Initial ADIOS2 implementation

example/adios/karman.adios.xml

@@ -0,0 +1,24 @@
+<?xml version="1.0"?>
+<adios-config>
+
+    <!--====================================
+           Configuration for the Writer 
+        ====================================-->
+
+    <io name="FlaggedGeometry">
+        <engine type="SST">
+            <parameter key="verbose" value="5"/>
+        </engine>
+    </io>
+
+
+    <!--====================================
+           Configuration for the Reader 
+        ====================================-->
+
+    <io name="FlaggedGeometry">
+        <engine type="SST">
+            <parameter key="verbose" value="5"/>
+        </engine>
+    </io>
+</adios-config>

example/adios/karman.xml

@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+
+<CLBConfig version="2.0" output="output/" permissive="true">
+	<Geometry nx="800" ny="800" nz="1">
+		<MRT>
+			<Box/>
+		</MRT>
+		<!-- <WVelocity name="Inlet">
+			<Inlet/>
+		</WVelocity>
+		<EPressure name="Outlet">
+			<Outlet/>
+		</EPressure>
+		<Inlet nx="1" dx="5">
+			<Box/>
+		</Inlet>
+		<Outlet nx="1" dx="-5">
+			<Box/>
+		</Outlet> -->
+		<Wall mask="ALL" dx="33" dy="10" nx="734" ny="734">
+			<Channel/>
+                        <ADIOS2 Stream="globalArray" Variable="GlobalArray" IOName="FlaggedGeometry" AdiosConfig="karman.adios.xml"/>
+
+		</Wall>
+	</Geometry>
+	<Model>
+		<Param name="VelocityX" value="0.01"/>
+		<Param name="Viscosity" value="0.02"/>
+		<Param name="Smag" value="0.16"/>
+		<Param name="PressDiffInObj" value="1"/>
+		<Param name="EOSScale" value="0.05"/>
+		<Param name="Tension" value="0.01"/>
+		<Param name="Coriolis" value="0.001"/>
+		<Param name="SolidAlfa" value="0.166"/>
+		<Param name="FluidAlfa" value="0.01"/>
+		<Param name="InitTemperature" value="0"/>
+		<Param name="InletTemperature" value="1"/>
+	</Model>
+	<VTK/>
+	<!-- <Solve Iterations="10000"/> -->
+</CLBConfig>

src/Geometry.cpp.Rt

@@ -4,6 +4,12 @@
     #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
 #endif
 
