Merge branch 'master' of https://github.com/TUM-I5/SWE

SConstruct

@@ -37,8 +37,8 @@ print '  Department of Informatics'
 print '  Chair of Scientific Computing'
 print '  http://www5.in.tum.de/SWE'
 print ''
-print 'This program comes with ABSOLUTELY NO WARRANTY.'
-print 'This is free software, and you are welcome to redistribute it'
+print 'SWE comes with ABSOLUTELY NO WARRANTY.'
+print 'SWE free software, and you are welcome to redistribute it'
 print 'under certain conditions.'
 print 'Details can be found in the file \'gpl.txt\'.'
 print ''
@@ -48,10 +48,16 @@ print ''
 #
 vars = Variables()
 
-# SWE specific variables
+# read parameters from a file if given
 vars.AddVariables(
-  PathVariable( 'xmlFile', 'location of the xml-file, which contains compile parameters', None, PathVariable.PathIsFile ),
+  PathVariable( 'buildVariablesFile', 'location of the python file, which contains the build variables', None, PathVariable.PathIsFile )
+)
+env = Environment(variables=vars)
+if 'buildVariablesFile' in env:
+  vars = Variables(env['buildVariablesFile'])
 
+# SWE specific variables
+vars.AddVariables(
   PathVariable( 'buildDir', 'where to build the code', 'build', PathVariable.PathIsDirCreate ),
 
   EnumVariable( 'compiler', 'used compiler', 'gnu',
@@ -83,6 +89,8 @@ vars.AddVariables(
 
 # external variables
 vars.AddVariables(
+  PathVariable( 'compilerPath', 'location of the C++ compiler', None, PathVariable.PathIsFile ),
+  PathVariable( 'linkerPath', 'location of the C++ linker', None, PathVariable.PathIsFile ),
   PathVariable( 'cudaToolkitDir', 'location of the CUDA toolkit', None ),
   PathVariable( 'cudaSDKDir', 'location of the CUDA SDK', None),
   PathVariable( 'netCDFDir', 'location of netCDF', None),
@@ -98,6 +106,12 @@ Help(vars.GenerateHelpText(env))
 
 # handle unknown, maybe misspelled variables
 unknownVariables = vars.UnknownVariables()
+
+# remove the buildVariablesFile from the list of unknown variables (used before)
+if 'buildVariablesFile' in unknownVariables:
+  unknownVariables.pop('buildVariablesFile')
+
+# exit in the case of unknown variables
 if unknownVariables:
   print "*** The following build variables are unknown:", unknownVariables.keys()
   Exit(1)
@@ -174,12 +188,18 @@ if env['parallelization'] in ['mpi_with_cuda']:
 # set the precompiler flags for MPI (C++)
 if env['parallelization'] in ['mpi_with_cuda', 'mpi']:
   env.Append(CPPDEFINES=['USEMPI'])
-  env['CXX'] = 'mpiCC.openmpi'
-  env['LINKERFORPROGRAMS'] = 'mpiCC.openmpi'
+  if 'compilerPath' in env:
+    env['CXX'] = env['compilerPath']
+  else:
+    env['CXX'] = 'mpiCC'
+  if 'linkerPath' in env:
+    env['LINKERFORPROGRAMS'] = env['linkerPath']
+  env['LINKERFORPROGRAMS'] = 'mpiCC'
 
 # set the precompiler flags and includes for netCDF
 if env['writeNetCDF'] == True:
   env.Append(CPPDEFINES=['WRITENETCDF'])
+  env.Append(LIBS=['netcdf','netcdf_c++'])
   # set netCDF location
   if 'netCDFDir' in env:
     env.Append(CPPPATH=[env['netCDFDir']+'/include'])
@@ -193,7 +213,7 @@ if env['asagi'] == True:
   env.Append(LIBS=['asagi'])
   if 'asagiDir' in env:
     env.Append(CPPPATH=[env['asagiDir']+'/include'])
-    env.Append(LIBPATH=[env['asagiDir']])
+    env.Append(LIBPATH=[env['asagiDir']+'/lib'])
   if 'netCDFDir' in env:
     env.Append(LIBPATH=[env['netCDFDir']+'/lib'])
 

