Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 362 (100.0%) | 2203 (100.0%) | 6.0 |
| dsunder | 36 (9.9%) | 1329 (60.3%) | 36.9 |
| dav | 49 (13.5%) | 259 (11.8%) | 5.2 |
| jas | 196 (54.1%) | 159 (7.2%) | 0.8 |
| ahumphrey | 53 (14.6%) | 132 (6.0%) | 2.4 |
| bpeterson | 10 (2.8%) | 122 (5.5%) | 12.2 |
| harman | 9 (2.5%) | 120 (5.4%) | 13.3 |
| jthornoc | 5 (1.4%) | 70 (3.2%) | 14.0 |
| jholmen | 2 (0.6%) | 12 (0.5%) | 6.0 |
| allen | 2 (0.6%) | 0 (0.0%) | 0.0 |
This patch has two parts. The first part changes the PerPatch variable so that uses C++11 shared_ptr so that it never makes a copy of the value, it instead preserves a pointer to a single value. This helps Wasatch who needs pointers to direct data. I've run this file against the full gold standard tests without issue. The others are some sizing fixes to the UnifiedScheduler knows how many PerPatch bytes to copy, before it was copying 0 bytes.
13 lines of code changed in 2 files:
* Refactor TaskGraph code prior to upcoming overhaul.
* Remove several unused _testdefs.h.in files
* Remove sci_algorithm.h, as this is no longer needed with c++11. Next step is to remove all sci_hashmap code, again we can simply use std::unordered_map/multimap now with c++11
* Remove some ancient _pgi code.
* Generate new configure script.
30 lines of code changed in 2 files:
white space clean up
0 lines of code changed in 2 files:
Reorganize the way we include MPI. Previously files were including the mpi_defs.h (configure generated file) to get mpi.h. Now they
include UintahMPI.h (from Core/Parallel/).
Note: MPI is now required (though for all intents and purposes it already was). You can still run a serial version of the code,
you just must compile/link with MPI first.
M configure
M configure.ac
- Fix check for xml2-config.
- Fix check for mpi.h location when using 'built-in' (fixes issue with non-mpich MPIs).
- Check to see if MPI handles const correctly.
- Fix some indentation.
- No longer define HAVE_MPI or HAVE_MPICH as we require MPI now.
- Added defines for MPI_CONST_WORKS, and MPI_MAX_THREADS and MPI3_ENABLED (thought the last 2 are hard-coded and need
to have configure tests written for them).
M include/sci_defs/mpi_testdefs.h.in
- Added MPI_CONST_WORKS, MPI_MAX_THREADS, and MPI3_ENABLED #defines.
- Moved the MPI wrappers into UintahMPI.h (thus out of this configure generated file).
D include/sci_mpi.h
- Removed sci_mpi.h as it is not used and its only purpose was to allow for compilation without MPI. This
is no-longer allowed (and probably hadn't worked in a long time).
A Core/Parallel/UintahMPI.h
- Added the new file UintahMPI.h which is used to #include <mpi.h> and wrap the MPI calls.
- These wrappers were in mpi_testdefs.h.
- Replaced most of the "const" with MPICONST so that on non-const-compliant MPIs they
can be turned off (this is done through a configure check).
- Grouped a lot of the UINTAH_ENABLE_MPI3 sections into single #if's instead of having a #if for each line.
M CCA/Components/Arches/fortran/sub.mk
- Remove tabs from where they are not supposed to be.
M CCA/Components/MPM/PetscSolver.h
M CCA/Components/ICE/PressureSolve/HypreStandAlone/Hierarchy.cc
M CCA/Components/ICE/PressureSolve/HypreStandAlone/mpitest.cc
M CCA/Components/ICE/Advection/FluxDatatypes.h
M CCA/Components/Schedulers/OnDemandDataWarehouse.h
M CCA/Components/Schedulers/BatchReceiveHandler.h
M CCA/Components/Schedulers/templates.cc
M CCA/Components/Schedulers/Relocate.h
M CCA/Components/Schedulers/MPIScheduler.cc
M CCA/Ports/PIDXOutputContext.h
M Core/Grid/Variables/Stencil4.cc
M Core/Grid/Variables/ReductionVariableBase.h
M Core/Grid/Variables/Stencil7.cc
M Core/Grid/Variables/SoleVariableBase.h
M Core/Parallel/ProcessorGroup.h
M Core/Parallel/PackBufferInfo.h
M Core/Parallel/BufferInfo.h
M Core/Disclosure/TypeDescription.h
M Core/Util/DOUT.hpp
M Core/Util/InfoMapper.h
M StandAlone/tools/mpi_test/async_mpi_test.cc
M StandAlone/tools/mpi_test/mpi_hang.cc
M StandAlone/tools/mpi_test/mpi_test.cc
M StandAlone/tools/fsspeed/fsspeed.cc
- Proper indentation.