+
+#ifdef ADIOS2_USE_MPI
+	#include <adios2.h>
+#endif
+
+
 <?R
  library(gvector,quiet=TRUE,warn.conflicts=FALSE)
  library(polyAlgebra,quiet=TRUE,warn.conflicts=FALSE)
@@ -1038,6 +1044,137 @@ int Geometry::Draw(pugi::xml_node & node)
 			    Dot(x, y, z);
 		    }
 	    fclose(f);
+	} else if (strcmp(n.name(), "ADIOS2") == 0) {
+	    lbRegion crop = getRegion(n.parent());
+	    crop = region.intersect(crop);
+	    crop.print();
+	    if (!n.attribute("IOName")) {
+			error("No 'IOName' attribute in 'ADIOS2' element in xml conf\n");
+			return -1;
+	    }
+
+
+	    if (!n.attribute("Stream")) {
+			error("No 'Stream' attribute in 'ADIOS2' element in xml conf\n");
+			return -1;
+	    }
+
+	    if (!n.attribute("Variable")) {
+			error("No 'Variable' attribute in 'ADIOS2' element in xml conf\n");
+			return -1;
+	    }
+
+	    if (!n.attribute("AdiosConfig")) {
+			error("No 'AdiosConfig' attribute in 'ADIOS2' element in xml conf\n");
+			return -1;
+	    }
+
+        /** ADIOS class factory of IO class objects */
+
+        adios2::ADIOS adios(n.attribute("AdiosConfig").value(),MPI_COMM_WORLD);
+
+        /*** IO class object: settings and factory of Settings: Variables,
+         * Parameters, Transports, and Execution: Engines */
+        adios2::IO adioIO = adios.DeclareIO(n.attribute("IOName").value());
+
+       	/** Engine derived class, spawned to start IO operations */
+        adios2::Engine AdiosReader = adioIO.Open(n.attribute("Stream").value(), adios2::Mode::Read);
+
+        const std::map<std::string, adios2::Params> variables = adioIO.AvailableVariables();
+
+        for (const auto variablePair : variables)
+        {
+            std::cout << "Name: " << variablePair.first;
+
+            for (const auto &parameter : variablePair.second)
+            {
+                std::cout << "\t" << parameter.first << ": " << parameter.second
+                          << "\n";
+            }
+        }
+
+        /** Write variable for buffering */
+		typedef std::uint8_t FTYPE; //TODO: this should be char_to_bool to save A LOT memory
+
+		adios2::Variable<FTYPE> Flags;
+
+	    if (true) 
+        {
+
+
+			std::cout << reg.dy << " R " << reg.ny<< std::endl;
+			std::cout << crop.dy << " C " << crop.ny<< std::endl;
+
+			size_t local_y0 = crop.dy - reg.dy;
+			size_t local_ny = crop.ny;
+
+			std::cout <<  "I need Y: " << local_y0 << " COUNT "<< local_ny << std::endl;
+
+
+            std::vector<FTYPE> FlagsBuffer((size_t)reg.nx*local_ny);
+
+            // read only the chunk corresponding to our rank
+            // myFloats.data is pre-allocated
+
+
+			for (int z = reg.dz; z < reg.dz + reg.nz; z++) {
+
+				size_t index = 0;
+
+				adios2::StepStatus status = AdiosReader.BeginStep(adios2::StepMode::Read, 60.0f);
+				if (status != adios2::StepStatus::OK)
+				{
+					ERROR("ADIOS stream ended or broken - NZ > Number of steps avalible");
+					break;
+				}
+
+		        Flags = adioIO.InquireVariable<FTYPE>(n.attribute("Variable").value());
+
+
+
+        	    Flags.SetSelection({{0,local_y0}, {(size_t)reg.nx, local_ny}});
+
+				AdiosReader.Get<FTYPE>(Flags, FlagsBuffer.data());
+
+				AdiosReader.EndStep();
+
+				size_t white = 0;
+
+
+
+
+				for (int x = reg.dx; x < reg.dx + reg.nx; x++)
+				for (int y = reg.dy; y < reg.dy + reg.ny; y++){
+					if (crop.isIn(x, y, z)){
+						const bool v = FlagsBuffer[index] == 1;
+						white = white + FlagsBuffer[index];
+						if (v) Dot(x, y, z);
+						index++;
+					}
+				}
+
+				std::cout << "I've read: MARKED: " << white << "  ALL: " << index << std::endl;
+
+			}
+
+        }
+		AdiosReader.Close();
+	    /** 
+		for (int x = reg.dx; x < reg.dx + reg.nx; x++)
+		for (int y = reg.dy; y < reg.dy + reg.ny; y++)
+		    for (int z = reg.dz; z < reg.dz + reg.nz; z++) {
+			int v;
+			int ret = fscanf(f, "%d", &v);
+                        if (ret == EOF) {
+                            ERROR("File (%s) ended while reading\n", n.attribute("file").value());
+                            return -1;
+                        }
+			if ((v != 0) && (crop.isIn(x, y, z)))
+			    Dot(x, y, z);
+		    }
+		**/
+
+
 	} else {
 	    pugi::xml_node node = fg_xml.find_child_by_attribute("Zone", "name", n.name());
 	    if (node) {

src/configure.ac

@@ -37,6 +37,16 @@ AC_ARG_WITH([hdf5-include],
 	AC_HELP_STRING([--with-hdf5-include=hdf5],
 		[specify the full path to your hdf5 installation (headers)]))
 
+AC_ARG_WITH([adios_dir],
+	AC_HELP_STRING([--with-adios_dir=adios_dir],
+		[specify the directory containing bin/adios_config /usr/local/adios2]),
+	[ADIOS_DIR="$withval"])
+
+AC_ARG_WITH([adios],
+	AC_HELP_STRING([--enable-adios],
+		[Enable ADIOS2 support (experimental)]),
+	[with_adios="$withval"])
+
 AC_ARG_ENABLE([graphics],
 	AC_HELP_STRING([--enable-graphics],
 		[make a GUI version]))
@@ -383,6 +393,24 @@ if test "x${with_hdf5}" != "xno"; then
 	fi
 fi
 
+if test "x${with_adios}" != "xno"; then
+	adios2_config="${ADIOS_DIR}/bin/adios2-config"
+	AC_CHECK_PROG(adios2_config,${adios2_config},${adios2_config},adios2-config)
+
+	AC_MSG_NOTICE([ADIOS2 config: ${adios2_config}])
+
+	AC_MSG_CHECKING([ADIOS2 embandinng: linker flags])
+	LD=$(${adios2_config} --cxx-libs)
+	LDFLAGS="${LDFLAGS} ${LD}"
+	AC_MSG_RESULT(["${LD}"])
+
+
+	AC_MSG_CHECKING([ADIOS2 embandinng: linker flags])
+	LD=$(${adios2_config} --cxx-flags)
+
+	CPPFLAGS="${CPPFLAGS} ${LD}"
+	AC_MSG_RESULT(["${LD}"])
+fi
 
 if  test "x${with_python}" == "xyes"; then