Merge pull request #528 from fmihpc/dev

Merge dev into master, for Vlasiator 5.1 release

.clang-format

@@ -0,0 +1,14 @@
+---
+BasedOnStyle:  LLVM
+UseTab: Never
+IndentWidth: 3
+TabWidth: 3
+BreakBeforeBraces: Attach
+PointerAlignment: Left
+AlignAfterOpenBracket: true
+AllowShortIfStatementsOnASingleLine: false
+IndentCaseLabels: false
+ColumnLimit: 120
+AccessModifierOffset: -3
+...
+

.gitignore

@@ -2,6 +2,8 @@
 *.vlsv
 *.silo
 *.o
+vscode/
+.vscode/
 version.cpp
 \#*\#
 *~

.vimrc

@@ -0,0 +1,6 @@
+set cindent
+set shiftwidth=3
+set tabstop=3
+set expandtab
+
+set equalprg=clang-format\ -style=file

MAKE/Makefile.Freezer

@@ -0,0 +1,106 @@
+CMP = mpic++
+LNK = mpic++
+
+# Markus' desktop computer
+
+#======== Vectorization ==========
+#Set vector backend type for vlasov solvers, sets precision and length. 
+#Options: 
+# AVX:	    VEC4D_AGNER, VEC4F_AGNER, VEC8F_AGNER
+# AVX512:   VEC8D_AGNER, VEC16F_AGNER
+# Fallback: VEC4D_FALLBACK, VEC4F_FALLBACK, VEC8F_FALLBACK
+
+ifeq ($(DISTRIBUTION_FP_PRECISION),SPF)
+#Single-precision        
+	VECTORCLASS = VEC8F_AGNER
+	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
+# 	VECTORCLASS = VEC8F_FALLBACK
+#	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/../vlasiator/vlasovsolver
+else
+#Double-precision
+#	VECTORCLASS = VEC4D_AGNER
+#	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
+	VECTORCLASS = VEC4D_FALLBACK
+	INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/../vlasiator/vlasovsolver
+endif
+
+#FLAGS = -ggdb
+
+#GNU flags:
+CC_BRAND = gcc
+CC_BRAND_VERSION = 6.2.0
+CXXFLAGS += -O3 -fopenmp -funroll-loops -std=c++17 -W -Wall -Wno-unused -fabi-version=0 -mavx2
+#CXXFLAGS += -ggdb -O0 -fopenmp -funroll-loops -std=c++17 -W -Wall -Wno-unused -fabi-version=0 -mavx2
+testpackage: CXXFLAGS = -g -ggdb -O2 -fopenmp -funroll-loops -std=c++17 -fabi-version=0  -mno-avx -mno-fma -fno-unsafe-math-optimizations
+
+MATHFLAGS = -ffast-math
+testpackage: MATHFLAGS =  -fno-unsafe-math-optimizations
+
+LDFLAGS =
+#-g -ggdb
+LIB_MPI = -lgomp -lgfortran -lpapi
+
+
+#======== PAPI ==========
+#Add PAPI_MEM define to use papi to report memory consumption?
+#CXXFLAGS += -DPAPI_MEM
+#testpackage: CXXFLAGS += -DPAPI_MEM
+
+#======== Allocator =========
+#Use jemalloc instead of system malloc to reduce memory fragmentation? https://github.com/jemalloc/jemalloc
+#Configure jemalloc with  --with-jemalloc-prefix=je_ when installing it
+#CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
+#testpackage: CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
+
+
+#======= Compiler and compilation flags =========
+# NOTES on compiler flags:
+# CXXFLAGS is for compiler flags, they are always used
+# MATHFLAGS are for special math etc. flags, these are only applied on solver functions
+# LDFLAGS flags for linker
+
+# BOOST_VERSION = current trilinos version
+# ZOLTAN_VERSION = current trilinos verson
+
+#======== Libraries ===========
+
+MPT_VERSION = 7.5.1
+JEMALLOC_VERSION = 4.0.4
+LIBRARY_PREFIX = /home/markusb/git/vlasiator-lib
+
+
+#compiled libraries
+# INC_BOOST = -I$(CRAY_TRILINOS_PREFIX_DIR)/include/boost
+# LIB_BOOST = -L$(CRAY_TRILINOS_PREFIX_DIR)/lib -lboost_program_options
+
+# INC_ZOLTAN = -I$(CRAY_TRILINOS_PREFIX_DIR)/include
+# LIB_ZOLTAN = -I$(CRAY_TRILINOS_PREFIX_DIR)/lib -lzoltan
+
+INC_BOOST = -I/usr/include/trilinos
+LIB_BOOST = -L/usr/include/trilinos -lboost_program_options
+
+INC_ZOLTAN = -I/usr/include/trilinos
+#LIB_ZOLTAN = -I/usr/lib/x86_64-linux-gnu -ltrilinos_zoltan
+LIB_ZOLTAN = -ltrilinos_zoltan
+USE_TRILINOS=1
+
+INC_JEMALLOC = -I$(LIBRARY_PREFIX)/jemalloc/include
+LIB_JEMALLOC = -L$(LIBRARY_PREFIX)/jemalloc/lib -ljemalloc -Wl,-rpath=$(LIBRARY_PREFIX)/jemalloc/lib
+
+
+INC_VLSV = -I$(LIBRARY_PREFIX)/vlsv
+LIB_VLSV = -L$(LIBRARY_PREFIX)/vlsv -lvlsv -Wl,-rpath=$(LIBRARY_PREFIX)/vlsv/lib
+
+LIB_PROFILE = -L$(LIBRARY_PREFIX)/phiprof/lib -lphiprof -Wl,-rpath=$(LIBRARY_PREFIX)/phiprof/lib
+INC_PROFILE = -I$(LIBRARY_PREFIX)/phiprof/include
+
+#header libraries
+
+INC_EIGEN = -I$(LIBRARY_PREFIX)/eigen
+#INC_EIGEN = -I$(LIBRARY_PREFIX)/eigen-eigen-07105f7124f9
+INC_DCCRG = -I$(LIBRARY_PREFIX)/dccrg_new_neighbours
+#INC_DCCRG = -I$(LIBRARY_PREFIX)/dccrg_master
+INC_FSGRID = -I$(LIBRARY_PREFIX)/fsgrid
+
+
+

