I/O adapted fully to use ADIOS2

Author: kshitij-v-mehta

Tutorial/brusselator/Makefile

@@ -7,14 +7,19 @@ CPP=-cpp
 	# All settings here for use Muite Laptop
 
 	COMPILER =  mpif90  
-	decompdir= ./2decomp_fft
+	decompdir=./2decomp_fft
 	FFTW_LINK=./fftwinstall
+	FFTW_DIR?=
+	ADIOS2_DIR?=
 	# compilation settings, optimization, precision, parallelization
-	FLAGS =  -O3  
-	LIBS = -I${FFTW_LINK}/include -L${FFTW_LINK}/lib -lfftw3 		
+	FLAGS = -O3 -DADIOS2
 
-	DECOMPLIB = -I${decompdir}/include -L${decompdir}/lib -l2decomp_fft 
+	INCLUDES = -I${FFTW_DIR}/include -I${decompdir}/include -I${ADIOS2_DIR}/include/fortran
 
+	FFTW_LIB = -L${FFTW_DIR}/lib -lfftw3
+	DECOMPLIB = -L${decompdir}/lib -l2decomp_fft
+	ADIOS2_LIB =-L${ADIOS2_DIR}/lib -ladios2_f -ladios2 -ladios2_sst -ladios2_evpath -ladios2_ffs -ladios2_dill -ladios2_atl
+	LIBS = ${FFTW_LIB} ${DECOMPLIB} ${ADIOS2_LIB}
 
 # libraries
 # source list for main program
@@ -27,12 +32,32 @@ OBJECTS = brusselator.o initialdata.o savedata.o getgrid.o \
 
 
 Brusselator: $(OBJECTS)
-		${COMPILER} -o Brusselator  $(OPTIONS) $(FLAGS) $(CPP) $(OBJECTS)  $(DECOMPLIB) $(LIBS)
+		${COMPILER} -o Brusselator  $(FLAGS) $(FLAGS) $(CPP) $(OBJECTS) $(LIBS)
+
+brusselator.o : brusselator.f90 savedata.o
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) brusselator.f90
+
+savedata.o : savedata.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) savedata.f90
+
+initialdata.o : initialdata.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) initialdata.f90
+
+getgrid.o : savedata.o  getgrid.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) getgrid.f90
+
+linear.o : linear.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) linear.f90
+
+nonlinear1.o : nonlinear1.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) nonlinear1.f90
+
+nonlinear2.o : nonlinear2.f90
+		${COMPILER} -c $(FLAGS) $(CPP) $(INCLUDES) nonlinear2.f90
 
-$(OBJECTS): $(SOURCES)
-		${COMPILER} -c $(OPTIONS) $(CPP) $(DECOMPLIB) $(LIBS) $(SOURCES)
 
 clean:
-	rm -f *.o
+	rm -f *.o *.mod
 clobber:	
 	rm -f Brusselator
+

Tutorial/brusselator/README

@@ -1,4 +1,8 @@
 The Brusselator source code has been forked from https://github.com/openmichigan/PSNM.
-
 Its dependency - 2decomp_fft, has been downloaded from http://www.2decomp.org. Current version is 1.5.847.
 
+Installation:
+
+First install the 2decomp_fft library ./2decomp_fft.
+Then, edit the Makefile to set the compiler etc. and run make.
+

Tutorial/brusselator/adios2_config.xml

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<adios-config>
+
+    <!--====================================
+           Configuration for the Writer 
+        ====================================-->
+
+    <io name="writer">
+        <engine type="BPFile">
+            
+            <!-- for vectorized memory operations, make sure your system 
+                 enables threads--> 
+            <parameter key="Threads" value="1"/>
+
+            <!-- Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+
+            <!-- XXKb, XXMb, or XXXGb supported, default=16Kb 
+                (applications might choose an optimal value) -->
+            <parameter key="InitialBufferSize" value="16Kb"/> 
+            
+            <!-- XXKb, XXMb, or XXXGb supported, default=Unlimited (until 
+                 fails), maximum at each time step  
+                (applications might choose an optimal value) -->
+            <!-- <parameter key="MaxBufferSize" value="2Gb"/> -->
+
+            <!-- exponential growth factor > 1, default = 1.05 
+                 1.05  is good for a few large variables, for many small
+                 variables increase the value to 1.5 to 2 
+                 (optimal value is application dependent)--> 
+            <!-- <parameter key="BufferGrowthFactor" value="1.05"/> -->
+            
+            <!-- Indicates how often (in number of steps), pick a large 
+                 number so metadata will only be written at Close  
+                (applications might choose an optimal value) -->
+            <parameter key="FlushStepsCount" value="1"/> 
+            
+        </engine>
+
+        <transport type="File">
+            
+            <!-- POSIX, stdio (C FILE*), fstream (C++) -->
+            <parameter key="Library" value="POSIX"/>
+            
+            <!-- For read/write, Microseconds (default), Milliseconds, Seconds, 
+                 Minutes, Hours. open/close always in Microseconds -->
+            <parameter key="ProfileUnits" value="Microseconds"/>
+            
+        </transport>
+        
+    </io>
+
+</adios-config>
+