Merge pull request #183 from Oden-EAG/next

Merging development branch into master for hp3D's JOSS paper release version.

.gitignore

@@ -13,6 +13,7 @@ fort.20
 *~
 m_options
 log.txt
+*__genmod.f90
 
 # Data files
 history

CHANGELOG

@@ -0,0 +1,31 @@
+
+=================
+Version 1.0 (dev)
+=================
+
+- Renamed preprocessor flags:
+  `C_MODE` --> `HP3D_COMPLEX`, `DEBUG_MODE` --> `HP3D_DEBUG`
+
+- Added preprocessor flag `HP3D_USE_X11` and `HP3D_USE_MPI_F08`
+
+- Added CI via GitHub actions for Linux and macOS.
+
+- New default configuration files in `m_options_linux` and `m_options_macos`. 
+  Both m_options files use PETSc's configuration for setting compiler options,
+  library paths, and include paths. The user only needs to provide the
+  corresponding PETSC_DIR and PETSC_ARCH.
+
+- Introduced global parameter `MAX_NRINDEX_HEV=31` used for binary-encoding
+  Dirichlet flags of (at most 31) H1, H(div), and H(curl) components.
+  This parameter replaces the previous global parameter MAX_NRINDEX.
+
+- Updated all of the remaining fixed-format (F77) legacy code.
+
+==========================================
+Version 1.0-beta, released on Sep 24, 2023
+==========================================
+
+- Release tag: 
+  https://github.com/Oden-EAG/hp3d/releases/tag/v1.0-beta
+
+- Initial pre-release.

README.md

@@ -52,13 +52,13 @@ Note: PETSc can also install MPI libraries if needed,
 e.g. `--download-openmpi=yes` or `--download-mpich=yes`.
 
 ## Compiler options
-Compilation is governed by preprocessing flags `COMPLEX` and `DEBUG`.
-- `COMPLEX = 0` , stiffness matrix, load vector(s) and solution DOFs are real-valued
-- `COMPLEX = 1` , stiffness matrix, load vector(s) and solution DOFs are complex-valued
-- `DEBUG   = 0` , compiler uses optimization flags, and the library performs only minimal checks during the computation
-- `DEBUG   = 1` , compiler uses debug flags, and the library performs additional checks during the computation
+Compilation is governed by preprocessing flags `HP3D_COMPLEX` and `HP3D_DEBUG`.
+- `HP3D_COMPLEX = 0` , stiffness matrix, load vector(s) and solution DOFs are real-valued
+- `HP3D_COMPLEX = 1` , stiffness matrix, load vector(s) and solution DOFs are complex-valued
+- `HP3D_DEBUG   = 0` , compiler uses optimization flags, and the library performs only minimal checks during the computation
+- `HP3D_DEBUG   = 1` , compiler uses debug flags, and the library performs additional checks during the computation
 
-Library will be created under either `hp3d/complex/` or `hp3d/real/`.
+Library will be created under either `hp3d/trunk/complex/` or `hp3d/trunk/real/`.
 
 Additional preprocessing flags for enabling/disabling dependencies on third-party libraries:
 - `HP3D_USE_INTEL_MKL = 0/1` , disable/enable dependency on Intel MKL package

trunk/m_options_files/custom/m_options_LC

@@ -7,8 +7,8 @@ HP3D_BASE_PATH  = /g/g92/keith10/Work/quartz/par_hp3d/trunk
 #------------------------------------------------------------------
 # PREPROCESSOR VARIABLES
 #------------------------------------------------------------------
-COMPLEX ?= 0
-DEBUG   ?= 0
+HP3D_COMPLEX ?= 0
+HP3D_DEBUG   ?= 0
 
 # Dependencies
 HP3D_USE_INTEL_MKL ?= 0
@@ -41,12 +41,12 @@ endif
 #FFLAGS += -Wpedantic
 
 # Optimization flags
-ifeq ($(DEBUG),0)
+ifeq ($(HP3D_DEBUG),0)
   FFLAGS += -O3
 endif
 
 # Debug flags
-ifeq ($(DEBUG),1)
+ifeq ($(HP3D_DEBUG),1)
   FFLAGS += -Og -g -fbacktrace -fcheck=all
 endif
 
@@ -78,7 +78,7 @@ MKL_INCS = -I/opt/intel/mkl/include
 # also adding Zoltan library dependence
 # also adding PETSC library dependence (petsc needs phdf5)
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   PETSC_LIB = /Users/stefan/hp3D/LIBS/petsc-3.13.1/arch-darwin-c-complex/lib
   PETSC_INC = /Users/stefan/hp3D/LIBS/petsc-3.13.1/arch-darwin-c-complex/include
 else
@@ -124,7 +124,7 @@ SRC_PATH          = src
 MODULE_PATH       = module
 LIB_PATH          = lib
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   HP3D_PATH       = $(HP3D_PATH_COMPLEX)
   OBJ_PATH        = $(OBJ_PATH_COMPLEX)
 else
@@ -159,7 +159,6 @@ HP3D_GMP        = $(HP3D_PATH)/lib/libhp3d_gmp.a
 
 HP3D_LINK_LIBS    = $(HP3D_LIB) $(HP3D_FRONTAL)
 HP3D_LINK_INCS    = -I$(HP3D_PATH)/common/hp3d \
-                    -I$(HP3D_PATH)/common/graphics \
                     -I$(HP3D_PATH)/module
 
 #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -191,7 +190,7 @@ PROB_INCS    += $(HP3D_LINK_INCS)   \
 # Files with ending in .F and .F90 (not .f and .f90)
 # are preprocessed according to certain directives
 
-PROB_PP_DEFS  = -D"C_MODE=$(COMPLEX)" \
-                -D"DEBUG_MODE=$(DEBUG)" \
+PROB_PP_DEFS  = -D"HP3D_COMPLEX=$(HP3D_COMPLEX)" \
+                -D"HP3D_DEBUG=$(HP3D_DEBUG)" \
                 -D"HP3D_USE_OPENMP=$(HP3D_USE_OPENMP)" \
                 -D"HP3D_USE_INTEL_MKL=$(HP3D_USE_INTEL_MKL)"

trunk/m_options_files/custom/m_options_TACC_intel18

@@ -7,8 +7,8 @@ HP3D_BASE_PATH  = ${WORK}/hp3d/trunk
 #------------------------------------------------------------------
 # PREPROCESSOR VARIABLES
 #------------------------------------------------------------------
-COMPLEX  ?= 0
-DEBUG    ?= 0
+HP3D_COMPLEX ?= 0
+HP3D_DEBUG   ?= 0
 
 #------------------------------------------------------------------
 # COMPILER SETTINGS (a 64bit processor architecture is assumed)
@@ -43,12 +43,12 @@ ifeq ($(HP3D_USE_OPENMP),1)
 endif
 
 # Optimization flags
-ifeq ($(DEBUG),0)
+ifeq ($(HP3D_DEBUG),0)
   FFLAGS += -O3 -xCORE-AVX512
 endif
 
 # Debug flags
-ifeq ($(DEBUG),1)
+ifeq ($(HP3D_DEBUG),1)
   FFLAGS += -O0 -g -traceback -check all -debug all
   FFLAGS += -check noarg_temp_created -assume noprotect_constants
 endif
@@ -92,7 +92,7 @@ MKL_INCS = -I${MKLROOT}/include/intel64/lp64 -I${MKLROOT}/include
 # also adding Zoltan library dependence
 # also adding PETSC library dependence (petsc needs phdf5)
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   TACC_PETSC32_LIB = /home1/apps/intel18/impi18_0/petsc/3.11/skylake-complex/lib
   TACC_PETSC32_INC = /home1/apps/intel18/impi18_0/petsc/3.11/skylake-complex/include
   TACC_PETSC64_LIB = /home1/apps/intel18/impi18_0/petsc/3.11/skylake-complexi64/lib
@@ -143,7 +143,7 @@ SRC_PATH          = src
 MODULE_PATH       = module
 LIB_PATH          = lib
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   HP3D_PATH       = $(HP3D_PATH_COMPLEX)
   OBJ_PATH        = $(OBJ_PATH_COMPLEX)
 else
@@ -174,7 +174,6 @@ HP3D_LINK_LIBS    = -Wl,--start-group \
 #HP3D_LINK_LIBS   += $(HP3D_COMMON) $(HP3D_GMP)
 HP3D_LINK_LIBS   += -Wl,--end-group
 HP3D_LINK_INCS    = -I$(HP3D_PATH)/common/hp3d \
-                    -I$(HP3D_PATH)/common/graphics \
                     -I$(HP3D_PATH)/module
 
 #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
@@ -217,7 +216,7 @@ PROB_INCS    += $(HP3D_LINK_INCS)   \
 # are preprocessed according to certain directives
 
 HP3D_USE_INTEL_MKL = 1
-PROB_PP_DEFS  = -D"C_MODE=$(COMPLEX)" \
-                -D"DEBUG_MODE=$(DEBUG)" \
+PROB_PP_DEFS  = -D"HP3D_COMPLEX=$(HP3D_COMPLEX)" \
+                -D"HP3D_DEBUG=$(HP3D_DEBUG)" \
                 -D"HP3D_USE_OPENMP=$(HP3D_USE_OPENMP)" \
                 -D"HP3D_USE_INTEL_MKL=$(HP3D_USE_INTEL_MKL)"

trunk/m_options_files/custom/m_options_TACC_intel19

@@ -7,8 +7,8 @@ HP3D_BASE_PATH  = ${WORK2}/hp3d/trunk
 #------------------------------------------------------------------
 # PREPROCESSOR VARIABLES
 #------------------------------------------------------------------
-COMPLEX  ?= 0
-DEBUG    ?= 0
+HP3D_COMPLEX ?= 0
+HP3D_DEBUG   ?= 0
 
 #------------------------------------------------------------------
 # COMPILER SETTINGS (a 64bit processor architecture is assumed)
@@ -43,12 +43,12 @@ ifeq ($(HP3D_USE_OPENMP),1)
 endif
 
 # Optimization flags
-ifeq ($(DEBUG),0)
+ifeq ($(HP3D_DEBUG),0)
   FFLAGS += -O3 -xCORE-AVX512
 endif
 
 # Debug flags
-ifeq ($(DEBUG),1)
+ifeq ($(HP3D_DEBUG),1)
   FFLAGS += -O0 -g -traceback -check all -debug all
   FFLAGS += -check noarg_temp_created -assume noprotect_constants
 endif
@@ -91,7 +91,7 @@ MKL_INCS = -I${MKLROOT}/include/intel64/lp64 -I${MKLROOT}/include
 # also adding Zoltan library dependence
 # also adding PETSC library dependence (petsc needs phdf5)
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   TACC_PETSC32_LIB = /home1/apps/intel19/impi19_0/petsc/3.15/clx-complex/lib
   TACC_PETSC32_INC = /home1/apps/intel19/impi19_0/petsc/3.15/clx-complex/include
   TACC_PETSC64_LIB = /home1/apps/intel19/impi19_0/petsc/3.15/clx-complexi64/lib
@@ -142,7 +142,7 @@ SRC_PATH          = src
 MODULE_PATH       = module
 LIB_PATH          = lib
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   HP3D_PATH       = $(HP3D_PATH_COMPLEX)
   OBJ_PATH        = $(OBJ_PATH_COMPLEX)
 else
@@ -173,7 +173,6 @@ HP3D_LINK_LIBS    = -Wl,--start-group \
 #HP3D_LINK_LIBS   += $(HP3D_COMMON) $(HP3D_GMP)
 HP3D_LINK_LIBS   += -Wl,--end-group
 HP3D_LINK_INCS    = -I$(HP3D_PATH)/common/hp3d \
-                    -I$(HP3D_PATH)/common/graphics \
                     -I$(HP3D_PATH)/module
 
 #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
@@ -216,7 +215,7 @@ PROB_INCS    += $(HP3D_LINK_INCS)   \
 # are preprocessed according to certain directives
 
 HP3D_USE_INTEL_MKL = 1
-PROB_PP_DEFS  = -D"C_MODE=$(COMPLEX)" \
-                -D"DEBUG_MODE=$(DEBUG)" \
+PROB_PP_DEFS  = -D"HP3D_COMPLEX=$(HP3D_COMPLEX)" \
+                -D"HP3D_DEBUG=$(HP3D_DEBUG)" \
                 -D"HP3D_USE_OPENMP=$(HP3D_USE_OPENMP)" \
                 -D"HP3D_USE_INTEL_MKL=$(HP3D_USE_INTEL_MKL)"

trunk/m_options_files/custom/m_options_cent_os_7

@@ -7,8 +7,8 @@ HP3D_BASE_PATH  = /home/stefan/hp3D/LIBS/hp3d/trunk
 #------------------------------------------------------------------
 # PREPROCESSOR VARIABLES
 #------------------------------------------------------------------
-COMPLEX ?= 0
-DEBUG   ?= 0
+HP3D_COMPLEX ?= 0
+HP3D_DEBUG   ?= 0
 
 # Dependencies
 HP3D_USE_INTEL_MKL ?= 0
@@ -39,12 +39,12 @@ endif
 #FFLAGS += -Wpedantic
 
 # Optimization flags
-ifeq ($(DEBUG),0)
+ifeq ($(HP3D_DEBUG),0)
   FFLAGS += -O3
 endif
 
 # Debug flags
-ifeq ($(DEBUG),1)
+ifeq ($(HP3D_DEBUG),1)
   FFLAGS += -Og -g -fbacktrace -fcheck=all
 endif
 
@@ -81,7 +81,7 @@ MKL_INCS = -I/opt/intel/mkl/include
 # also adding Zoltan library dependence
 # also adding PETSC library dependence (petsc needs phdf5)
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   PETSC_LIB = /home/stefan/hp3D/LIBS/petsc-3.13.5/arch-centos-complex/lib
   PETSC_INC = /home/stefan/hp3D/LIBS/petsc-3.13.5/arch-centos-complex/include
 else
@@ -133,7 +133,7 @@ SRC_PATH          = src
 MODULE_PATH       = module
 LIB_PATH          = lib
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   HP3D_PATH       = $(HP3D_PATH_COMPLEX)
   OBJ_PATH        = $(OBJ_PATH_COMPLEX)
 else
@@ -168,7 +168,6 @@ HP3D_LINK_LIBS   += -Wl,--end-group
 
