CMakeLists.txt

# ##############################################################################
# CMAKE CONFIGURATION FILE FOR DENDRO DIRECTORY
#
# This file in particular contains all of the options that apply specificially
# to the Dendro directory as it is compiled. This includes the example solvers
# as well as the library itself.
#
# NOTE: there is a CMakeLists-NonLibraryDefs.txt file which contains more options.
# The options in there must be included in the root directory of your project
# that you are using this library with. This will configure everything for building,
# but the options must be propagated to your own solvers and projects.
# 
# ##############################################################################

cmake_minimum_required(VERSION 3.1)
project(Dendro-5.0-Library C CXX Fortran)

option(DENDROLIB_ISOLATED_DIR "Only modify this if Dendro is not a library" OFF)

# we need a lot of other definitions if we are calling cmake directly for this folder.
if(DENDROLIB_ISOLATED_DIR)
  include("CMakeLists-NonLibraryDefs.txt")
endif()

message(STATUS "Now setting the CMake files for the Dendro Library...")

set(DENDRO_INCLUDE_FILES
    include/point.h
    include/pointT.h
    include/seqUtils.h
    include/seqUtils.tcc
    include/ompUtils.h
    include/ompUtils.tcc
    include/dendro.h
    include/binUtils.h
    include/hcurvedata.h
    include/genPts_par.h
    include/TreeNode.h
    include/key.h
    include/skey.h
    include/node.h
    include/treenode2vtk.h
    include/parUtils.h
    include/parUtils.tcc
    include/mesh.h
    include/mesh.tcc
    include/meshE2NUtils.tcc
    include/dendro.h
    include/colors.h
    include/dtypes.h
    include/sfcSort.h
    include/sfcSearch.h
    include/octUtils.h
    include/dendroIO.h
    include/mathMeshUtils.h
    include/mathUtils.h
    include/mathUtils.tcc
    include/memory_pool.h
    include/stencil.h
    include/dollar.hpp
    include/block.h
    include/sc_flops.h
    include/wavelet.h
    include/profiler.h
    include/dendroProfileParams.h
    include/daUtils.h
    include/daUtils.tcc
    include/oda.h
    include/oda.tcc
    include/odaUtils.h
    include/asyncExchangeContex.h
    include/matRecord.h
    include/nufft.h
    include/sub_oda.h
    include/sub_oda.tcc
    include/dvec.h
    include/meshUtils.h
    include/waveletRefEl.h
    include/waveletAMR.h
    include/waveletAMR.tcc
    test/include/testUtils.h
    test/include/testUtils.tcc
    test/include/meshTestUtils.h
    include/launcher.h
    include/device.h)

set(DENDRO_SOURCE_FILES
    src/dendro.cpp
    src/point.cpp
    src/binUtils.cpp
    src/hcurvedata.cpp
    src/genPts_par.cpp
    src/TreeNode.cpp
    src/treenode2vtk.cpp
    src/parUtils.cpp
    src/mesh.cpp
    src/octUtils.cpp
    src/dendroIO.cpp
    src/block.cpp
    src/sc_flops.cpp
    src/profiler.cpp
    src/dendroProfileParams.cpp
    src/oda.cpp
    src/odaUtils.cpp
    src/sub_oda.cpp
    src/meshUtils.cpp
    src/waveletRefEl.cpp
    test/src/meshTestUtils.cpp)

set(FEM_INC
    FEM/include/basis.h
    FEM/include/lapac.h
    FEM/include/tensor.h
    FEM/include/matvec.h
    FEM/include/workspace.h
    FEM/include/operators.h
    FEM/include/feMat.h
    FEM/include/feMatrix.h
    FEM/include/feVec.h
    FEM/include/feVector.h)

set(FEM_SRC FEM/examples/src/laplace.cpp FEM/src/basis.cpp FEM/src/refel.cpp
            FEM/src/tensor.cpp FEM/src/workspace.cpp)

set(LINALG_INC LinAlg/include/cg.h)

