Directory include/sci_defs/

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dav 2016-10-12 15:09 Rev.: 55863

Update configure to remove Wasatch .o files when W3P changes (need to rebuild configure but wanted to get tihs in).

11 lines of code changed in 2 files:

• include/sci_defs: wasatch_testdefs.h.in (new)

jas 2016-08-05 12:17 Rev.: 55575

Adds an additional preprocessor define to handle the case between cblas.h from macports and the native MacOSX native veclib.

3 lines of code changed in 2 files:

• include/sci_defs: blas_testdefs.h.in (+3 -2)

cgritton 2016-07-18 09:19 Rev.: 55524

Added a finite folume component to solve electrostatics problems

1 lines of code changed in 2 files:

• include/sci_defs: uintah_testdefs.h.in (new)

ahumphrey 2016-06-27 12:54 Rev.: 55477

* 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.

0 lines of code changed in 14 files:

• include/sci_defs: collab_vis_testdefs.h.in (del), dynamic_cast_testdefs.h.in (del), exe_testdefs.h.in (del), framework_testdefs.h.in (del), image_testdefs.h.in (del), kepler_testdefs.h.in (del), loki_testdefs.h.in (del), mdsplus_testdefs.h.in (del), scisock_testdefs.h.in (del), ssl_testdefs.h.in (del), tao_testdefs.h.in (del), tena_testdefs.h.in (del), tena_testdefs.in (del), vdt_testdefs.h.in (del)

dav 2016-06-22 17:18 Rev.: 55462

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.

18 lines of code changed in 2 files:

• include/sci_defs: mpi_testdefs.h.in (new)

ahumphrey 2016-06-21 13:57 Rev.: 55453

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.

1938 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+1938 -8)

ahumphrey 2016-06-14 21:26 Rev.: 55445

Revert -r55443, until folks can get compilers upgraded and buildbot MPI is updated.

8 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+8 -1938)

dsunder 2016-06-14 15:05 Rev.: 55444

Replace thread_local with __thread to support compilers which do not fully support c++11 thread API

1 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+1 -1)

ahumphrey 2016-06-14 13:47 Rev.: 55443

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.

1938 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+1938 -8)

ahumphrey 2016-06-10 12:31 Rev.: 55430

Revert r55429.

Still having an MPICH/OpenMPI compatibility problem.

8 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+8 -2002)

ahumphrey 2016-06-10 11:38 Rev.: 55429

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.

2002 lines of code changed in 1 file:

• include/sci_defs: mpi_testdefs.h.in (+2002 -8)

ahumphrey 2016-06-07 09:19 Rev.: 55420

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 2 files:

• include/sci_defs: config_testdefs.h.in (new)

dav 2016-05-17 11:29 Rev.: 55360

Additions to get PoKitt (Cantera) linking in properly.

M configure
M configure.ac

- Find Cantera libs and add them to PoKiTT linking.

M configVars.mk.in

- Just a few comments about where libs come from.

M include/sci_defs/wasatch_testdefs.h.in

- PoKiTT define implies Cantera so don't need separate define.

2 lines of code changed in 1 file:

• include/sci_defs: wasatch_testdefs.h.in (+2 -3)

dav 2016-05-16 14:48 Rev.: 55353

Fix the problem with fortran .h files (in Arches) not being generated correctly (on the binary
side) when CUDA is turned on.

Update the make system so that the dependency rules for CUDA enabled files are created
automatically. The user no-longer has to specify that each CUDA_ENABLED_SRCS .cu file
depends on the corresponding .cc file. Updated both Wasatch and Arches to use the
new approach.

M Makefile.in

- Add a 'function' (make-cuda-target) that will create CUDA dependency rules automatically,
instead of having the developer have to list the rules manually. This function must
be called in each sub.mk file that creates a CUDA_ENABLED_SRCS list.
- Remove all .cu and (mostly fortran) .h files from the <bin> side when
"make cleanreally" is called.

M configure
M configure.ac

- Put in check to verify that Uintah and Wasatch 3P are both (or neither) being
built with CUDA.
- Will also add Candera check once I get more info.

A include/sci_defs/wasatch_testdefs.h.in

- Place PoKitt and Candera defines in new (configure generated binary side) wasatch_defs.h
file.