- Replaced mpi_defs.h with UintahMPI.h.
- Use <> for includes and not "" per Uintah conding standard.
- Added comment for the #endif of the #ifndef compiler guard for the .h file.
Moved some #ifndef .h compiler guards to the very top of the file.
M testprograms/Malloc/test11.cc
M testprograms/Malloc/test12.cc
M testprograms/Malloc/test13.cc
- Fix indentation.
- "__linux" doesn't exist on some systems, so added "__linux__".
Probably could remove the __linux, but not sure so I didn't.
M VisIt/libsim/visit_libsim.cc
- Use #include <>.
M StandAlone/sus.cc
- Remove the code for old MPI versions. We don't support MPI v1 any more.
13 lines of code changed in 8 files:
Redirect all MPI calls through the lightweight wrapper (header only)
This allows for standardized error checking and easy collection of runtime stats. All MPI funtions can be called from the wrapper by replacing:
MPI_ with Uintah::MPI::
e.g.
Uintah::MPI::Isend(...)
Uintah::MPI::Reduce(...)
Also enables MPI3 wrappers when MPI3 is available and protects against these when not. Will want MPI3 for non-blocking collectives. MPI3 is availalbe on Mira but not Titan yet.
* Note src/scripts/wrap_mpi_calls.sh has been added to the src tree. This has the sed foo to do this replacement src tree-wide.
* Have tested this with OpenMPI, MPICH, IntelMPI and also built on Titan and Mira.
17 lines of code changed in 12 files:
Revert -r55443, until folks can get compilers upgraded and buildbot MPI is updated.
17 lines of code changed in 7 files:
Redirect all MPI calls through the lightweight wrapper (header only)
This allows for standardized error checking and easy collection of runtime stats. All MPI funtions can be called from the wrapper by replacing:
MPI_ with Uintah::MPI::
e.g.
Uintah::MPI::Isend(...)
Uintah::MPI::Reduce(...)
Also enables MPI3 wrappers when MPI3 is available and protects against these when not. Will want MPI3 for non-blocking collectives. MPI3 is availalbe on Mira but not Titan yet.
* Note src/scripts/wrap_mpi_calls.sh has been added to the src tree. This has the sed foo to do this replacement src tree-wide.
* Have tested this with OpenMPI, MPICH, IntelMPI and also built on Titan and Mira.
17 lines of code changed in 7 files:
Replace usage of NULL macro (type int) with nullptr (pointer literal of type: nullptr_t).
nullptr is implicitly convertible and comparable to any pointer type or pointer-to-member type, but is not implicitly comparable to integral types, except that it is convertible to bool (explicitly).
14 lines of code changed in 8 files:
Revert r55429.
Still having an MPICH/OpenMPI compatibility problem.
17 lines of code changed in 7 files:
Redirect all MPI calls through the lightweight wrapper (header only)
This allows for standardized error checking and easy collection of runtime stats. All MPI funtions can be called from the wrapper by replacing:
MPI_ with Uintah::MPI::
e.g.
Uintah::MPI::Isend(...)
Uintah::MPI::Reduce(...)
Also enables MPI3 wrappers when MPI3 is available and protects against these when not. Will want MPI3 for non-blocking collectives. MPI3 is availalbe on Mira but not Titan yet.
* Note src/scripts/wrap_mpi_calls.sh has been added to the src tree. This has the sed foo to do this replacement src tree-wide.
17 lines of code changed in 7 files:
Removal of src/Core/Thread and related refactoring throughout the code-base.