build/options/hpcsccs3_SWE_gnu_cuda_asagi.py

+#! /usr/bin/python
+
+# @file
+# This file is part of SWE.
+#
+# @author Alexander Breuer (breuera AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Dipl.-Math._Alexander_Breuer)
+#
+# @section LICENSE
+#
+# SWE is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# SWE is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with SWE.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# @section DESCRIPTION
+#
+# Example build parameters a "gnu, cuda, asagi" setting.
+#
+
+#build options
+parallelization='cuda'
+computeCapability='sm_21'
+solver='fwave'
+asagi='yes'
+
+# libraries (machine dependent)
+cudaToolkitDir='/work/breuera/software/cuda'
+cudaSDKDir='/work/breuera/workspace/NVIDIA_GPU_Computing_SDK'
+asagiDir='/work/breuera/software/asagi_nompi'
+netCDFDir='/home_local/breuera/software/netcdf/netcdf-4.1.3'

build/options/hpcsccs3_SWE_gnu_mpi_with_cuda_asagi.py

+#! /usr/bin/python
+
+# @file
+# This file is part of SWE.
+#
+# @author Alexander Breuer (breuera AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Dipl.-Math._Alexander_Breuer)
+#
+# @section LICENSE
+#
+# SWE is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# SWE is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with SWE.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# @section DESCRIPTION
+#
+# Example build parameters a "gnu, mpi_with_cuda, asagi" setting.
+#
+
+#build options
+parallelization='mpi_with_cuda'
+computeCapability='sm_21'
+solver='fwave'
+asagi='yes'
+writeNetCDF='yes'
+
+# libraries (machine dependent)
+cudaToolkitDir='/work/breuera/software/cuda'
+cudaSDKDir='/work/breuera/workspace/NVIDIA_GPU_Computing_SDK'
+asagiDir='/work/breuera/software/asagi_nompi'
+netCDFDir='/home_local/breuera/software/netcdf/netcdf-4.1.3/'

build/options/npsgpu_SWE_gnu_mpi_with_cuda_asagi.py

+#! /usr/bin/python
+
+# @file
+# This file is part of SWE.
+#
+# @author Alexander Breuer (breuera AT in.tum.de, http://www5.in.tum.de/wiki/index.php/Dipl.-Math._Alexander_Breuer)
+#
+# @section LICENSE
+#
+# SWE is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# SWE is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with SWE.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+# @section DESCRIPTION
+#
+# Example build parameters for the NPS GPU-cluster.
+#
+
+#build options
+parallelization='mpi_with_cuda'
+computeCapability='sm_20'
+solver='fwave'
+asagi='yes'
+writeNetCDF='yes'
+
+# libraries (machine dependent)
+compilerPath='/usr/lib64/openmpi/bin/mpiCC'
+linkerPath='/usr/lib64/openmpi/bin/mpiCC'
+cudaSDKDir='/'
+asagiDir='/home/prof2/software/asagi/mpi'
+netCDFDir='/home/prof2/software/netcdf'

src/SConscript

@@ -57,7 +57,7 @@ sourceFiles = ['SWE_Block.cpp']
 
 # netCDF writer
 if env['writeNetCDF'] == True:
-  sourceFiles.append( ['io/NetCdfWriter.cpp'] )
+  sourceFiles.append( ['tools/NetCdfWriter.cpp'] )
 
 # xml reader
 if env['xmlRuntime'] == True:

src/SWE_Block.cpp

@@ -61,7 +61,7 @@ SWE_Block::SWE_Block(float _offsetX, float _offsetY)
 {
   // set WALL as default boundary condition
   for(int i=0; i<4;i++) {
-     boundary[i] = WALL;
+     boundary[i] = PASSIVE;
      neighbour[i] = NULL;
   };
   
@@ -80,53 +80,44 @@ SWE_Block::~SWE_Block() {
 //==================================================================
 