M CCA/Components/Arches/sub.mk

- Fix fortran .h file dependency problem. Note, these dependencies are have been (and
continue to be) manually entered into the sub.mk file. However, previously, they
used multiple lines (eg: Source.$(OBJEXT) was written 5 times. You don't need to
do this, you can just list it once and then put all the files it depends on.

When building without CUDA, the fortran .h files are needed to create
the object files (eg: Source.o). However, if CUDA is turned on, then they are
needed to create the CUDA .cu file (eg: <bin>/Source.cu). Perviously, at least
on some machines (though the problem should have shown up on all machines?), the fortran
.h files were not being generated.

It appears that currently Arches/sub.mk is the only directory that has CUDA files that
are dependent on fortran .h files. If this occurs in other sub-dirs for Arches (as
CUDA is added to the code), then the same approach should be taken in those files.

M CCA/Components/Arches/ChemMix/sub.mk
M CCA/Components/Arches/CoalModels/sub.mk
M CCA/Components/Arches/LagrangianParticles/sub.mk
M CCA/Components/Arches/Operators/sub.mk
M CCA/Components/Arches/ParticleModels/sub.mk
M CCA/Components/Arches/PropertyModels/sub.mk
M CCA/Components/Arches/PropertyModelsV2/sub.mk
M CCA/Components/Arches/SourceTerms/sub.mk
M CCA/Components/Arches/Task/sub.mk
M CCA/Components/Arches/Transport/sub.mk
M CCA/Components/Arches/TransportEqns/sub.mk
M CCA/Components/Arches/Utility/sub.mk
M CCA/Components/Arches/WallHTModels/sub.mk
M CCA/Components/Wasatch/Expressions/BoundaryConditions/sub.mk
M CCA/Components/Wasatch/Expressions/MMS/sub.mk
M CCA/Components/Wasatch/Expressions/PostProcessing/sub.mk
M CCA/Components/Wasatch/Expressions/Turbulence/sub.mk
M CCA/Components/Wasatch/Expressions/sub.mk
M CCA/Components/Wasatch/Operators/sub.mk
M CCA/Components/Wasatch/Transport/sub.mk
M CCA/Components/Wasatch/sub.mk

- Call make system function make-cuda-target to generate CUDA .cu dependencies.

34 lines of code changed in 1 file:

• include/sci_defs: wasatch_testdefs.h.in (+34)

jas 2016-01-08 15:45 Rev.: 54640

Update copyright date to 2016.

41 lines of code changed in 65 files:

• include/sci_defs: bits_testdefs.h.in (+1 -1), blas_testdefs.h.in (+1 -1), boost_testdefs.h.in (+1 -1), collab_vis_testdefs.h.in (new 1), compile_testdefs.h.in (+1 -1), cuda_testdefs.h.in (+1 -1), dynamic_cast_testdefs.h.in (new 1), environment_testdefs.h.in (+1 -1), error_testdefs.h.in (new), exe_testdefs.h.in (new 1), framework_testdefs.h.in (new 1), gperftools_testdefs.h.in (+1 -1), hashmap_testdefs.h.in (new), hypre_testdefs.h.in (new), ieeefp_testdefs.h.in (new), image_testdefs.h.in (new 1), ipm_testdefs.h.in (+1 -1), kepler_testdefs.h.in (new 1), lapack_testdefs.h.in (+1 -1), loki_testdefs.h.in (new 1), magma_testdefs.h.in (new), malloc_testdefs.h.in (new), mdsplus_testdefs.h.in (new 1), mpi_testdefs.h.in (+1 -1), osx_testdefs.h.in (+1 -1), papi_testdefs.h.in (+1 -1), petsc_testdefs.h.in (new), pidx_testdefs.h.in (+1 -1), scisock_testdefs.h.in (new 1), ssl_testdefs.h.in (new 1), stat64_testdefs.h.in (new), tao_testdefs.h.in (new 1), template_testdefs.h.in (new), tena_testdefs.h.in (new 1), tena_testdefs.in (new 1), thread_testdefs.h.in (+1 -1), uintah_testdefs.h.in (+1 -1), vdt_testdefs.h.in (new 1), visit_testdefs.h.in (+1 -1), visus_testdefs.h.in (new), z_testdefs.h.in (new)