to
allow PIDX to truly run in parallel. At some point it would be good to update puda/compare_uda/etc
to run in parallel...
- See previous comments from PIDX branch for more details on the PIDX communicators that are necessary
to transfer data as some data does not live on all cores and thus can't use the golbal comm.
- Rename a few functions (queryAndSetParticlePositionName()) to be more accurate as to what they do.
- There are still a number of hacks in this code that need to be addressed (eg: var_materials map).
M Core/Geometry/IntVector.h
- Mostly cosmetics...
White space for readability.
Place 1-line functions in .h on one line to make it easier to see all provided functions.
M Core/Grid/Grid.cc
- White space, variable alignment for readability.
M Core/Grid/Level.h
M Core/Grid/Level.cc
- White space, coding standard (return type on its own line).
- Fix logic error in computeVariableExtents() that did not handle periodic boundaries correctly.
This fix was suggested as probably the correct way to do it by Todd... seems to pass tests and did fix
the issue (PIDX saving a particular something or other) that led me to it.
M Core/Grid/Patch.cc
- Place "else" on its own line for readability.
M Core/Grid/Variables/GridVariable.h
- Added emitPIDX().
- Opening "{" for functions in .h files goes on same line.
M Core/Grid/Variables/GridVariableBase.h
M Core/Grid/Variables/GridVariableBase.cc
- Organize #includes.
- White space, line up vars, etc for better readability.
- Return type on its own line.
M Core/Grid/Variables/ParticleData.h
- #include ParticleSubset.h for particleIndex.
M Core/Grid/Variables/ParticleSubset.h
- Cosmetic white space.
M Core/Grid/Variables/ParticleVariable.h
- White space, variable line up, etc.
- Added emitPIDX() function for particles. Note, particles do not fully work yet (on PIDX side).
And thus, this function hasn't really been tested.
M Core/Grid/Variables/ParticleVariableBase.h
M Core/Grid/Variables/ParticleVariableBase.cc
M Core/Grid/Variables/PerPatchBase.h
M Core/Grid/Variables/PerPatchBase.cc
M Core/Grid/Variables/ReductionVariableBase.h
M Core/Grid/Variables/ReductionVariableBase.cc
- Cosmetic white space. Coding standards. Etc.
M Core/Grid/Variables/Variable.h
M Core/Grid/Variables/Variable.cc
- Organize #includes.
- Use "const" on params that are const.
- Cosmetic white space, etc.
M Core/Grid/Variables/VarnameMatlPatch.h
- Pass non-changing strings by const reference (instead of copying them).
- White space for readability.
M Core/ProblemSpec/ProblemSpec.cc
- Line up vars, white space.
M R_Tester/helpers/compare_dat_files.pl
- Strip "/" from end of uda names.
- Clean up output to make it more readable (Todd I hope this doesn't break some of your scripts...)
M R_Tester/helpers/compare_dats
- White space.
M R_Tester/helpers/runSusTests.py
- Fix typo.
M StandAlone/compare_uda.cc
- White space.
- Line up vars.
- Coding standard.
- Line up case statement for better readability.
- 0 => nullptr
- query() now returns if the var was found (because PIDX has a list of all variables the simulation starts with
and the vars may not actually exist in the UDA.
- var => var_name (as it is actually the name, and not the var).
- Use 80+ columns.
M StandAlone/partvarRange.cco
M StandAlone/selectpart.cc
M StandAlone/tools/compute_Lnorm_udas.cc
M StandAlone/tools/dumpfields/dumpfields.cc
M StandAlone/tools/extractors/extractF.cc
M StandAlone/tools/extractors/extractS.cc
M StandAlone/tools/extractors/extractV.cc
M StandAlone/tools/extractors/faceextract.cc
M StandAlone/tools/extractors/lineextract.cc
M StandAlone/tools/extractors/partextract.cc
M StandAlone/tools/extractors/particle2tiff.cc
M StandAlone/tools/extractors/timeextract.cc
M StandAlone/tools/puda/AA_MMS.cc
M StandAlone/tools/puda/ER_MMS.cc
M StandAlone/tools/puda/GV_MMS.cc
M StandAlone/tools/puda/ICE_momentum.cc
M StandAlone/tools/puda/PIC.cc
M StandAlone/tools/puda/POL.cc
M StandAlone/tools/puda/asci.cc
M StandAlone/tools/puda/jacquie.cc
M StandAlone/tools/puda/jim1.cc
M StandAlone/tools/puda/jim2.cc
M StandAlone/tools/puda/jim3.cc
M StandAlone/tools/puda/pressure.cc
M StandAlone/tools/puda/puda.cc
M VisIt/interfaces/archiveInterface.cc
- queryVariables() now returns number of materials.
M StandAlone/tools/puda/varsummary.h
M StandAlone/tools/puda/varsummary.cc
- Swat some evil endls.
M build_scripts/build_pidx.sh
- FYI... Not sure if changing PIDX_TAG to "master" actually works...
M buildbot_try.sh
- Added a number of comments about use of this script.
- Fixed some typos.
- Spread command to multiple lines for readability.
2102 lines of code changed in 106 files:
Fix for potentail fatal bug when putting variables into the Datawarehouse (DW) when the variable type is
different from the type specified by the VarLabel. I'm surprised that we did not validate this previously
and more surprised that many things did not fail because of this. I'm guessing that for the most part
people didn't accidentally trigger this issue, and when it did happen, the underlying data was close enough
that it didn't cause issues.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
- Put in a check to validate that the variable and var label types match when allocateAndPut() is called.
Only makes this check if assertions are configured on (ie, debug builds).
M CCA/Components/Arches/ExplicitSolver.cc
- Fix error where SFCYVariable as being put into the DW as a SFCXVariable (X instead of Y).
M CCA/Components/Arches/SourceTerms/RMCRT.cc
- Fix error where abskg and sigmaT4 were being put into the DW as doubles before being converted into float vars
in RMCRT later on.
M Core/Grid/Variables/GridVariable.h
- Add some whitespace and use {} for one line if statements.
61 lines of code changed in 4 files:
Cosmetic white space cleanup
58 lines of code changed in 1 file:
Mostly cosemetic commit. Added in a number of "const" declarations and cleaned up
the code around them.
M CCA/Components/DataArchiver/DataArchiver.h
M CCA/Components/DataArchiver/DataArchiver.cc
- Mark methods as const if they don't change object data.
- Pass (all) params as constants where appropriate.
- Return const pointers to object data (as appropriate).
- Align params, white space.
- Rename findAllVariableTypes() to the more accurate findAllVariablesWithType().
- The "d_" vars are being phased out, so using direct getMPIRank() call instead.
M CCA/Ports/LoadBalancer.h
- Rename enum to use CAPITAL names for clarity. (The enum itself should probably be a named type.)
This makes grep'ing for them much easier.
- Remove tabs, white space.
M CCA/Components/LoadBalancers/DynamicLoadBalancer.cc
M CCA/Components/LoadBalancers/LoadBalancerCommon.cc
M CCA/Components/LoadBalancers/ParticleLoadBalancer.cc
M CCA/Components/SimulationController/AMRSimulationController.cc
- White space.
- Remove some "d_" usage.
- Use new LoadBalancer enum NAMES.
- Single line "if" statements need to use {}.
427 lines of code changed in 7 files:
Fix static build when Examples are not built.
2 lines of code changed in 1 file:
Cosmetic update: Consolidate one line functions in .h file to be more easily read (in terms of a class spec). Added a few comments about what data the variables hold.
9 lines of code changed in 1 file: