Removing Makefiles

570f604b · Atkins, Charles Vernon · 36ad24cb · 36ad24cb · 36ad24cb · 36ad24cb
Commit 570f604b authored 8 years ago by Atkins, Charles Vernon
--- a/Makefile
+++ b/Makefile
-# Makefile for testing purposes, will build libadios.a, libadios_nompi.a 
-# Created on: Oct 4, 2016
-#     Author: wfg
-#DEFAULT COMPILERS IN PATH, LIBS will be modified in Makefile.libs
-CC:=g++
-MPICC:=mpic++
-LIBS:=
-SHARED:=no
-CFLAGS:=-c -Wall -Wpedantic -std=c++11 -O0 -g
-LINKERMPI:=ar
-LINKERNoMPI:=ar
-LINKERFLAGS:= rcs
-LIBEXT:=a
-ifeq ($(SHARED),yes)
-	CFLAGS+= -fPIC
-	LINKERMPI=$(MPICC) 
-	LINKERNoMPI=$(CC)
-	LINKERFLAGS= -shared -o
-	LIBEXT=so
-endif
-#ADIOS 
-HFiles:=$(shell find ./include -type f -name "*.h")
-CPPFiles:=$(shell find ./src -type f -name "*.cpp")
-INC:=-I./include
-VPATH = ./src ./src/core ./src/functions \
-        ./src/engine/bp ./src/engine/dataman ./src/engine/adios1 \
-		./src/transport/file ./src/transport/wan \
-		./src/capsule/heap ./src/capsule/shmem \
-		./src/transform \
-		./src/format
-#SEPARATE EXTERNAL HEADERS AND LIBRARIES HANDLING in Makefile.libs, export variables 
-export $(HFiles) $(CPPFiles) $(CFLAGS) $(INC) $(LIBS)  
-include Makefile.libs
-OBJMPI:=$(patsubst %.cpp, ./bin/mpi/%.o, $(notdir $(CPPFiles)) )
-OBJMPI:=$(patsubst ./bin/mpi/mpidummy.o, ,$(OBJMPI) )  #remove mpidummy from compilation
-OBJNoMPI:=$(patsubst %.cpp, ./bin/nompi/%.o, $(notdir $(CPPFiles)) )
-OBJNoMPI:=$(patsubst ./bin/nompi/MPIFile.o, ,$(OBJNoMPI) )  #remove MPIFile from compilation (not supported in serial)
-.PHONY: all clean mpi nompi
-all: mpi nompi
-mpi: $(HFiles) $(OBJMPI)
-	@( mkdir -p ./lib );
-	$(LINKERMPI) $(LINKERFLAGS) ./lib/libadios.$(LIBEXT) $(OBJMPI)
-	@echo "Finished building MPI library ./lib/libadios.$(LIBEXT)";
-	@echo
-./bin/mpi/%.o: %.cpp $(HFiles)
-	@( mkdir -p ./bin/mpi );
-	$(MPICC) $(CFLAGS) $(INC) -o $@ $<
-nompi: $(HFiles) $(OBJNoMPI)
-	@( mkdir -p ./lib );
-	$(LINKERNoMPI) $(LINKERFLAGS) ./lib/libadios_nompi.$(LIBEXT) $(OBJNoMPI)
-	@echo "Finished building noMPI library ./lib/libadios.$(LIBEXT)";
-	@echo
-./bin/nompi/%.o: %.cpp $(HFiles)
-	@( mkdir -p ./bin/nompi );
-	$(CC) $(CFLAGS) $(INC) -DADIOS_NOMPI -o $@ $<
-clean:
-	rm ./bin/mpi/*.o ./bin/nompi/*.o ./lib/*	
--- a/Makefile.libs
+++ b/Makefile.libs
-#Language API
-LANGUAGE_INC:=./include
-LANGUAGE_SRC:=./src
-ifeq ($(C_API),yes)
-else
-    HFiles:=$(filter-out $(LANGUAGE_INC)/ADIOS_C.h,$(HFiles))
-    CPPFiles:=$(filter-out $(LANGUAGE_SRC)/ADIOS_C.cpp,$(CPPFiles))     
-endif
-#EXTERNAL DEPENDECIES
-ENGINE_INC:=./include/engine
-ENGINE_SRC:=./src/engine
-TRANSPORT_INC:=./include/transport
-TRANSPORT_SRC:=./src/transport
-ifeq ($(HAVE_DATAMAN),yes)
-    DATAMAN_LOC:=/Users/w4g/Dropbox/lib/DataMan# need to change this to your local dataman location
-    CFLAGS += -DHAVE_DATAMAN
-    INC += -I$(DATAMAN_LOC)/include
-    LIBS += -L$(DATAMAN_LOC)/lib -ldataman
-else
-    HFiles:=$(filter-out $(ENGINE_INC)/dataman/DataManWriter.h,$(HFiles))
-    HFiles:=$(filter-out $(ENGINE_INC)/dataman/DataManReader.h,$(HFiles))