set(ODE_INC
    ODE/include/fdCoefficient.h
    ODE/include/rk.h
    ODE/include/rkMaxwell.h
    ODE/include/rkTransport.h
    ODE/include/rkTransportUtils.h
    ODE/include/ts.h
    ODE/include/blkAsync.h
    ODE/include/ctx.h
    ODE/include/ets.h
    ODE/include/enuts.h
    ODE/include/enutsUtils.tcc
    ODE/include/asyncCtxByLev.h
    ODE/include/subSM.h
    ODE/include/enutsOp.h
    ODE/include/sdc.h
    ODE/include/inverseCtx.h)

set(ODE_SRC ODE/src/rk.cpp ODE/src/subSM.cpp ODE/src/rkMaxwell.cpp
            ODE/src/rkTransport.cpp ODE/src/enutsOp.cpp)

set(IO_INC
    IO/vtk/include/oct2vtk.h IO/vtk/include/json.hpp
    IO/vtk/include/checkPoint.h IO/vtk/include/cencode.h IO/include/rawIO.h)

set(IO_SRC IO/vtk/src/oct2vtk.cpp IO/vtk/src/checkPoint.cpp)

set(ZLIB_INC
    IO/zlib/inc/crc32.h
    IO/zlib/inc/deflate.h
    IO/zlib/inc/gzguts.h
    IO/zlib/inc/inffast.h
    IO/zlib/inc/inffixed.h
    IO/zlib/inc/inflate.h
    IO/zlib/inc/inftrees.h
    IO/zlib/inc/trees.h
    IO/zlib/inc/zlib.h
    IO/zlib/inc/zconf.h
    IO/zlib/inc/zutil.h)

set(ZLIB_SRC
    IO/zlib/src/adler32.c
    IO/zlib/src/compress.c
    IO/zlib/src/crc32.c
    IO/zlib/src/deflate.c
    IO/zlib/src/gzclose.c
    IO/zlib/src/gzlib.c
    IO/zlib/src/gzread.c
    IO/zlib/src/gzwrite.c
    IO/zlib/src/infback.c
    IO/zlib/src/inffast.c
    IO/zlib/src/inflate.c
    IO/zlib/src/inftrees.c
    IO/zlib/src/trees.c
    IO/zlib/src/uncompr.c
    IO/zlib/src/zutil.c)

if(WITH_CUDA)
  set(DENDRO_INCLUDE_FILES ${DENDRO_INCLUDE_FILES} include/cudaUtils.h)
  set(DENDRO_SOURCE_FILES ${DENDRO_SOURCE_FILES} src/cudaUtils.cpp src/oda.cpp
                          FEM/examples/src/heatMat.cpp)
endif()

# ==========================
# DENDRO LIBRARY DEFINITION -- Starting with CUDA
# ==========================
if(WITH_CUDA)
  set(SOURCE_FILES
      ${DENDRO_SOURCE_FILES}
      ${FEM_SRC}
      ${ODE_SRC}
      ${IO_SRC}
      ${ZLIB_SRC}
      GPU/include/derivs_cu.cuh
      GPU/src/refel_const.cu
      GPU/src/mesh_gpu.cu)
  cuda_add_library(dendro5_cuda ${SOURCE_FILES})
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/GPU/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
  target_include_directories(
    dendro5_cuda PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/FEM/examples/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
  target_include_directories(dendro5_cuda
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/include)
  target_include_directories(dendro5_cuda PUBLIC ${MPI_INCLUDE_PATH})
  target_include_directories(dendro5_cuda PUBLIC ${CUDA_INCLUDE_DIRS})
  target_link_libraries(dendro5_cuda ${CUDA_LIBRARIES})
endif()

