Initial commit

BoxLib.license.txt

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+SOURCE CODE LICENSE AGREEMENT
+BoxLib Version 2014-02-28, Copyright (c) 2013, 
+The Regents of the University of California, 
+through Lawrence Berkeley National Laboratory 
+(subject to receipt of any required approvals from the U.S.
+Dept. of Energy).  All rights reserved."
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+(1) Redistributions of source code must retain the above copyright
+notice, this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence
+Berkeley National Laboratory, U.S. Dept. of Energy nor the names of
+its contributors may be used to endorse or promote products derived
+from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes,
+patches, or upgrades to the features, functionality or performance of
+the source code ("Enhancements") to anyone; however, if you choose to
+make your Enhancements available either publicly, or directly to
+Lawrence Berkeley National Laboratory, without imposing a separate
+written license agreement for such Enhancements, then you hereby grant
+the following license: a  non-exclusive, royalty-free perpetual
+license to install, use, modify, prepare derivative works, incorporate
+into other computer software, distribute, and sublicense such
+enhancements or derivative works thereof, in binary and source code
+form.

GNUmakefile

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+#MPI := 
+MPI := t
+
+#OMP := 
+OMP := t
+
+NDEBUG := t
+#NDEBUG := 
+
+### Edit compiler options in comps/$(COMP).mak
+COMP := GNU
+# COMP := Intel
+
+### 
+ifdef MPI
+  # Set USE_MPI_WRAPPERS := t to use mpif90 or mpiifort, 
+  # otherwise you need to specify mpi_include_dir, mpi_lib_dir, and mpi_libraries.
+  USE_MPI_WRAPPERS := t
+  ifndef USE_MPI_WRAPPERS
+    MPI_HOME := /usr/local
+    mpi_include_dir = $(strip $(MPI_HOME))/include
+    mpi_lib_dir = $(strip $(MPI_HOME))/lib
+    mpi_libraries += -lmpich -lpthread
+  endif
+endif
+
+MKVERBOSE := t
+
+#########################################################################
+
+COMP := $(strip $(COMP))
+
+ifdef MPI
+  mpi_suffix 	:= .mpi
+endif
+ifdef OMP
+  omp_suffix 	:= .omp
+endif
+ifndef NDEBUG
+  debug_suffix 	:= .debug
+endif
+
+suf=$(COMP)$(debug_suffix)$(mpi_suffix)$(omp_suffix)
+
+odir=.
+mdir=.
+tdir=.
+
+tdir = t/$(suf)
+odir = $(tdir)/o
+mdir = $(tdir)/m
+
+F_C_LINK := UNDERSCORE
+
+SOURCE_HOME := src
+
+fsources    := $(notdir $(wildcard $(SOURCE_HOME)/*.f))
+f90sources  := $(notdir $(wildcard $(SOURCE_HOME)/*.f90))
+F90sources  := $(notdir $(wildcard $(SOURCE_HOME)/*.F90))
+csources    := $(notdir $(wildcard $(SOURCE_HOME)/*.c))
+
+ifdef MPI
+  f90sources := $(filter-out parallel_stubs.f90,$(f90sources))
+else
+  f90sources := $(filter-out parallel.f90,$(f90sources))
+endif
+
+ifdef OMP
+  f90sources := $(filter-out omp_stubs.f90,$(f90sources))
+else
+  f90sources := $(filter-out omp.f90,$(f90sources))
+endif
+
+libraries =
+
+fpp_flags =
+fld_flags =
+
+ifeq ($(wildcard comps/$(COMP).mak),)
+   $(error "comps/$(COMP).mak does not exist")   
+else 
+  include comps/$(COMP).mak
+endif
+
+ifdef mpi_include_dir
+  fpp_flags += -I $(mpi_include_dir)
+endif
+
+ifdef mpi_lib_dir
+  fld_flags += -L $(mpi_lib_dir)
+endif
+
+MODDEP  :=  scripts/moddep.pl
+MKDEP   :=  scripts/mkdep.pl
+
+FPPFLAGS += $(fpp_flags) -I $(SOURCE_HOME)
+LDFLAGS  += $(fld_flags) 
+libraries += $(mpi_libraries)
+
+CPPFLAGS += -DBL_FORT_USE_$(F_C_LINK) -I $(SOURCE_HOME)
+
+objects = $(addprefix $(odir)/,       \
+	$(sort $(f90sources:.f90=.o)) \
+	$(sort $(F90sources:.F90=.o)) \
+	$(sort $(fsources:.f=.o))     \
+	$(sort $(csources:.c=.o))     \
+	)
+sources =                     \
+	$(sort $(f90sources)) \
+	$(sort $(F90sources)) \
+	$(sort $(fsources)  ) \
+	$(sort $(csources)  )
+
+c_includes = $(SOURCE_HOME)
+f_includes = $(SOURCE_HOME)
+
+vpath %.c $(SOURCE_HOME)
+vpath %.f $(SOURCE_HOME)
+vpath %.f90 $(SOURCE_HOME)
+vpath %.F90 $(SOURCE_HOME)
+
+COMPILE.f   = $(FC)  $(FFLAGS) $(FPPFLAGS) -c
+COMPILE.f90 = $(F90) $(F90FLAGS) $(FPPFLAGS) -c
+COMPILE.F90 = $(F90) $(F90FLAGS) $(F90PPFLAGS) $(FPPFLAGS) -c
+
+LINK.f90    = $(F90) $(F90FLAGS) $(FPPFLAGS) $(LDFLAGS)
+
+default: main.$(suf).exe
+
+main.$(suf).exe: $(objects)
+	$(LINK.f90) -o main.$(suf).exe $(objects) $(libraries)
+
+clean::
+	$(RM) ./*.o ./*.mod $(mdir)/*.mod $(odir)/*.o *.$(suf).exe *~
+	$(RM) $(tdir)/f90.depends $(tdir)/c.depends
+	$(RM) TAGS tags
+
+realclean:: clean
+	$(RM) -fr t
+	$(RM) *.exe
+
+TAGS:	$(sources)
+	ctags -e --verbose=yes --fortran-kinds=+i $(abspath $^)
+
+tags:	$(sources)
+	ctags --verbose=yes --fortran-kinds=+i $^
+
+# should prevent deletion of .o files
+.SECONDARY: $(objects)
+
+
+%.$(suf).exe:%.f90 $(objects)
+ifdef MKVERBOSE
+	$(LINK.f90) -o main.$(suf).exe $< $(objects) $(libraries)
+else
+	@echo "Linking $@ ..."
+	@$(LINK.f90) -o main.$(suf).exe $< $(objects) $(libraries)
+endif
+
+${odir}/%.o: %.f
+	@if [ ! -d $(odir) ]; then mkdir -p $(odir); fi
+	@if [ ! -d $(mdir) ]; then mkdir -p $(mdir); fi
+ifdef MKVERBOSE
+	$(COMPILE.f) -o $@ $<
+else
+	@echo "Building $< ..."
+	@$(COMPILE.f) -o $@ $<
+endif
+
+${odir}/%.o: %.f90
+	@if [ ! -d $(odir) ]; then mkdir -p $(odir); fi
+	@if [ ! -d $(mdir) ]; then mkdir -p $(mdir); fi
+ifdef MKVERBOSE
+	$(COMPILE.f90) -o $@ $<
+else
+	@echo "Building $< ..."
+	@$(COMPILE.f90) -o $@ $<
+endif
+
+${odir}/%.o: %.F90
+	@if [ ! -d $(odir) ]; then mkdir -p $(odir); fi
+	@if [ ! -d $(mdir) ]; then mkdir -p $(mdir); fi
+ifdef MKVERBOSE
+	$(COMPILE.F90) -o $@ $<
+else
+	@echo "Building $< ..."
+	@$(COMPILE.F90) -o $@ $<
+endif
+
+${odir}/%.o: %.c
+	@if [ ! -d $(odir) ]; then mkdir -p $(odir); fi
+ifdef MKVERBOSE
+	$(COMPILE.c) -o $@ $<
+else
+	@echo "Building $< ..."
+	@$(COMPILE.c) -o $@ $<
+endif
+
+$(tdir)/f90.depends: $(fsources) $(f90sources) $(F90sources)
+	@if [ ! -d $(tdir) ]; then mkdir -p $(tdir); fi
+ifdef MKVERBOSE
+	perl $(MODDEP) $(f_includes) --odir $(odir)  $^ > $(tdir)/f90.depends 
+else
+	@echo "Building f90/f dependency File ..."
+	@perl $(MODDEP) $(f_includes) --odir $(odir) $^ > $(tdir)/f90.depends 
+endif
+
+$(tdir)/c.depends:  $(csources)
+	@if [ ! -d $(tdir) ]; then mkdir -p $(tdir); fi
+ifdef MKVERBOSE
+	perl $(MKDEP) $(c_includes) --odir $(odir) $^ > $(tdir)/c.depends 
+else
+	@echo "Building c dependency File ..."
+	@perl $(MKDEP) $(c_includes) --odir $(odir) $^ > $(tdir)/c.depends 
+endif
+
+ifneq ($(MAKECMDGOALS),realclean)
+ifneq ($(MAKECMDGOALS),clean)
+include $(tdir)/f90.depends
+
+ifdef csources
+include $(tdir)/c.depends
+endif
+endif
+endif
+
+#-----------------------------------------------------------------------------
+# for debugging.  To see the value of a Makefile variable,
+# e.g. Fmlocs, simply do "make print-Fmlocs".  This will
+# print out the value.
+print-%: ; @echo $* is $($*)
+
+#-----------------------------------------------------------------------------
+# If a file requires special compiler flags (say -O0), one can do
+# something like below, where SPECIALF90FLAGS is modified based on the
+# result of "make print-F90FLAGS".
+#
+#SPECIALF90FLAGS := -O0 -Jt/GNU.mpi.omp/m -I t/GNU.mpi.omp/m -ftree-vectorize -fno-range-check -fopenmp
+#${odir}/xxx.o: src/xxx.f90
+#	$(F90) $(SPECIALF90FLAGS) $(FPPFLAGS) -c -o $@ $<