-    HFiles:=$(filter-out $(TRANSPORT_INC)/wan/MdtmMan.h,$(HFiles))
-    CPPFiles:=$(filter-out $(ENGINE_SRC)/dataman/DataManWriter.cpp,$(CPPFiles))
-    CPPFiles:=$(filter-out $(ENGINE_SRC)/dataman/DataManReader.cpp,$(CPPFiles))
-    CPPFiles:=$(filter-out $(TRANSPORT_SRC)/wan/MdtmMan.cpp,$(CPPFiles))
-endif
-ifeq ($(HAVE_ADIOS1),yes)
-    ADIOS1_DIR=/opt/adios/lean/1.11# need to change this to your local adios 1.x installation
-    CFLAGS += -DHAVE_ADIOS1
-    INC += -I$(ADIOS1_DIR)/include
-    LIBS += $(shell ${ADIOS1_DIR}/bin/adios_config -l)
-else
-    HFiles:=$(filter-out $(ENGINE_INC)/adios1/ADIOS1Writer.h,$(HFiles))
-    HFiles:=$(filter-out $(ENGINE_INC)/adios1/ADIOS1Reader.h,$(HFiles))
-    CPPFiles:=$(filter-out $(ENGINE_SRC)/adios1/ADIOS1Writer.cpp,$(CPPFiles))
-    CPPFiles:=$(filter-out $(ENGINE_SRC)/adios1/ADIOS1Reader.cpp,$(CPPFiles))
-endif
-#EXTERNAL DEPENDENCIES
-ifeq ($(HAVE_NETCDF),yes)
-    LIBS += -lnetcdf
-    CFLAGS += -DHAVE_NETCDF
-else
-    HFiles:=$(filter-out $(TRANSPORT_INC)/NetCDF4.h,$(HFiles))
-    CPPFiles:=$(filter-out $(TRANSPORT_SRC)/NetCDF4.cpp,$(CPPFiles))     
-endif
-ifeq ($(HAVE_PHDF5),yes)
-    LIBS += -lhdf5
-    CFLAGS += -DHAVE_PHDF5
-else
-    HFiles:=$(filter-out $(TRANSPORT_INC)/PHDF5.h,$(HFiles))
-    CPPFiles:=$(filter-out $(TRANSPORT_SRC)/PHDF5.cpp,$(CPPFiles))     
-endif
-ifeq ($(HAVE_BZIP2),yes)
-    LIBS += -lbz2
-    CFLAGS += -DHAVE_BZIP2
-else
-    HFiles:=$(filter-out $(TRANSFORM_INC)/BZIP2.h,$(HFiles))
-    CPPFiles:=$(filter-out $(TRANSFORM_SRC)/BZIP2.cpp,$(CPPFiles))     
-endif
-ifeq ($(HAVE_SZIP),yes)
-    LIBS += -lsz
-    CFLAGS += -DHAVE_SZIP
-else
-    HFiles:=$(filter-out $(TRANSFORM_INC)/SZIP.h,$(HFiles))
-    CPPFiles:=$(filter-out $(TRANSFORM_SRC)/SZIP.cpp,$(CPPFiles))     
-endif
-ifeq ($(HAVE_ZLIB),yes)
-    LIBS += -lz
-    CFLAGS += -DHAVE_ZLIB
-else
-    HFiles:=$(filter-out $(TRANSFORM_INC)/ZLIB.h,$(HFiles))
-    CPPFiles:=$(filter-out $(TRANSFORM_SRC)/ZLIB.cpp,$(CPPFiles))     
-endif
--- a/bindings/python/Makefile
+++ b/bindings/python/Makefile
-#Makefile
-# Created on: Mar 13, 2017
-#     Author: wfg
-MPICC:=mpic++
-CPPFiles:=$(shell find ./src -type f -name "*.cpp")
-OBJS:=$(patsubst %.cpp, ./bin/%.o, $(notdir $(CPPFiles)) )
-# location of the Python header files
-PYTHON_VERSION:= 2.7
-PYTHON_INC:= /usr/include/python$(PYTHON_VERSION)
-PYTHON_LIBLOC:= /usr/lib/python$(PYTHON_VERSION)/config-x86_64-linux-gnu/
-ifeq ($(HAVE_PYBIND11),yes)  # USE PYBIND11 (headers only)
-    BIND_FLAG:= -DHAVE_PYBIND11
-    BIND_INC:= /home/wfg/workspace/pybind11/include
-    BIND_LIBS:=
-    OBJS:=$(patsubst ./bin/glueBoostPython.o, ,$(OBJS) ) #remove BoostPython
-else                             # USE BOOST PYTHON (default)
-	BIND_FLAG:= -DHAVE_BOOSTPYTHON
-	BIND_INC:= /opt/boost_1_63_0/
-	BIND_LIBS:= -L/opt/boost_1_63_0/stage/lib/ -lboost_python -lboost_numpy
-	OBJS:=$(patsubst ./bin/gluePyBind11.o, ,$(OBJS) ) #remove PyBind11
-endif
-# location of ADIOS include and lib
-ADIOS_INC:= /home/wfg/workspace/ADIOSPP/include
-ADIOS_LIB:= /home/wfg/workspace/ADIOSPP/lib
-ADIOSPy_INC:=./include
-CFLAGS:=-c -Wall -fPIC -O0 -g -std=c++11 -Wno-deprecated-declarations $(BIND_FLAG)
-INC:= -I$(PYTHON_INC) -I$(BIND_INC) -I$(ADIOS_INC) -I$(ADIOSPy_INC)
-LIBS:= -L$(ADIOS_LIB) -ladios $(BIND_LIBS) -L$(PYTHON_LIBLOC) -lpython$(PYTHON_VERSION)
-# compile mesh classes
-TARGET = ADIOSPy
-all: $(TARGET).so
-$(TARGET).so: $(OBJS)
-	$(MPICC) -shared -o $(TARGET).so -Wl,--export-dynamic $(OBJS) $(LIBS) 
-./bin/%.o: ./src/%.cpp
-	@( mkdir -p ./bin );
-	$(MPICC) $(INC) $(CFLAGS) -o $@ $<
-clean:
-	rm ./bin/*.o *.so
\ No newline at end of file
--- a/buildADIOS1.sh
+++ b/buildADIOS1.sh
-#!/bin/bash
-# buildTest.sh for ADIOS1 Writer example
-# Created on: Mar 27, 2017
-#     Author: pnb
-# Recommended: do a "make clean" the first time 
-MPICOMPILER=mpic++
-ADIOS1_DIR=/opt/adios/1.11
-if [ "$(uname)" == "Darwin" ]; then
-	CCOMPILER=clang++
-elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
-	CCOMPILER=g++
-fi
-echo "######################################################################################"
-echo "Start building ADIOS ./lib/libadios.a ./libadios_nompi.a" 
-echo "######################################################################################"
-echo
-make -j4 HAVE_ADIOS1=yes ADIOS1_DIR=${ADIOS1_DIR} CC=$CCOMPILER MPICC=$MPICOMPILER       #build the ./lib/libadios.a and ./libadios_nompi.a
-echo
-echo "#################################################################"
-echo "Building ADIOS1Writer example"
-echo "#################################################################"
-make -j4 -C ./examples/hello/adios1Writer CC=$CCOMPILER MPICC=$MPICOMPILER mpi
-#make -j4 -C ./examples/hello/adios1Reader CC=$CCOMPILER MPICC=$MPICOMPILER mpi
-echo
-echo
-echo
-echo "#################################################################"
-echo "Running the MPI example"
-echo "#################################################################"
-echo
-echo
-echo "#################################################################"
-echo "ADIOS1 writer"
-echo "#################################################################"
-mpirun -np 4 ./examples/hello/adios1Writer/helloADIOS1Writer.exe
-echo "DONE...check for myDoubles.bp directory"
-echo "#################################################################"
-echo "ADIOS1 reader..not ready yet"
-echo "#################################################################"
-#./examples/hello/adios1Writer/helloADIOS1Reader.exe
-echo
-echo
-echo "#################################################################"
-echo "To run mpi version with 4 mpi processes: "
-echo "mpirun -n 4 ./examples/hello/bpWriter/helloBPWriter.exe"
-echo "mpirun -n 4 ./examples/hello/bpReader/helloBPReader.exe"
-echo "END"
-echo "################################################################"
--- a/buildBP.sh
+++ b/buildBP.sh
-#!/bin/bash
-# buildTest.sh for BP Writer example
-# Created on: Feb 9, 2017
-#     Author: wfg
-# Recommended: do a "make clean" the first time 
-MPICOMPILER=mpic++
-if [ "$(uname)" == "Darwin" ]; then
-	CCOMPILER=clang++
-elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
-	CCOMPILER=g++
-fi
-echo "######################################################################################"
-echo "Start building ADIOS ./lib/libadios.a ./libadios_nompi.a" 
-echo "######################################################################################"
-echo
-make -j4 CC=$CCOMPILER MPICC=$MPICOMPILER       #build the ./lib/libadios.a and ./libadios_nompi.a
-echo
-echo "#################################################################"
-echo "Building BPWriter example"
-echo "#################################################################"
-make -j4 -C ./examples/hello/bpWriter CC=$CCOMPILER MPICC=$MPICOMPILER
-#make -j4 -C ./examples/hello/bpReader CC=$CCOMPILER MPICC=$MPICOMPILER
-echo
-echo
-echo
-echo "#################################################################"
-echo "Running nompi.exe example"
-echo "#################################################################"
-echo
-echo
-echo "#################################################################"
-echo "BP writer"
-echo "#################################################################"
-./examples/hello/bpWriter/helloBPWriter_nompi.exe
-echo "DONE...check for myDoubles_nompi.bp directory"
-echo "#################################################################"
-echo "BP reader..not ready yet"
-echo "#################################################################"
-#./examples/hello/bpWriter/helloBPReader.exe
-echo
-echo
-echo "#################################################################"
-echo "To run mpi version with 4 mpi processes: "
-echo "mpirun -n 4 ./examples/hello/bpWriter/helloBPWriter.exe"
-echo "mpirun -n 4 ./examples/hello/bpReader/helloBPReader.exe"
-echo "END"
-echo "################################################################"
--- a/buildDataMan.sh
+++ b/buildDataMan.sh
-#!/bin/bash
-# buildTest.sh for Dataman example
-# Created on: Feb 9, 2017
-#     Author: wfg
-DATAMAN_LOCATION=/Users/w4g/Dropbox/lib/DataMan
-MPICOMPILER=mpic++
-if [ "$(uname)" == "Darwin" ]; then
-	CCOMPILER=g++
-	export DYLD_LIBRARY_PATH=$DATAMAN_LOCATION/lib:$DYLD_LIBRARY_PATH
-elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
-	CCOMPILER=g++
-	export LD_LIBRARY_PATH=$DATAMAN_LOCATION/lib:$LD_LIBRARY_PATH
-fi
-echo "######################################################################################"
-echo "Start building ADIOS ./lib/libadios.a ./libadios_nompi.a with DataMan library" 
-echo "######################################################################################"
-echo
-make -j4 HAVE_DATAMAN=yes DATAMAN_LOC=$DATAMAN_LOCATION CC=$CCOMPILER MPICC=$MPICOMPILER       #build the ./lib/libadios.a and ./libadios_nompi.a
-echo
-echo "#################################################################"
-echo "Building Dataman Reader and Writer examples"
-echo "#################################################################"