This is the first step in a series of infrastrucutre overhauls to modernize Uintah. Though this all passes local RT (both CPU and GPU tests), I expect some fallout we haven't considered and will be standing by to deal with any issues. Once the dust settles, we will move to replacing Core/Malloc with jemalloc.
* We are now using the standard library for all multi-threading needs within the infrastructure, e.g. std::atomic, std::thread, std::mutex, etc.
* The Unified Scheduler is now the only multi-threaded scheduler, e.g. ThreadedMPIScheduler no longer exists (though the source will soon be placed into an attic).
* Threads spawned by the Unified Scheduler are detached by default (not joinable), allowing for easy, clean and independent execution. There are no longer ConditionVariables used to signal worker threads, just a simple enum for thread-state.
* What was Core/Thread/Time.* is now Core/Util/Time.* - a next step will be to migrate all internal timers, etc to use std::chrono.
* NOTE: Though much cleanup has occurred with this commit, there is still significant cleanup and formatting to be done. The scope of this commit neccessitates a more incremental approach.
3 lines of code changed in 3 files:
Simplify the flux limiter operations by going to Array3.
Modified BlockRange to allow for operator() with an option
in addition to the (i,j,k).
Added a FaceVelocity class which computes the face velocities for the
various staggered grid faces.
29 lines of code changed in 2 files:
Refactor Array3 to remove iterator to make it possible to merge trunk
into the kokkos_dev branch
512 lines of code changed in 8 files:
For Dan S.:
Only get a kokkos view is d_window is not NULL.
Use a brace constructor for Array3 rather than default.
From Jeremy:
Simplify some of the lambda captures using a shortened [&] notation.
19 lines of code changed in 1 file:
Array3 operator[] forwards to Kokkos if enabled
214 lines of code changed in 2 files:
Move pragma ivdep above omp directive and implement
const correct copy constructors for KokkosArray3
-For Dan S.
22 lines of code changed in 2 files:
Update Array3 operator(i,j,k) to call through to Kokkos if enabled
56 lines of code changed in 4 files:
add vectorization hints to parallel_for
6 lines of code changed in 1 file:
This commit should fix the previous commit with respect to Uintah Variable
types. Additionally, it adds support for Arches files to be pushed through
NVCC as needed.
M CCA/Components/Wasatch/sub.mk
- Added a brief comment on use of CUDA_ENABLED_SRCS.
M CCA/Components/Arches/TransportEqns/CQMOM_Convection.h
M CCA/Components/Arches/TransportEqns/Discretization_new.h
M CCA/Components/Arches/TransportEqns/CQMOMEqn.h
M CCA/Components/Arches/TransportEqns/DQMOMEqn.h
M CCA/Components/Arches/Task/TaskInterface.h
- Minor cleanups:
- Fix warning message.
- Some white space for readability.
- Remove an empty "private:" block.
M CCA/Components/Arches/CoalModels/sub.mk
M CCA/Components/Arches/TransportEqns/sub.mk
M CCA/Components/Arches/Transport/sub.mk
M CCA/Components/Arches/sub.mk
M CCA/Components/Arches/ParticleModels/sub.mk
M CCA/Components/Arches/PropertyModels/sub.mk
M CCA/Components/Arches/ChemMix/sub.mk
M CCA/Components/Arches/PropertyModelsV2/sub.mk
M CCA/Components/Arches/Task/sub.mk
M CCA/Components/Arches/SourceTerms/sub.mk
M CCA/Components/Arches/Operators/sub.mk
M CCA/Components/Arches/WallHTModels/sub.mk
M CCA/Components/Arches/Utility/sub.mk
M CCA/Components/Arches/LagrangianParticles/sub.mk
- Update Arches sub.mk files to correctly specify which files
need CUDA (nvcc) compilation.
M Core/Grid/Variables/CCVariable.h
M Core/Grid/Variables/SFCYVariable.h
M Core/Grid/Variables/NCVariable.h
M Core/Grid/Variables/SFCXVariable.h
M Core/Grid/Variables/SFCZVariable.h
M Core/Grid/Variables/ParticleVariable.h
M Core/Disclosure/TypeDescription.h
- Turns out that the registerMe variable was needed. There was an erroneous comment
in the previous version that implied that it wasn't needed (that the work happened
in the Variable constructor, but this was not the case. I have added a number of
comments to clarify how this works so the next person to dig into it will have an
easier time.