# ------ Non-CUDA version of library
add_library(dendro5 ${DENDRO_SOURCE_FILES} ${FEM_SRC} ${ODE_SRC} ${IO_SRC}
                    ${ZLIB_SRC})
target_link_libraries(dendro5 PUBLIC ${MPI_LIBRARIES} m)
target_include_directories(dendro5 PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(
  dendro5 PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/FEM/examples/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(dendro5
                           PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/include)
target_include_directories(dendro5 PUBLIC ${MPI_INCLUDE_PATH})
target_include_directories(dendro5 PUBLIC ${GSL_INCLUDE_DIRS})
if(WITH_CUDA)
  target_include_directories(dendro5 PUBLIC ${CUDA_INCLUDE_DIRS})
endif()

if(WITH_BLAS_LAPACK)
  target_include_directories(dendro5 PUBLIC ${LAPACK_INCLUDE_DIR})
  target_link_libraries(dendro5 PUBLIC ${LAPACK_LIBRARIES})
endif()

if(BUILD_WITH_PETSC)
  target_include_directories(dendro5 PUBLIC ${PETSC_INCLUDES})
  target_link_libraries(dendro5 PUBLIC ${PETSC_LIBRARIES})
endif()

# =======================
# =======================
# TESTS AND EXAMPLE PROGRAMS
# =======================
# =======================
if(WITH_CUDA)
  cuda_add_executable(run_meshgpu_tests
                      ${CMAKE_CURRENT_SOURCE_DIR}/GPU/src/run_meshgpu_tests.cu)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/GPU/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
  target_include_directories(run_meshgpu_tests
                             PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/IO/include)
  target_include_directories(run_meshgpu_tests PUBLIC ${MPI_INCLUDE_PATH})
  target_include_directories(run_meshgpu_tests PUBLIC ${CUDA_INCLUDE_DIRS})
  target_link_libraries(run_meshgpu_tests dendro5 dendro5_cuda)
endif(WITH_CUDA)

set(SOURCE_FILES Hilbert/src/genHTables.cpp include/radix.h)
add_executable(genHtables ${SOURCE_FILES})
target_include_directories(genHtables
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)

set(SOURCE_FILES Hilbert/src/sfcMatvecTable.cpp include/dendro.h)
add_executable(genSFCMatVecTables ${SOURCE_FILES})
target_link_libraries(genSFCMatVecTables m)
target_include_directories(genSFCMatVecTables
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)

set(SOURCE_FILES examples/src/ptsSort.cpp)
add_executable(ptsSort ${SOURCE_FILES})
target_include_directories(ptsSort PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(ptsSort
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(ptsSort
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(ptsSort PRIVATE ${MPI_INCLUDE_PATH})
target_link_libraries(ptsSort dendro5 ${MPI_LIBRARIES} m)