-make -j4 -C ./examples/hello/datamanWriter HAVE_DATAMAN=yes DATAMAN_LOC=$DATAMAN_LOCATION CC=$CCOMPILER MPICC=$MPICOMPILER
-echo
-make -j4 -C ./examples/hello/datamanReader HAVE_DATAMAN=yes DATAMAN_LOC=$DATAMAN_LOCATION CC=$CCOMPILER MPICC=$MPICOMPILER
-echo
-echo
-echo "#################################################################"
-echo "Running nompi.exe examples"
-echo "#################################################################"
-echo
-echo
-echo "#################################################################"
-echo "DataMan writer"
-echo "#################################################################"
-./examples/hello/datamanWriter/helloDataManWriter_nompi.exe
-echo "#################################################################"
-echo "DataMan reader"
-echo "#################################################################"
-#./examples/hello/datamanReader/helloDataManReader_nompi.exe
-echo
-echo
-echo "#################################################################"
-echo "To run mpi version with 4 mpi processes: "
-echo "mpirun -n 4 ./examples/hello/datamanWriter/helloDatamanWriter.exe"
-echo "mpirun -n 4 ./examples/hello/datamanReader/helloDatamanReader.exe"
-echo "END"
-echo "################################################################"
--- a/examples/globalArray/Makefile
+++ b/examples/globalArray/Makefile
-# Makefile for testing purposes, will build libadios.a 
-# Created on: Oct 31, 2016
-#     Author: pnorbert
-BASE_NAME=globalArrayXML
-TOOL_DIR=/usr/bin
-CC=$(TOOL_DIR)/g++ # Compiling with mpicc for now
-MPICC:=/usr/local/bin/mpic++
-AR=$(TOOL_DIR)/ar
-#ADIOS LOCATION
-ADIOS_DIR=../..
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-#FLAGS
-CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
-all: mpi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME)_mpi $(ADIOS_LIB)
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME)_nompi $(ADIOS_NOMPI_LIB)
-clean:
-	rm -f *_mpi *_nompi *.o 
-	rm -rf *.dSYM
--- a/examples/groupless/basic/Makefile
+++ b/examples/groupless/basic/Makefile
-# Makefile for testing purposes, will build writer_mpi (make or make mpi) or writer_nompi (make nompi) 
-# Created on: Feb 13, 2017
-#     Author: pnorbert
-#COMPILERS
-CC=g++ 
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -Woverloaded-virtual -std=c++11 -O0 -g
-LDFLAGS=
-all: writer reader 
-writer reader: $(ADIOS_LIB) $(ADIOS_HFiles)
-	    $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $@.cpp -o $@ $(ADIOS_LIB) $(LDFLAGS) -lpthread  \
-clean:
-	rm -f writer reader
--- a/examples/groupless/compound/Makefile
+++ b/examples/groupless/compound/Makefile
-# Makefile for testing purposes, will build writer_mpi (make or make mpi) or writer_nompi (make nompi) 
-# Created on: Feb 13, 2017
-#     Author: pnorbert
-#COMPILERS
-CC=g++ 
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -Woverloaded-virtual -std=c++11 -O0 -g
-LDFLAGS=
-all: writer reader 
-writer reader: $(ADIOS_LIB) $(ADIOS_HFiles)
-	    $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $@.cpp -o $@ $(ADIOS_LIB) $(LDFLAGS) -lpthread  \
-clean:
-	rm -f writer reader
--- a/examples/groupless/multistep/Makefile
+++ b/examples/groupless/multistep/Makefile
-# Makefile for testing purposes, will build writer_mpi (make or make mpi) or writer_nompi (make nompi) 
-# Created on: Feb 13, 2017
-#     Author: pnorbert
-#COMPILERS
-CC=g++ 
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -Woverloaded-virtual -std=c++11 -O0 -g
-LDFLAGS=
-all: writer_multistep reader_allsteps reader_stepping
-writer_multistep reader_allsteps reader_stepping: $(ADIOS_LIB) $(ADIOS_HFiles)
-	    $(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $@.cpp -o $@ $(ADIOS_LIB) $(LDFLAGS) -lpthread  \
-clean:
-	rm -f writer_multistep reader_allsteps reader_stepping
--- a/examples/heatTransfer/Makefile
+++ b/examples/heatTransfer/Makefile
-# Makefile
-# Created on: Feb 13, 2017
-#     Author: pnorbert
-#
-#   SYSTEM SPECIFIC SETTINGS
-#
-#COMPILERS
-CC=g++ 
-MPICC=mpic++
-#FLAGS
-CFLAGS=-Wall -Wpedantic -Woverloaded-virtual -std=c++11 -O0 -g
-LDFLAGS=-lpthread
-#ADIOS1 LOCATION
-ADIOS1_DIR=/opt/adios/1.11
-#ADIOS2 LOCATION
-ADIOS2_DIR=../..
-# SEQUENTIAL HDF5 LOCATION
-HDF5_DIR=/opt/hdf5-1.8.17
-HDF5_INCLUDE=-I$(HDF5_DIR)/include 
-HDF5_LIB=$(HDF5_DIR)/lib/libhdf5.la
-#
-#   SHOULD NOT NEED TO CHANGE ANYTHING BELOW
-#
-ADIOS1_INCLUDE=-I$(ADIOS1_DIR)/include
-ADIOS1_LIB=`${ADIOS1_DIR}/bin/adios_config -l`
-ADIOS2_INCLUDE= -DHAVE_MPI -I$(ADIOS2_DIR)/include
-ADIOS2_LIB=$(ADIOS2_DIR)/lib/libadios.a
-default: 
-	@echo "Make targets: ascii hdf5_a hdf5_b phdf5 adios1 adios2"
-	@echo "  ascii:    build example with text output(IO_ascii.cpp)"
-	@echo "  hdf5_a:   build example with HDF5, separate timesteps (IO_hdf5_a.cpp)"
-	@echo "  hdf5_b:   build example with HDF5, combined timesteps (IO_hdf5_b.cpp)"
-	@echo "  phdf5:    build example with Parallel HDF5  (IO_phdf5.cpp)"
-	@echo "  adios1:   build example with ADIOS 1.x  (IO_adios1.cpp)"
-	@echo "  adios2:   build example with ADIOS2  (IO_adios2.cpp)"
-all: default
-help: default
-ascii: main.cpp HeatTransfer.cpp Settings.cpp IO_ascii.cpp 
-	    $(MPICC) $(CFLAGS) -o heatTransfer_ascii $^ $(LDFLAGS)   
-hdf5_a: main.cpp HeatTransfer.cpp Settings.cpp IO_hdf5_a.cpp 
-	    libtool --mode=link --tag=CC $(MPICC) $(CFLAGS) $(HDF5_INCLUDE) -o heatTransfer_hdf5_a $^ $(HDF5_LIB) $(LDFLAGS)
-adios1: main.cpp HeatTransfer.cpp Settings.cpp IO_adios1.cpp 
-	    $(MPICC) $(CFLAGS) $(ADIOS1_INCLUDE) -o heatTransfer_adios1 $^ $(ADIOS1_LIB) $(LDFLAGS)  
-adios2: main.cpp HeatTransfer.cpp Settings.cpp IO_adios2.cpp 
-	    $(MPICC) $(CFLAGS) $(ADIOS2_INCLUDE) -o heatTransfer_adios2 $^ $(ADIOS2_LIB) $(LDFLAGS)  
-clean:
-	rm -f heatTransfer_ascii heatTransfer_hdf5_a heatTransfer_adios1 heatTransfer_adios2
--- a/examples/hello/Makefile
+++ b/examples/hello/Makefile
-# Makefile for testing purposes, will build libadios.a 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloADIOSNoXML_OOP
-TOOL_DIR=/usr/bin
-CC=$(TOOL_DIR)/g++ # Compiling with mpicc for now
-MPICC=$(TOOL_DIR)/mpic++
-AR=$(TOOL_DIR)/ar
-#ADIOS LOCATION
-ADIOS_DIR=../..