M Core/Disclosure/TypeDescription.cc
- Update file global variables to be designated as such to help avoid confusion.
- Assign to NULL as they are pointers and not integers.
89 lines of code changed in 11 files:
Remove more unused 'Register' stuff. Commit update to aclocal.m4 that is in configure already, but still not sure why these changes (from John or Tony) are necessary.
0 lines of code changed in 1 file:
A number of fixes for Titan (CUDA) and static builds in general. Also, with this commit, the stand-alone
tools such as puda and compare_uda should now work on machines that require static builds.
M configure
M configure.ac
- Turn back on the C++11 check.
- Fix check for broken exceptions (on Titan) that fails because the code is cross-compiled.
- When MPI is specified as built-in, the NVCC compiler fails to find mpi.h (as we don't specify
the -I/path/to/mpi/ flag). This commit uses the built-in compiler to find the location of mpi, and
provides the location to the NVCC compiler (using INC_MPI_H_NVCC).
- Remove some old debugging statements.
- Fix (hack) on Titan for problem with CUDA 7.0 and Boost. Must specify two -D flags.
M configVars.mk.in
- Add the INC_MPI_H_NVCC flag to the NVCC_CXXFLAGS var.
- Fix (copy/paste?) bug where cuda .d files were being deleted as thus make dependency information
was lost. I'm guessing that before this fix, Uintah CUDA developers must have experienced
strange behavior when modifying .h files as the code would not have re-built like it should have.
- Remove all .d files from the base directory... This is due to the fact that Titan's NVCC compiler
is leaving around many bogus/tmp .d files and not cleaning up after itself. It might be that
we should make a check for being on Titan (or a more general test for problematic NVCC .d
generation - though I'm not sure right off on how to write this check) - but for now the removing
of all .d files in the base dir should have no effect on anything else.
- Make verbose output not suppress the "rm" call.
M CCA/Components/Wasatch/Wasatch.h
M CCA/Components/Wasatch/Wasatch.cc
- Fix compiler warning about "const" return variables.
- White space.
M CCA/Components/ProblemSpecification/ProblemSpecReader.cc
- Allow for validation of .ups file on machines where the executable is not in build tree (eg: on Titan,
before running sus, you must move it to a file system visible to the compute nodes). In order
to use this functionality, you must copy the "inputs/" directory to the same location you move sus to.
- It appears that, when validating the .ups file, sus was doing the validation on every process. This
doesn't seem like it is necessary, so only do so now on proc 0...
M Core/Exceptions/ErrnoException.cc
- White space, {}s.
M Core/Grid/Variables/CCVariable.h
M Core/Grid/Variables/SFCYVariable.h
M Core/Grid/Variables/NCVariable.h
M Core/Grid/Variables/SFCXVariable.h
M Core/Grid/Variables/SFCZVariable.h
- Remove the "registerMe" code that is not used. Perhaps it was replaced with the current method of
registering Uintah variables but not cleaned up? Regardless, it doesn't do anything now, and
just makes tracking what is going on more difficult, so it is best that it be removed.
- Put one-line functions in a .h file on a single line to make it easier to view the class spec.
M Core/Grid/Variables/sub.mk
- Add the StaticInstantiate.cc file. This file is used to force Uintah variable registration on
machines that use static builds and don't register the variables in the normal/correct way
when the shared library (static constructors fire) is loaded.
A Core/Grid/Variables/StaticInstantiate.h
A Core/Grid/Variables/StaticInstantiate.cc
- Uintah relies on our variable types (CCVariable, NCVariable, etc) being registered with Uintah
before it allows components to create a variable of the given type. On most systems (and
specifically for shared lib builds), when the CCVariable.o code is loaded from libCore_Grid.so
static constructors fire and register the variables. However, on some machines that use static
builds (such as Titan) appear to "optimize out" these constructors, and thus the variables
never register themselves and when puda or compare_uda (etc) try to load data, the Uintah
type system says it does not recognize the type and dies. This commit adds the (hack) function
instantiateVariableTypes() which sole purpose is to create variables of all types that Uintah
uses so that they will register themselves with the type system. This function is called the
first time a DataArchive is created (on static builds). All the variables it creates go away
as soon as the function is done, but have by then registered themselves.