set(SOURCE_FILES examples/include/testOctUtils.h examples/src/testOCtUtils.cpp)
add_executable(testOctUtils ${SOURCE_FILES})
target_link_libraries(testOctUtils dendro5 ${MPI_LIBRARIES} m)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(testOctUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(testOctUtils PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(testOctUtils PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/tstTreeSearch.cpp)
add_executable(tstTreeSearch ${SOURCE_FILES})
target_link_libraries(tstTreeSearch dendro5 ${MPI_LIBRARIES} m)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(tstTreeSearch
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(tstTreeSearch PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(tstTreeSearch PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/octUtilsBenchmark.cpp)
add_executable(octUtilBenchmark ${SOURCE_FILES})
target_link_libraries(octUtilBenchmark dendro5 ${MPI_LIBRARIES} m)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(octUtilBenchmark
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(octUtilBenchmark PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(octUtilBenchmark PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/bucketBench.cpp)
add_executable(bucketBench ${SOURCE_FILES})
target_link_libraries(bucketBench dendro5 ${MPI_LIBRARIES} m)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(bucketBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(bucketBench PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(bucketBench PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/mfreeTest.cpp)
add_executable(mfreeBench ${SOURCE_FILES})
target_link_libraries(mfreeBench dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(mfreeBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(mfreeBench PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(mfreeBench PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/meshBenchmark.cpp)
add_executable(meshBench ${SOURCE_FILES})
target_link_libraries(meshBench dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(meshBench
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(meshBench PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(meshBench PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/meshE2NCheck.cpp)
add_executable(meshE2NCheck ${SOURCE_FILES})
target_link_libraries(meshE2NCheck dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES}
                      m)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(meshE2NCheck
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(meshE2NCheck PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(meshE2NCheck PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES test/src/run_all_tests.cpp)
add_executable(run_all_tests ${SOURCE_FILES})
target_link_libraries(run_all_tests dendro5 ${LAPACK_LIBRARIES}
                      ${MPI_LIBRARIES} m)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(run_all_tests
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(run_all_tests PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(run_all_tests PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES test/src/benchUtils.cpp)
add_executable(benchUtils ${SOURCE_FILES})
target_link_libraries(benchUtils dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(benchUtils
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(benchUtils PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(benchUtils PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES ODE/examples/testLTSBlkVec.cpp)
add_executable(testLTSBlkVec ${SOURCE_FILES})
target_link_libraries(testLTSBlkVec dendro5 ${LAPACK_LIBRARIES}
                      ${MPI_LIBRARIES} m)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(testLTSBlkVec
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(testLTSBlkVec PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(testLTSBlkVec PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/dgVecTest.cpp)
add_executable(dgVecTest ${SOURCE_FILES})
target_link_libraries(dgVecTest dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(dgVecTest
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(dgVecTest PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(dgVecTest PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/testInterp.cpp)
add_executable(testInterp ${SOURCE_FILES})
target_link_libraries(testInterp dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(testInterp
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(testInterp PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(testInterp PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES examples/src/meshLooping.cpp)
add_executable(meshLoop ${SOURCE_FILES})
target_link_libraries(meshLoop dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(meshLoop PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(meshLoop
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(meshLoop PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(meshLoop PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/refelExample.cpp)
add_executable(refEl ${SOURCE_FILES})
target_link_libraries(refEl dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(refEl PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(refEl
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(refEl PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(refEl PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/refelOctreeExample.cpp)
add_executable(refElOctree ${SOURCE_FILES})
target_link_libraries(refElOctree dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES}
                      m)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(refElOctree
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(refElOctree PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(refElOctree PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES ODE/examples/transportEq.cpp)
add_executable(transportEq ${SOURCE_FILES})
target_link_libraries(transportEq dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES}
                      m)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(transportEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(transportEq PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(transportEq PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/laplace.cpp)
add_executable(laplaceEq ${SOURCE_FILES})
target_link_libraries(laplaceEq dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(laplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(laplaceEq PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(laplaceEq PRIVATE ${GSL_INCLUDE_DIRS})

set(SOURCE_FILES FEM/examples/src/heatMat.cpp FEM/examples/src/heatVec.cpp
                 FEM/examples/src/heatEq.cpp)
add_executable(heatEq ${SOURCE_FILES})
target_link_libraries(heatEq dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES} m)
target_include_directories(heatEq PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(
  heatEq PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/examples/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(heatEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(heatEq PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(heatEq PRIVATE ${GSL_INCLUDE_DIRS})

# this is not working, carving things out from octree domain
set(SOURCE_FILES FEM/examples/src/subdaExample.cpp)
add_executable(subDAExample ${SOURCE_FILES})
target_link_libraries(subDAExample dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES}
                      m)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(
  subDAExample PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/examples/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(subDAExample
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(subDAExample PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(subDAExample PRIVATE ${GSL_INCLUDE_DIRS})

# apply the metric in a different way - traversing the tree without using the datastructures
set(SOURCE_FILES FEM/examples/src/sfcLaplace.cpp)
add_executable(sfcLaplaceEq ${SOURCE_FILES})
target_link_libraries(sfcLaplaceEq dendro5 ${LAPACK_LIBRARIES} ${MPI_LIBRARIES}
                      m)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/test/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/examples/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/FEM/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/ODE/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/LinAlg/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/vtk/include)
target_include_directories(sfcLaplaceEq
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/IO/zlib/inc)
target_include_directories(sfcLaplaceEq PRIVATE ${MPI_INCLUDE_PATH})
target_include_directories(sfcLaplaceEq PRIVATE ${GSL_INCLUDE_DIRS})