Include What You Use

[chapman39]

Updating serac and system includes based on whether we're using them in the file directly using include-what-you-use.

This PR:

• adds (or removes) standard library includes that's directly used (or not used) in each file
• adds (or removes) serac includes that's directly used (or not used) in each file'
• tries to group include headers by class header (if cpp), system, tpl, and project includes

also,

• removes usage of using namespace serac::profiling; to better track profiling function usage (e.g. concat, SERAC_MARK_SCOPE, etc)

TODO

• run iwyu again and double check things in functional and functional tests
• going thru non-test serac_physics

my setup for iwyu

# build iwyu outside serac proj
git clone [email protected]:include-what-you-use/include-what-you-use.git
git checkout clang_14
cd include-what-you-use
mkdir build && cd build
module load clang/14.0.6
cmake -G "Unix Makefiles" -DCMAKE_PREFIX_PATH=/usr/tce/packages/clang/clang-14.0.6 ..
srun -N1 make -j

# add build to path
# PATH=/usr/workspace/meemee/iwyu/include-what-you-use/build/bin/:$PATH
# PATH=/usr/workspace/meemee/iwyu/include-what-you-use/:$PATH

# build serac with clang 14
module load python
./config-build.py -DCMAKE_CXX_INCLUDE_WHAT_YOU_USE=include-what-you-use
srun -N1 make -j 2> /tmp/iwyu.out
fix_includes.py -b < ../iwyu.out

after this, i one-by-one remove the comments and check if the header they added is worth adding or not. there is a --nocomments option, but it's useful to see why iwyu added the header.

workaround petsc circular includes

• Petsc internally has a circular include error, so I commented out this error in the iwyu source. I emailed the petsc team so they could be aware of this.
• Cycles are actually ignored in iwyu develop, but since we needed the clang_14 branch this workaround was needed.

Error running 'include-what-you-use': Cycle in include-mapping:
  <petscmacros.h> ->
  <petsc/private/petscadvancedmacros.h> ->
  <petsc/private/petscadvancedmacros.h>

[white238]

Suggested change

	#include <mpi.h>
	#include "mpi.h"

[chapman39]

should i do the same for googletest headers?