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-#FLAGS
-CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
-all: mpi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME)_mpi $(ADIOS_LIB)
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME)_nompi $(ADIOS_NOMPI_LIB)
-clean:
-	rm *_mpi; rm *_nompi
--- a/examples/hello/adios1Writer/Makefile
+++ b/examples/hello/adios1Writer/Makefile
-# Makefile for testing purposes, will build helloADIOS1Writer (make or make mpi) or helloADIOS1Writer_nompi (make nompi) 
-# Created on: Mar 27, 2017
-#     Author: pnb
-BASE_NAME=helloADIOS1Writer
-#COMPILERS
-CC=g++
-MPICC=mpic++
-#ADIOS 1.x  LOCATION
-ADIOS1_DIR=/opt/adios/1.11
-ADIOS1_LIB=$(shell ${ADIOS1_DIR}/bin/adios_config -l)
-ADIOS1_NOMPI_LIB=$(shell ${ADIOS1_DIR}/bin/adios_config -ls)
-#ADIOS 2.x LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -std=c++11 -O0 -g
-LDFLAGS=
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) $(ADIOS1_LIB) $(LDFLAGS) -lpthread
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) -DADIOS_NOMPI $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) $(ADIOS1_NOMPI_LIB) $(LDFLAGS) -lpthread
-clean:
-	rm *.exe
--- a/examples/hello/bpReader/Makefile
+++ b/examples/hello/bpReader/Makefile
-# Makefile for testing purposes, will build helloWriter_OOP_mpi (make or make mpi) or helloWriter_OOP_nompi (make nompi) 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloBPReader
-#COMPILERS
-CC=g++
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -std=c++11 -O0 -g
-LDFLAGS=
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) $(LDFLAGS) -lpthread
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) $(LDFLAGS) -lpthread
-clean:
-	rm *.exe
\ No newline at end of file
--- a/examples/hello/bpWriter/Makefile
+++ b/examples/hello/bpWriter/Makefile
-# Makefile for testing purposes, will build helloWriter_OOP_mpi (make or make mpi) or helloWriter_OOP_nompi (make nompi) 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloBPWriter
-#COMPILERS
-CC=g++
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -std=c++11 -O0 -g
-LDFLAGS=
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) $(LDFLAGS) -lpthread
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) -DADIOS_NOMPI $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) $(LDFLAGS) -lpthread
-clean:
-	rm *.exe
\ No newline at end of file
--- a/examples/hello/compound/Makefile
+++ b/examples/hello/compound/Makefile
-# Makefile for testing purposes, will build helloWriter_OOP_mpi (make or make mpi) or helloWriter_OOP_nompi (make nompi) 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloCompound
-#COMPILERS
-CC=g++
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -std=c++11 -O0 -g
-LDFLAGS=
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) -DHAVE_MPI $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) $(LDFLAGS) -lpthread
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) $(LDFLAGS) -lpthread
-clean:
-	rm *.exe
\ No newline at end of file
--- a/examples/hello/datamanReader/Makefile
+++ b/examples/hello/datamanReader/Makefile
-# Makefile for testing purposes, will build libadios.a 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloDataManReader
-CC=g++ # Compiling with defaults
-MPICC=mpic++
-INC=
-LIB=
-LIB_NOMPI=
-#ADIOS
-ADIOS_DIR=../../..