README

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+
+This is a minimalist version of SMC, a combustion code that solves
+compressible Navier-Stokes equations for viscous multi-component
+reacting flows.  SMC is developed at the Center for Computational
+Sciences and Engineering (CCSE) at Lawrence Berkeley National
+Laboratory.  It uses the BoxLib library
+(https://ccse.lbl.gov/BoxLib/), also developed at CCSE.  This
+minimalist version of SMC includes a stripped down version of BoxLib.
+Therefore, the full version of BoxLib is not needed.
+
+The code is mainly written in Fortran 90, with some parts in C.
+Parallelization is implemented with hybrid MPI/OpenMP.  However, SMC
+can also be built with pure MPI, or pure OpenMP, or neither.
+
+GNU make is used to build the code.  The following options can be
+specified in the GNUmakefile:
+
+* MPI := t 
+  This determines whether we are using the Message Passing
+  Interface (MPI) library.  Leaving this option empty will disable
+  MPI.  If MPI is enabled, you need to specify how to link to the MPI
+  library.  You can set USE_MPI_WRAPPERS := t, then mpif90 will be
+  used.  Or you can set "mpi_include_dir", "mpi_lib_dir", and
+  "mpi_libraries" to appropriate values in GNUmakefile.
+
+* OMP := 
+  This determines whether we are using OpenMP.  Leaving this option
+  empty disables OpenMP.
+
+* NDEBUG := 
+  This option determines whether we compile with support for debugging
+  (usually also enabling some runtime checks). Setting NDEBUG := t
+  turns off debugging.
+
+* COMP := GNU
+  Set this to your compiler of choice (e.g., GNU).  Specific options
+  for a certain compiler are stored in the comps/$(COMP).mak file.   
+
+* MIC :=
+  Set this if compiling for Intel Xeon Phi.
+
+* MKVERBOSE := t
+  This determines the verbosity of the building process.
+
+To build an executable, type "make" in the SMC directory.  The
+executable will have a name like main.GNU.debug.mpi.exe depending
+on the compiler and some other options specified in the GNUmakefile.
+There are some other options provided by the GNUmakefile.  You can
+type "make TAGS" or "make tags" to generate tag file for Email or vi.
+You can type "make clean" or "make realclean" to remove files
+generated during the make process.
+
+Runtime parameters can be specified in the inputs_SMC file, which must
+be placed in the directory where the executable is run.  Below are a
+list of selected runtime parameters and default values.
+
+* n_cellx = -1
+* n_celly = -1
+* n_cellz = -1
+
+  Number of cells in the x, y, and z-directions.  They must be greater than 4.
+
+* max_grid_size = 64 
+
+  This determines the largest grid size of a box.  If max_grid_size is
+  too big, there might be fewer boxes than MPI tasks, and then some
+  processors will be idle.  However, if it is too small, each MPI task
+  may have too many small boxes, and the performance will be affected.
+  Thus, max_grid_size must be chosen according to the number of cells
+  and the number of MPI tasks.  Ideally, you would like to have one
+  box for each MPI task to minimize the communication cost.
+
+* verbose = 0
+
+  This determines verbosity.
+
+* stop_time = -1.d0
+
+  Simulation stop time.
+
+* max_step = 1
+
+  Maximum number of timesteps in the simulation.
+
+Note that there are a number of OMP COLLAPSE clauses in the code.
+These tend to trigger compiler bugs.  If the code crashes, try to run
+it without "COLLAPSE". 
+
+More information about SMC can be found in the paper "High-Order
+Algorithms for Compressible Reacting Flow with Complex Chemistry" by
+M. Emmett, W. Zhang, and J.B. Bell
+(http://arxiv.org/abs/1309.7327). If you have any questions, please
+contact Weiqun Zhang ([email protected]).