 /**
- * Initialise unknowns and bathymetry in all grid cells 
- * according to the specified SWE_Scenario
- * Note: unknowns hu and hv represent momentum, while parameters u and v are velocities! 
+ * Initializes the unknowns and bathymetry in all grid cells according to the given SWE_Scenario.
+ *
+ * In the case of multiple SWE_Blocks at this point, it is not clear how the boundary conditions
+ * should be set. This is because an isolated SWE_Block doesn't have any in information about the grid.
+ * Therefore the calling routine, which has the information about multiple blocks, has to take care about setting
+ * the right boundary conditions.
  * 
+ * @param i_scenario scenario, which is used during the setup.
+ * @param i_multipleBlocks are the multiple SWE_blocks?
  */
-void SWE_Block::initScenario(SWE_Scenario &scene) {
+void SWE_Block::initScenario( SWE_Scenario &i_scenario,
+                              const bool i_multipleBlocks ) {
 
   // initialize water height and discharge
   for(int i=1; i<=nx; i++)
     for(int j=1; j<=ny; j++) {
       float x = offsetX + (i-0.5f)*dx;
       float y = offsetY + (j-0.5f)*dy;
-      h[i][j] =  scene.getWaterHeight(x,y);
-      hu[i][j] = scene.getVeloc_u(x,y) * h[i][j];
-      hv[i][j] = scene.getVeloc_v(x,y) * h[i][j]; 
+      h[i][j] =  i_scenario.getWaterHeight(x,y);
+      hu[i][j] = i_scenario.getVeloc_u(x,y) * h[i][j];
+      hv[i][j] = i_scenario.getVeloc_v(x,y) * h[i][j]; 
     };
 
-  // initialise bathymetry
+  // initialize bathymetry
   for(int i=0; i<=nx+1; i++) {
     for(int j=0; j<=ny+1; j++) {
-      b[i][j] = scene.getBathymetry(offsetX + (i-0.5f)*dx,
-                                    offsetY + (j-0.5f)*dy );
+      b[i][j] = i_scenario.getBathymetry( offsetX + (i-0.5f)*dx,
+                                          offsetY + (j-0.5f)*dy );
     }
   }
 
-  // obtain boundary conditions for all four edges from scenario
-  boundary[BND_LEFT]   = scene.getBoundaryType(BND_LEFT); 
-  boundary[BND_RIGHT]  = scene.getBoundaryType(BND_RIGHT); 
-  boundary[BND_BOTTOM] = scene.getBoundaryType(BND_BOTTOM); 
-  boundary[BND_TOP]    = scene.getBoundaryType(BND_TOP); 
-
-  // set bathymetry values in the ghost layer, if necessary
-  for(int j=0; j<=ny+1; j++) {
-    if( boundary[BND_LEFT] == OUTFLOW || boundary[BND_LEFT] == WALL ) {
-      b[0][j] = b[1][j];
-    }
-    if( boundary[BND_RIGHT] == OUTFLOW || boundary[BND_RIGHT] == WALL ) {
-      b[nx+1][j] = b[nx][j];
-    }
-  }
-  for(int i=0; i<=nx+1; i++) {
-    if( boundary[BND_BOTTOM] == OUTFLOW || boundary[BND_BOTTOM] == WALL ) {
-      b[i][0] = b[i][1];
-    }
-    if( boundary[BND_TOP] == OUTFLOW || boundary[BND_TOP] == WALL ) {
-      b[i][ny+1] = b[i][ny];
-    }
+  // in the case of multiple blocks the calling routine takes care about proper boundary conditions.
+  if( i_multipleBlocks == false ) {
+    // obtain boundary conditions for all four edges from scenario
+    setBoundaryType(BND_LEFT, i_scenario.getBoundaryType(BND_LEFT));
+    setBoundaryType(BND_RIGHT, i_scenario.getBoundaryType(BND_RIGHT));
+    setBoundaryType(BND_BOTTOM, i_scenario.getBoundaryType(BND_BOTTOM));
+    setBoundaryType(BND_TOP, i_scenario.getBoundaryType(BND_TOP));
   }
 
   // perform update after external write to variables 
@@ -339,16 +330,38 @@ void SWE_Block::setOutflowBoundaries() {
 }
 