MAKE/Makefile.docker

@@ -18,15 +18,27 @@ else
 	VECTORCLASS = VEC4D_AGNER
 endif
 
+FLAGS = 
+
+#GNU flags:
+CXXFLAGS += -O3 -fopenmp -funroll-loops -std=c++17 -W -Wall -Wno-unused -fabi-version=0 -mavx2
+testpackage: CXXFLAGS = -O2 -fopenmp -funroll-loops -std=c++17 -fabi-version=0  -mavx
+
+MATHFLAGS = -ffast-math
+LDFLAGS = -g
+LIB_MPI = -lgomp
+
 #======== PAPI ==========
 #Add PAPI_MEM define to use papi to report memory consumption?
 CXXFLAGS +=  -DPAPI_MEM
+testpackage: CXXFLAGS +=  -DPAPI_MEM
 
 
 #======== Allocator =========
 #Use jemalloc instead of system malloc to reduce memory fragmentation? https://github.com/jemalloc/jemalloc
 #Configure jemalloc with  --with-jemalloc-prefix=je_ when installing it
 CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
+testpackage: CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
 
 
 #======= Compiler and compilation flags =========
@@ -42,16 +54,7 @@ CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
 #                         mpi.h in c++ on Cray
 
 CXXFLAGS += -DMPICH_IGNORE_CXX_SEEK
-
-FLAGS = 
-
-#GNU flags:
-CXXFLAGS += -O3 -fopenmp -funroll-loops -std=c++11 -W -Wall -Wno-unused -fabi-version=0 -mavx2
-testpackage: CXXFLAGS = -O2 -fopenmp -funroll-loops -std=c++0x -fabi-version=0  -mavx
-
-MATHFLAGS = -ffast-math
-LDFLAGS = -g
-LIB_MPI = -lgomp
+testpackage: CXXFLAGS += -DMPICH_IGNORE_CXX_SEEK
 
 # BOOST_VERSION = current trilinos version
 # ZOLTAN_VERSION = current trilinos verson