M Core/DataArchive/DataArchive.h
M Core/DataArchive/DataArchive.cc
- Use the instantiateVariableTypes() function the 1st time a DataArchive is created (on static builds).
- Add a few more 'const's for variables that must not change.
- Indent properly, white space.
- Move some private data to the main private section.
M Core/Disclosure/TypeUtils.cc
- Move to 80+ columns for better readability.
M Core/Disclosure/TypeDescription.cc
- Remove the (non-used) Register section.
115 lines of code changed in 9 files:
remove get3DPointer from Array3Data
0 lines of code changed in 4 files:
Revert "BlockRange: restore ability to extract indices from linear index"
This requires c++11
This reverts commit 82ffe5ccd4f75851449b565c01f3a75c5044da30.
0 lines of code changed in 1 file:
BlockRange: restore ability to extract indices from linear index
31 lines of code changed in 1 file:
With the removal of the SCIRun namespace, there were a number of
places where 'SCIRun::' was replaced with 'Uintah::'. However,
some of these were already inside of the "using namespace Uintah {"
sections which causes the icc compiler to emit 1000s of warnings.
I have removed the "Uintah::" from these locations. Basically
this is a purely cosmetic update to remove warnings.
42 lines of code changed in 20 files:
* Included Array3.h to support Kokkos-based builds using KokkosView3
4 lines of code changed in 1 file:
Move non-conflicting classes that were in SCIRun namespace to Uintah namespace.
68 lines of code changed in 72 files:
avoid constructing IntVectors when using operator()(int i, int j, int k) with Array3
13 lines of code changed in 4 files:
protect omp pragma in Uintah::parallel_for with an enable macro
16 lines of code changed in 1 file:
Add operator()(int i, int j, int k) to constVariable and update Poisson1 to always use a functor
32 lines of code changed in 2 files:
add operator()(i,j,k) to Array3 if Kokkos is NOT enabled
9 lines of code changed in 1 file:
* Fixed OpenMP reductions for Intel compilers
8 lines of code changed in 1 file:
Level.h - pullled a weed.
Variable.cc/h
- added readPIDX() method which passes an pidxBuffer into an Array3
- commented emitPIDX()
DataArchive.cc
query() PIDX section
-Now pushing pidxBuffer into an Array3 via readPIDX()
With this commit the user can output:PIDX and read:PIDX. Also:
compare_uda -exact PIDX.uda stock.uda
compares exactly. Only 1 variable in index.xml works. There's a bug with multiple variables.
37 lines of code changed in 2 files:
Added ability to outputDoublesAsFloats in PIDX. Not Verified.
DataArchiver.cc
- saveLabels_PIDX() - top of the stack for writing PIDX
set pc.setOutputDoubleAsFloat()
Variable.cc
- added dividers
- emitPIDX()
pass in expected bufferSize and check against it.
Pass into emitNormal() outputDoubleAsFloat argument
PIDXOutputContext.*
- added methods setOutputDoubleAsFloat() and isOutputDoubleAsFloat()
DataWarehouse.h OnDemandDataWarehouse.h
- updated parameters for emitPIDX()
OnDemandDataWarehouse::emitPIDX()
- added {}
- passing expect buffer size through to var->emitPIDX()
67 lines of code changed in 2 files:
Implement parallel_for and parallel_reduce over 3D ranges
79 lines of code changed in 1 file:
DataArchiver: outputVariables()
- now saving to the runTimeStats the number of bytes saved during file IO. Both stock and PIDX formats
OnDemandDataWarehouse, DataWarehouse, Variables:
- emit() now returns the number of bytes written.
Simulation State:
- changed units from bytes/sec -> MBytes/sec.
We can now monitor the IO rates per MPI rank.
8 lines of code changed in 2 files:
Add getKokkosView() to Array3
Wrap the Array3 memory with an unmanaged Kokkos::View.
113 lines of code changed in 4 files:
<< operators
output "null PatchSubset" or "null Material Subset" if they are null.
0 lines of code changed in 2 files:
Improve interface to RowMajor and ColumnMajor ranges
110 lines of code changed in 1 file:
Create RowMajor and ColumnMajor Ranges to which map from a linear index to a mult-dimensional index
138 lines of code changed in 1 file:
(3 more)