 /**
- * set boundary type for a specific block boundary
- * @param edge	specifies boundary (LEFT, RIGHT, BOTTOM, TOP)
- * @param boundtype	type of boundary condition
- * @param inflow	pointer to an SWE_block1D that specifies 
- * 			inflow (should be NULL for WALL or OUTFLOW boundary) 
+ * Set the boundary type for specific block boundary.
+ *
+ * @param i_edge location of the edge relative to the SWE_block.
+ * @param i_boundaryType type of the boundary condition.
+ * @param i_inflow pointer to an SWE_Block1D, which specifies the inflow (should be NULL for WALL or OUTFLOW boundary)
  */
-void SWE_Block::setBoundaryType(BoundaryEdge edge, BoundaryType boundtype, 
-                                const SWE_Block1D* inflow) {
-  boundary[edge] = boundtype;
-  neighbour[edge] = inflow;
+void SWE_Block::setBoundaryType( const BoundaryEdge i_edge,
+                                 const BoundaryType i_boundaryType,
+                                 const SWE_Block1D* i_inflow) {
+  boundary[i_edge] = i_boundaryType;
+  neighbour[i_edge] = i_inflow;
+
+  // set bathymetry values in the ghost layer, if necessary
+  for(int j=0; j<=ny+1; j++) {
+    if( boundary[BND_LEFT] == OUTFLOW || boundary[BND_LEFT] == WALL ) {
+      b[0][j] = b[1][j];
+    }
+    if( boundary[BND_RIGHT] == OUTFLOW || boundary[BND_RIGHT] == WALL ) {
+      b[nx+1][j] = b[nx][j];
+    }
+  }
+  for(int i=0; i<=nx+1; i++) {
+    if( boundary[BND_BOTTOM] == OUTFLOW || boundary[BND_BOTTOM] == WALL ) {
+      b[i][0] = b[i][1];
+    }
+    if( boundary[BND_TOP] == OUTFLOW || boundary[BND_TOP] == WALL ) {
+      b[i][ny+1] = b[i][ny];
+    }
+  }
+
+  // synchronize after an external update of the bathymetry
+  synchBathymetryAfterWrite();
 }
 
 // /**
@@ -529,7 +542,6 @@ void SWE_Block::setBoundaryConditions() {
         h[0][j] = h[1][j];
         hu[0][j] = -hu[1][j];
         hv[0][j] = hv[1][j];
-        b[0][j] = b[1][j];
       };
       break;
     }
@@ -539,7 +551,6 @@ void SWE_Block::setBoundaryConditions() {
         h[0][j] = h[1][j];
         hu[0][j] = hu[1][j];
         hv[0][j] = hv[1][j];
-        b[0][j] = b[1][j];
       };
       break;
     }
@@ -559,7 +570,6 @@ void SWE_Block::setBoundaryConditions() {
         h[nx+1][j] = h[nx][j];
         hu[nx+1][j] = -hu[nx][j];
         hv[nx+1][j] = hv[nx][j];
-        b[nx+1][j] = b[nx][j];
       };
       break;
     }
@@ -569,7 +579,6 @@ void SWE_Block::setBoundaryConditions() {
         h[nx+1][j] = h[nx][j];
         hu[nx+1][j] = hu[nx][j];
         hv[nx+1][j] = hv[nx][j];
-        b[nx+1][j] = b[nx][j];
       };
       break;
     }
@@ -589,7 +598,6 @@ void SWE_Block::setBoundaryConditions() {
         h[i][0] = h[i][1];
         hu[i][0] = hu[i][1];
         hv[i][0] = -hv[i][1];
-        b[i][0] = b[i][1];
       };
       break;
     }
@@ -599,7 +607,6 @@ void SWE_Block::setBoundaryConditions() {
         h[i][0] = h[i][1];
         hu[i][0] = hu[i][1];
         hv[i][0] = hv[i][1];
-        b[i][0] = b[i][1];
       };
       break;
     }
@@ -619,7 +626,6 @@ void SWE_Block::setBoundaryConditions() {
         h[i][ny+1] = h[i][ny];
         hu[i][ny+1] = hu[i][ny];
         hv[i][ny+1] = -hv[i][ny];
-        b[i][ny+1] = b[i][ny];
       };
       break;
     }
@@ -629,7 +635,6 @@ void SWE_Block::setBoundaryConditions() {
         h[i][ny+1] = h[i][ny];
         hu[i][ny+1] = hu[i][ny];
         hv[i][ny+1] = hv[i][ny];
-        b[i][ny+1] = b[i][ny];
       };
       break;
     }

