Merge branch 'master' of https://github.com/fmihpc/vlasiator

COPYING

@@ -1,13 +1,14 @@
 
 Vlasiator is a significant investment made by the Finnish
-Meteorological Institute, and its development has taken many years.
+Meteorological Institute and the University of Helsinki,
+and its development has taken many years.
 
 While we are publishing the entirety of the source code under the GPL-2
 open-source license (see below) for the benefit of the entire scientific
 comunity, we strongly advise any user to comply with the Vlasiator
 "Rules of the Road" available at
 
-                     http://vlasiator.fmi.fi
+                     http://www.physics.helsinki.fi/vlasiator
 
 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 

MAKE/Makefile.hornet_gcc

@@ -67,6 +67,7 @@ INC_PROFILE = -I$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_V
 
 INC_EIGEN = -I$(LIBRARY_PREFIX)/eigen/
 INC_DCCRG = -I$(LIBRARY_PREFIX)/dccrg/
+INC_FSGRID = -I/zhome/academic/HLRS/pri/ipryakem/fsgrid/
 INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
 
 

MAKE/Makefile.marconi

@@ -12,7 +12,6 @@
 
 #======== Vectorization ==========
 #Set vector backend type for vlasov solvers, sets precision and length. 
-#NOTE this has to have the same precision as the distribution function define (DISTRIBUTION_FP_PRECISION)
 #Options: 
 # AVX:	    VEC4D_AGNER, VEC4F_AGNER, VEC8F_AGNER
 # AVX512:   VEC8D_AGNER, VEC16F_AGNER
@@ -33,7 +32,8 @@ CXXFLAGS +=  -DPAPI_MEM
 
 #======== Allocator =========
 #Use TBB malloc
-LDFLAGS += -L$(TBBROOT)/lib/intel64/gcc4.7/ -ltbbmalloc_proxy -ltbbmalloc
+#LDFLAGS += -L$(TBBROOT)/lib/intel64/gcc4.7/ -ltbbmalloc_proxy -ltbbmalloc
+CXXFLAGS += -DUSE_JEMALLOC -DJEMALLOC_NO_DEMANGLE
 
 
 #======= Compiler and compilation flags =========
@@ -47,7 +47,7 @@ CC_BRAND_VERSION = 17.0.1
 CXXFLAGS +=  -O2 -g -DMAX_VECTOR_SIZE=512 -xMIC-AVX512 -std=c++11 -qopenmp -ansi-alias
 testpackage: CXXFLAGS = -O2 -g -DMAX_VECTOR_SIZE=512 -xMIC-AVX512 -std=c++11 -qopenmp -ansi-alias
 MATHFLAGS = 
-LDFLAGS += -qopenmp -lifcore 
+LDFLAGS += -qopenmp -lifcore -Wl,-rpath,/cineca/prod/opt/libraries/boost/1.61.0/intelmpi--2017--binary/lib,-rpath,/marconi_work/Pra14_3521/libraries/phiprof/lib,-rpath,/marconi_work/Pra14_3521/libraries/papi/lib
 CMP = mpicxx
 LNK = mpicxx
 
@@ -58,19 +58,23 @@ HEADER_LIBRARY_PREFIX = /marconi_work/Pra14_3521/libraries
 LIBRARY_PREFIX = /marconi_work/Pra14_3521/libraries
 
 
-INC_BOOST = -I$(BOOST_INC)
-LIB_BOOST = -L$(BOOST_LIB) -lboost_program_options
+INC_BOOST = -I/cineca/prod/opt/libraries/boost/1.61.0/intelmpi--2017--binary/include
+LIB_BOOST = -L/cineca/prod/opt/libraries/boost/1.61.0/intelmpi--2017--binary/lib -lboost_program_options
 
 INC_ZOLTAN = -I$(LIBRARY_PREFIX)/zoltan/include
 LIB_ZOLTAN = -L$(LIBRARY_PREFIX)/zoltan/lib -lzoltan
 
-INC_VLSV = -I$(LIBRARY_PREFIX)/vlsv
-LIB_VLSV = -L$(LIBRARY_PREFIX)/vlsv -lvlsv
+INC_VLSV = -I$(LIBRARY_PREFIX)/vlsv_debug
+LIB_VLSV = -L$(LIBRARY_PREFIX)/vlsv_debug -lvlsv
 
+INC_FSGRID = -I$(HEADER_LIBRARY_PREFIX)/fsgrid
 
 LIB_PROFILE = -L$(LIBRARY_PREFIX)/phiprof/lib -lphiprof
 INC_PROFILE = -I$(LIBRARY_PREFIX)/phiprof/include
 