-LIB+= $(ADIOS_DIR)/lib/libadios.a
-LIB_NOMPI+= $(ADIOS_DIR)/lib/libadios_nompi.a
-INC+= -I$(ADIOS_DIR)/include
-#DATAMAN
-DATAMAN_LOC=/Users/w4g/Dropbox/lib/DataMan
-INC+= -I$(DATAMAN_LOC)/include
-LIB+= -L$(DATAMAN_LOC)/lib -ldataman # -lcacheman -lstreamman -lzmqman
-LIB_NOMPI+= -L$(DATAMAN_LOC)/lib -ldataman
-#COMPILER FLAGS
-CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
-#SYSTEM LIBS
-LIB+= -lpthread
-LIB_NOMPI+= -ldl -lpthread
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(INC) $(BASE_NAME).cpp -o $(BASE_NAME).exe $(LIB)
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(INC) -DADIOS_NOMPI $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(LIB_NOMPI)
-clean:
-	rm *.exe;
--- a/examples/hello/datamanWriter/Makefile
+++ b/examples/hello/datamanWriter/Makefile
-# Makefile for testing purposes, will build libadios.a 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=helloDataManWriter
-CC=g++ # Compiling with defaults
-MPICC=mpic++
-INC=
-LIB=
-LIB_NOMPI=
-#ADIOS
-ADIOS_DIR=../../..
-LIB+= $(ADIOS_DIR)/lib/libadios.a
-LIB_NOMPI+= $(ADIOS_DIR)/lib/libadios_nompi.a
-INC+= -I$(ADIOS_DIR)/include
-#DATAMAN
-DATAMAN_LOC=/Users/w4g/Dropbox/lib/DataMan
-INC+= -I$(DATAMAN_LOC)/include
-LIB+= -L$(DATAMAN_LOC)/lib -ldataman # -lcacheman -lstreamman -lzmqman
-LIB_NOMPI+= -L$(DATAMAN_LOC)/lib -ldataman # -lcacheman -lstreamman -lzmqman
-#COMPILER FLAGS
-CFLAGS=-Wall -O0 -g -Wpedantic -std=c++11
-#SYSTEM LIBS
-LIB+= -lpthread
-LIB_NOMPI+= -ldl -lpthread 
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(INC) $(BASE_NAME).cpp -o $(BASE_NAME).exe $(LIB)
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(INC) -DADIOS_NOMPI $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(LIB_NOMPI)
-clean:
-	rm *.exe;
--- a/examples/hello/timeBP/Makefile
+++ b/examples/hello/timeBP/Makefile
-# Makefile for testing purposes, will build helloWriter_OOP_mpi (make or make mpi) or helloWriter_OOP_nompi (make nompi) 
-# Created on: Oct 4, 2016
-#     Author: wfg
-BASE_NAME=timeBPWriter
-#COMPILERS
-CC=g++
-MPICC=mpic++
-#ADIOS LOCATION
-ADIOS_DIR=../../..
-ADIOS_INCLUDE=-I$(ADIOS_DIR)/include
-ADIOS_LIB=$(ADIOS_DIR)/lib/libadios.a
-ADIOS_NOMPI_LIB=$(ADIOS_DIR)/lib/libadios_nompi.a
-#FLAGS
-CFLAGS=-Wall -Wpedantic -std=c++11 -O0 -g
-LDFLAGS=
-all: mpi nompi
-mpi: $(ADIOS_LIB) $(ADIOS_HFiles)
-	$(MPICC) $(CFLAGS) $(ADIOS_INCLUDE) $(BASE_NAME).cpp -o $(BASE_NAME).exe $(ADIOS_LIB) $(LDFLAGS) -lpthread
-nompi: $(ADIOS_NOMPI_LIB) $(NoMPI_HFiles)
-	$(CC) $(CFLAGS) $(ADIOS_INCLUDE) -DADIOS_NOMPI $(BASE_NAME)_nompi.cpp -o $(BASE_NAME)_nompi.exe $(ADIOS_NOMPI_LIB) $(LDFLAGS) -lpthread
-clean:
-	rm *.exe
\ No newline at end of file
--- a/examples/hello/timeBP/test.sh
+++ b/examples/hello/timeBP/test.sh
-#!/bin/bash
-rm -fr *.bp
-make clean
-make -j4