src/SWE_Block.hh

@@ -118,7 +118,7 @@ class SWE_Block {
   public:
   // object methods
     /// initialise unknowns to a specific scenario:
-    void initScenario(SWE_Scenario &scene);
+    void initScenario(SWE_Scenario &i_scenario, const bool i_multipleBlocks = false );
     // set unknowns
     /// set the water height to a uniform value
     void setWaterHeight(float _h);

src/examples/swe_mpi.cpp

@@ -23,21 +23,34 @@
  *
  * @section DESCRIPTION
  *
- * Very basic setting of SWE, which uses a wave propagation solver and an artificial scenario on a single block.
+ * Setting of SWE, which uses a wave propagation solver and an artificial or ASAGI scenario on multiple blocks.
  */
 
 #include <mpi.h>
-#include "../tools/help.hh"
+#include <cassert>
+#include <cmath>
 #include <cstdlib>
 #include <string>
 
+#include "../tools/help.hh"
+
 #include "../SWE_Block.hh"
+
 #ifndef CUDA
 #include "../SWE_WavePropagationBlock.hh"
 #else
 #include "../SWE_WavePropagationBlockCuda.hh"
 #endif
+
+#ifdef WRITENETCDF
+#include "../tools/NetCdfWriter.hh"
+#endif
+
+#ifdef ASAGI
+#include "../scenarios/SWE_AsagiScenario.hpp"
+#else
 #include "../scenarios/SWE_simple_scenarios.h"
+#endif
 
 #ifdef READXML
 #include "../tools/CXMLConfig.hpp"
@@ -136,6 +149,7 @@ int main( int argc, char** argv ) {
 
   // read xml file
   #ifdef READXML
+  assert(false); //TODO: not implemented.
   if(argc != 2) {
     l_sweLogger.printString("Aborting. Please provide a proper input file.");
     l_sweLogger.printString("Example: ./SWE_gnu_debug_none_augrie config.xml");
@@ -169,8 +183,34 @@ int main( int argc, char** argv ) {
   l_blockPositionX = l_mpiRank / l_blocksY;
   l_blockPositionY = l_mpiRank % l_blocksY;
 
+  #ifdef ASAGI
+  /*
+   * Pixel node registration used [Cartesian grid]
+   * Grid file format: nf = GMT netCDF format (float)  (COARDS-compliant)
+   * x_min: -500000 x_max: 6500000 x_inc: 500 name: x nx: 14000
+   * y_min: -2500000 y_max: 1500000 y_inc: 500 name: y ny: 8000
+   * z_min: -6.48760175705 z_max: 16.1780223846 name: z
+   * scale_factor: 1 add_offset: 0
+   * mean: 0.00217145586762 stdev: 0.245563641735 rms: 0.245573241263
+   */
+
+  //simulation area
+  float simulationArea[4];
+  simulationArea[0] = -450000;
+  simulationArea[1] = 6450000;
+  simulationArea[2] = -2450000;
+  simulationArea[3] = 1450000;
+
+  //  scenarios::Asagi scene( "/naslx/ptmp/2/di56dok/data/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+  //                          "/naslx/ptmp/2/di56dok/data/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+  //                          (float) 300., simulationArea);
+  SWE_AsagiScenario l_scenario( "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+                                "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+                                (float) 14400., simulationArea, true);
+  #else
   // create a simple artificial scenario
   SWE_BathymetryDamBreakScenario l_scenario;
+  #endif
 
   //! number of checkpoints for visualization (at each checkpoint in time, an output file is written).
   int l_numberOfCheckPoints = 40;
@@ -218,7 +258,7 @@ int main( int argc, char** argv ) {
   #endif
 
   // initialize the wave propgation block
-  l_wavePropgationBlock.initScenario(l_scenario);
+  l_wavePropgationBlock.initScenario( l_scenario, true );
 
   //! time when the simulation ends.
   float l_endSimulation = l_scenario.endSimulation();
@@ -330,8 +370,27 @@ int main( int argc, char** argv ) {
 
   // write the output at time zero
   l_sweLogger.printOutputTime(0);
+  #ifdef WRITENETCDF
+  //boundary size of the ghost layers
+  int l_boundarySize[4];
+  l_boundarySize[0] = l_boundarySize[1] = l_boundarySize[2] = l_boundarySize[3] = 1;
+
+  //construct a NetCdfWriter
+  std::string l_fileName = generateFileName(l_baseName,l_blockPositionX,l_blockPositionY);
+  io::NetCdfWriter l_netCdfWriter( l_fileName, l_nXLocal, l_nYLocal );
+  //create the netCDF-file
+  l_netCdfWriter.createNetCdfFile( l_dX, l_dY,
+                                   l_originX, l_originY );
+  l_netCdfWriter.writeBathymetry( l_wavePropgationBlock.getBathymetry(),
+                                  l_boundarySize );
+  l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                l_wavePropgationBlock.getDischarge_hu(),
+                                l_wavePropgationBlock.getDischarge_hv(),
+                                l_boundarySize, (float) 0.);
+#else
   l_wavePropgationBlock.writeVTKFileXML( generateFileName(l_baseName,0,l_blockPositionX,l_blockPositionY),
                                          l_nXLocal*l_blockPositionX, l_nYLocal*l_blockPositionY);
+#endif
 
 
   /**
@@ -352,7 +411,6 @@ int main( int argc, char** argv ) {
     // do time steps until next checkpoint is reached
     while( l_t < l_checkPoints[c] ) {
       // exchange ghost and copy layers
-      l_sweLogger.printString("Exchanging ghost and copy layers.");
       exchangeLeftRightGhostLayers( l_leftNeighborRank,  l_leftInflow,  l_leftOutflow,
                       l_rightNeighborRank, l_rightInflow, l_rightOutflow,
                       l_mpiCol );
@@ -364,7 +422,7 @@ int main( int argc, char** argv ) {
       // reset the cpu clock
       l_sweLogger.resetCpuClockToCurrentTime();
 
-      // set values in ghost cells:
+      // set values in ghost cells
       l_wavePropgationBlock.setGhostLayer();
 
       // compute numerical flux on each edge
@@ -396,9 +454,16 @@ int main( int argc, char** argv ) {
     // print current simulation time
     l_sweLogger.printOutputTime(l_t);
 
-    // write vtk output
+    // write output
+    #ifdef WRITENETCDF
+    l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                  l_wavePropgationBlock.getDischarge_hu(),
+                                  l_wavePropgationBlock.getDischarge_hv(),
+                                  l_boundarySize, l_t);
+    #else
     l_wavePropgationBlock.writeVTKFileXML( generateFileName(l_baseName,c,l_blockPositionX,l_blockPositionY),
                                           l_blockPositionX*l_nXLocal, l_blockPositionY*l_nYLocal);
+    #endif
   }
 
   /**

src/examples/swe_wavepropagation.cpp

@@ -23,21 +23,35 @@
  *
  * @section DESCRIPTION
  *
- * Very basic setting of SWE, which uses a wave propagation solver and an artificial scenario on a single block.
+ * Basic setting of SWE, which uses a wave propagation solver and an artificial or ASAGI scenario on a single block.
  */
 
-#include "../tools/help.hh"
+#include <cassert>
 #include <cstdlib>
 #include <string>
+#include "../tools/help.hh"
 
 #include "../SWE_Block.hh"
+
 #ifndef CUDA
 #include "../SWE_WavePropagationBlock.hh"
 #else
 #include "../SWE_WavePropagationBlockCuda.hh"
 #endif
+
+#ifdef WRITENETCDF
+#include "../tools/NetCdfWriter.hh"
+#endif
+
+#ifdef ASAGI
+#include "../scenarios/SWE_AsagiScenario.hpp"
+#else
 #include "../scenarios/SWE_simple_scenarios.h"
-#include "../tools/Logger.hpp"
+#endif
+
+#ifdef READXML
+#include "../tools/CXMLConfig.hpp"
+#endif
 
 #ifndef STATICLOGGER
 #define STATICLOGGER
@@ -53,12 +67,14 @@ int main( int argc, char** argv ) {
    * Initialization.
    */
   // check if the necessary command line input parameters are given
+  #ifndef READXML
   if(argc != 4) {
     std::cout << "Aborting ... please provide proper input parameters." << std::endl
               << "Example: ./SWE_parallel 200 300 /work/openmp_out" << std::endl
               << "\tfor a single block of size 200 * 300" << std::endl;
     return 1;
   }
+  #endif
 
   //! number of grid cells in x- and y-direction.
   int l_nX, l_nY;
@@ -67,15 +83,58 @@ int main( int argc, char** argv ) {
   std::string l_baseName;
 
   // read command line parameters
+  #ifndef READXML
   l_nY = l_nX = atoi(argv[1]);
   l_nY = atoi(argv[2]);
   l_baseName = std::string(argv[3]);
+  #endif
 
-  //create a simple artificial scenario
+  // read xml file
+  #ifdef READXML
+  assert(false); //TODO: not implemented.
+  if(argc != 2) {
+    s_sweLogger.printString("Aborting. Please provide a proper input file.");
+    s_sweLogger.printString("Example: ./SWE_gnu_debug_none_augrie config.xml");
+    return 1;
+  }
+  s_sweLogger.printString("Reading xml-file.");
+
+  std::string l_xmlFile = std::string(argv[1]);
+  s_sweLogger.printString(l_xmlFile);
+
+  CXMLConfig l_xmlConfig;
+  l_xmlConfig.loadConfig(l_xmlFile.c_str());
+  #endif
+
+  #ifdef ASAGI
+  /* Information about the example bathymetry grid (tohoku_gebco_ucsb3_500m_hawaii_bath.nc):
+   *
+   * Pixel node registration used [Cartesian grid]
+   * Grid file format: nf = GMT netCDF format (float)  (COARDS-compliant)
+   * x_min: -500000 x_max: 6500000 x_inc: 500 name: x nx: 14000
+   * y_min: -2500000 y_max: 1500000 y_inc: 500 name: y ny: 8000
+   * z_min: -6.48760175705 z_max: 16.1780223846 name: z
+   * scale_factor: 1 add_offset: 0
+   * mean: 0.00217145586762 stdev: 0.245563641735 rms: 0.245573241263
+   */
+
+  //simulation area
+  float simulationArea[4];
+  simulationArea[0] = -450000;
+  simulationArea[1] = 6450000;
+  simulationArea[2] = -2450000;
+  simulationArea[3] = 1450000;
+
+  SWE_AsagiScenario l_scenario( "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_bath.nc",
+                                "/work/breuera/workspace/geo_information/output/tohoku_gebco_ucsb3_500m_hawaii_displ.nc",
+                                (float) 28800., simulationArea, true);
+  #else
+  // create a simple artificial scenario
   SWE_BathymetryDamBreakScenario l_scenario;
+  #endif
 
   //! number of checkpoints for visualization (at each checkpoint in time, an output file is written).
-  int l_numberOfCheckPoints = 40;
+  int l_numberOfCheckPoints = 20;
 
   //! size of a single cell in x- and y-direction
   float l_dX, l_dY;
@@ -116,8 +175,27 @@ int main( int argc, char** argv ) {
      l_checkPoints[cp] = cp*(l_endSimulation/l_numberOfCheckPoints);
   }
 
+
   // write the output at time zero
+  s_sweLogger.printOutputTime((float) 0.);
+  #ifdef WRITENETCDF
+  //boundary size of the ghost layers
+  int l_boundarySize[4];
+  l_boundarySize[0] = l_boundarySize[1] = l_boundarySize[2] = l_boundarySize[3] = 1;
+
+  //construct a NetCdfWriter
+  std::string l_fileName = l_baseName;
+  io::NetCdfWriter l_netCdfWriter( l_fileName, l_nX, l_nY );
+  //create the netCDF-file
+  l_netCdfWriter.createNetCdfFile(l_dX, l_dY, l_originX, l_originY);
+  l_netCdfWriter.writeBathymetry(l_wavePropgationBlock.getBathymetry(), l_boundarySize);
+  l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                l_wavePropgationBlock.getDischarge_hu(),
+                                l_wavePropgationBlock.getDischarge_hv(),
+                                l_boundarySize, (float) 0.);
+  #else
   l_wavePropgationBlock.writeVTKFileXML(generateFileName(l_baseName,0,0,0), l_nX, l_nY);
+  #endif
 