 #HP3D_LINK_LIBS    = $(HP3D_LIB) $(HP3D_FRONTAL)
 HP3D_LINK_INCS    = -I$(HP3D_PATH)/common/hp3d \
-                    -I$(HP3D_PATH)/common/graphics \
                     -I$(HP3D_PATH)/module
 
 #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -202,7 +201,7 @@ PROB_INCS    += $(HP3D_LINK_INCS)   \
 # Files with ending in .F and .F90 (not .f and .f90)
 # are preprocessed according to certain directives
 
-PROB_PP_DEFS  = -D"C_MODE=$(COMPLEX)" \
-                -D"DEBUG_MODE=$(DEBUG)" \
+PROB_PP_DEFS  = -D"HP3D_COMPLEX=$(HP3D_COMPLEX)" \
+                -D"HP3D_DEBUG=$(HP3D_DEBUG)" \
                 -D"HP3D_USE_OPENMP=$(HP3D_USE_OPENMP)" \
                 -D"HP3D_USE_INTEL_MKL=$(HP3D_USE_INTEL_MKL)"

trunk/m_options_files/custom/m_options_debian_10

@@ -7,8 +7,8 @@ HP3D_BASE_PATH  = /home/stefan/hp3D/LIBS/hp3d/trunk
 #------------------------------------------------------------------
 # PREPROCESSOR VARIABLES
 #------------------------------------------------------------------
-COMPLEX ?= 0
-DEBUG   ?= 0
+HP3D_COMPLEX ?= 0
+HP3D_DEBUG   ?= 0
 
 # Dependencies
 HP3D_USE_INTEL_MKL ?= 0
@@ -39,12 +39,12 @@ endif
 #FFLAGS += -Wpedantic
 
 # Optimization flags
-ifeq ($(DEBUG),0)
+ifeq ($(HP3D_DEBUG),0)
   FFLAGS += -O3
 endif
 
 # Debug flags
-ifeq ($(DEBUG),1)
+ifeq ($(HP3D_DEBUG),1)
   FFLAGS += -Og -g -fbacktrace -fcheck=all
 endif
 
@@ -81,7 +81,7 @@ MKL_INCS = -I/opt/intel/mkl/include
 # also adding Zoltan library dependence
 # also adding PETSC library dependence (petsc needs phdf5)
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   PETSC_LIB = /home/stefan/hp3D/LIBS/petsc-3.13.5/arch-debian-complex/lib
   PETSC_INC = /home/stefan/hp3D/LIBS/petsc-3.13.5/arch-debian-complex/include
 else
@@ -133,7 +133,7 @@ SRC_PATH          = src
 MODULE_PATH       = module
 LIB_PATH          = lib
 
-ifeq ($(COMPLEX),1)
+ifeq ($(HP3D_COMPLEX),1)
   HP3D_PATH       = $(HP3D_PATH_COMPLEX)
   OBJ_PATH        = $(OBJ_PATH_COMPLEX)
 else
@@ -168,7 +168,6 @@ HP3D_LINK_LIBS   += -Wl,--end-group
 
 #HP3D_LINK_LIBS    = $(HP3D_LIB) $(HP3D_FRONTAL)
 HP3D_LINK_INCS    = -I$(HP3D_PATH)/common/hp3d \
-                    -I$(HP3D_PATH)/common/graphics \
                     -I$(HP3D_PATH)/module
 
 #- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -202,7 +201,7 @@ PROB_INCS    += $(HP3D_LINK_INCS)   \
 # Files with ending in .F and .F90 (not .f and .f90)
 # are preprocessed according to certain directives
 
-PROB_PP_DEFS  = -D"C_MODE=$(COMPLEX)" \
-                -D"DEBUG_MODE=$(DEBUG)" \
+PROB_PP_DEFS  = -D"HP3D_COMPLEX=$(HP3D_COMPLEX)" \
+                -D"HP3D_DEBUG=$(HP3D_DEBUG)" \
                 -D"HP3D_USE_OPENMP=$(HP3D_USE_OPENMP)" \
                 -D"HP3D_USE_INTEL_MKL=$(HP3D_USE_INTEL_MKL)"