+INC_JEMALLOC = -I$(LIBRARY_PREFIX)/jemalloc/include
+LIB_JEMALLOC = -L$(LIBRARY_PREFIX)/jemalloc/lib -ljemalloc -Wl,-rpath,$(LIBRARY_PREFIX)/jemalloc/lib
+
 #system
 INC_PAPI = -I$(LIBRARY_PREFIX)/papi/include
 LIB_PAPI = -L$(LIBRARY_PREFIX)/papi/lib -lpapi -lpfm

MAKE/Makefile.sisu_gcc

@@ -3,7 +3,6 @@ LNK = CC
 
 #======== Vectorization ==========
 #Set vector backend type for vlasov solvers, sets precision and length. 
-#NOTE this has to have the same precision as the distribution function define (DISTRIBUTION_FP_PRECISION)
 #Options: 
 # AVX:	    VEC4D_AGNER, VEC4F_AGNER, VEC8F_AGNER
 # AVX512:   VEC8D_AGNER, VEC16F_AGNER
@@ -77,7 +76,6 @@ LIB_JEMALLOC = -L$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_
 INC_VLSV = -I$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_VERSION)/vlsv
 LIB_VLSV = -L$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_VERSION)/vlsv -lvlsv
 
-
 LIB_PROFILE = -L$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_VERSION)/phiprof/2.0/lib -lphiprof
 INC_PROFILE = -I$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_VERSION)/phiprof/2.0/include
 
@@ -86,7 +84,7 @@ INC_PROFILE = -I$(LIBRARY_PREFIX)/mpich2/$(MPT_VERSION)/$(CC_BRAND)/$(CC_BRAND_V
 INC_EIGEN = -I$(LIBRARY_PREFIX)/eigen/
 INC_DCCRG = -I$(LIBRARY_PREFIX)/dccrg/
 INC_VECTORCLASS = -I$(LIBRARY_PREFIX)/vectorclass
-
+INC_FSGRID = -I$(LIBRARY_PREFIX)/fsgrid
 
 
 

MAKE/Makefile.taito_gcc

@@ -3,7 +3,6 @@ LNK = mpiCC
 
 #======== Vectorization ==========
 #Set vector backend type for vlasov solvers, sets precision and length. 
-#NOTE this has to have the same precision as the distribution function define (DISTRIBUTION_FP_PRECISION)
 #Options: 
 # AVX:	    VEC4D_AGNER, VEC4F_AGNER, VEC8F_AGNER
 # AVX512:   VEC8D_AGNER, VEC16F_AGNER

MAKE/Makefile.voima

@@ -53,6 +53,7 @@ LIB_PROFILE = -L$(LIBRARY_PREFIX_COMPILED)/phiprof2/lib -lphiprof
 INC_PROFILE = -I$(LIBRARY_PREFIX_COMPILED)/phiprof2/include
 INC_SILO = -I$(LIBRARY_PREFIX_COMPILED)/silo/$(SILO_VERSION)/include
 LIB_SILO = -L$(LIBRARY_PREFIX_COMPILED)/silo/$(SILO_VERSION)/lib -lsilo
+INC_FSGRID = -I$(LIBRARY_PREFIX)/fsgrid
 
 #header libraries
 

MAKE/Makefile.yann

@@ -53,20 +53,22 @@ LIB_MPI = -lgomp
 
 LIBRARY_PREFIX = $(HOME)
 
-INC_BOOST = -I$(LIBRARY_PREFIX)/include
-LIB_BOOST = -L$(LIBRARY_PREFIX)/lib -lboost_program_options
+INC_BOOST = -I/usr/include/boost/
+LIB_BOOST = -L/usr/lib/x86_64-linux-gnu/ -lboost_program_options
 
 INC_ZOLTAN = -I$(LIBRARY_PREFIX)/include
 LIB_ZOLTAN = -L$(LIBRARY_PREFIX)/lib -lzoltan
 
-INC_VLSV = -I$(LIBRARY_PREFIX)/Codes/vlsv
-LIB_VLSV = -L$(LIBRARY_PREFIX)/Codes/vlsv -lvlsv
+INC_VLSV = -I$(LIBRARY_PREFIX)/Development/vlsv
+LIB_VLSV = -L$(LIBRARY_PREFIX)/Development/vlsv -lvlsv
 
 INC_SILO = -I$(LIBRARY_PREFIX)/include
 LIB_SILO = -L$(LIBRARY_PREFIX)/lib -lsilo
 
 INC_DCCRG = -I$(LIBRARY_PREFIX)/include
 
+INC_FSGRID = -I$(LIBRARY_PREFIX)/Development/fsgrid
+
 INC_JEMALLOC = -I$(LIBRARY_PREFIX)/include/jemalloc
 LIB_JEMALLOC = -L$(LIBRARY_PREFIX)/lib -ljemalloc