 
   /**
@@ -159,11 +237,18 @@ int main( int argc, char** argv ) {
     // update the cpu time in the logger
     s_sweLogger.updateCpuTime();
 
-    // print current simulation time
+    // print current simulation time of the output
     s_sweLogger.printOutputTime(l_t);
 
-    // write vtk output
+    // write output
+#ifdef WRITENETCDF
+    l_netCdfWriter.writeUnknowns( l_wavePropgationBlock.getWaterHeight(),
+                                  l_wavePropgationBlock.getDischarge_hu(),
+                                  l_wavePropgationBlock.getDischarge_hv(),
+                                  l_boundarySize, l_t);
+#else
     l_wavePropgationBlock.writeVTKFileXML(generateFileName(l_baseName,c,0,0), l_nX, l_nY);
+#endif
   }
 
   /**
@@ -173,7 +258,7 @@ int main( int argc, char** argv ) {
   s_sweLogger.printStatisticsMessage();
 
   // print the cpu time
-  s_sweLogger.printCpuTime("CPU/GPU time");
+  s_sweLogger.printCpuTime();
 
   // print the wall clock time (includes plotting)
   s_sweLogger.printWallClockTime(time(NULL));

src/scenarios/SWE_AsagiScenario.hpp

@@ -25,19 +25,15 @@
  * Access to bathymetry and displacement files with ASAGI.
  */
 
-#ifndef ASAGI_HPP_
-#define ASAGI_HPP_
+#ifndef SWEASAGISCENARIO_HPP_
+#define SWEASAGISCENARIO_HPP_
 
 #include <cassert>
 #include <string>
 #include <asagi.h>
 #include "SWE_Scenario.h"
 
-namespace scenarios {
-  class Asagi;
-}
-
-class scenarios::Asagi: public SWE_Scenario {
+class SWE_AsagiScenario: public SWE_Scenario {
 //private:
     //! pointer to the Asagi bathymetry grid
     asagi::Grid* bathymetryGrid;
@@ -75,17 +71,17 @@ class scenarios::Asagi: public SWE_Scenario {
      * @param i_displacementFile path to the netCDF-displacement file
      * @param i_duration time the simulation runs (in seconds)
      */
-    Asagi ( const std::string i_bathymetryFile,
-            const std::string i_displacementFile,
-            const float i_duration,
-            const float i_simulationArea[4],
-            const bool i_dynamicDisplacement = false ):
-              dynamicDisplacement(i_dynamicDisplacement),
-              duration(i_duration) {
-      //create the bathymetry grid
-      bathymetryGrid = asagi::Grid::create( asagi::Grid::FLOAT );
-      //create the displacement grid
-      displacementGrid = asagi::Grid::create( asagi::Grid::FLOAT );
+   SWE_AsagiScenario ( const std::string i_bathymetryFile,
+                       const std::string i_displacementFile,
+                       const float i_duration,
+                       const float i_simulationArea[4],
+                       const bool i_dynamicDisplacement = false ):
+                       dynamicDisplacement(i_dynamicDisplacement),
+                       duration(i_duration) {
+                       //create the bathymetry grid
+                       bathymetryGrid = asagi::Grid::create( asagi::Grid::FLOAT );
+                       //create the displacement grid
+                       displacementGrid = asagi::Grid::create( asagi::Grid::FLOAT );
 
       int l_asagiOpen = bathymetryGrid->open(i_bathymetryFile.c_str());
       //open the bathymetry grid
@@ -154,7 +150,7 @@ class scenarios::Asagi: public SWE_Scenario {
 
     }
 
-    virtual ~Asagi() {
+    virtual ~SWE_AsagiScenario() {
     }
 
     void deleteGrids() {
@@ -287,4 +283,4 @@ class scenarios::Asagi: public SWE_Scenario {
     };
 };
 
-#endif /* ASAGI_HPP_ */
+#endif /* SWEASAGISCENARIO_HPP_ */

src/tools/Logger.hpp

@@ -72,6 +72,9 @@ class tools::Logger {
   //! definition of the welcome message
   const std::string welcomeMessage;
 
+  //! definition of the copyrights
+  const std::string copyRights;
+
   //! definition of the finish message
   const std::string finishMessage;
 
@@ -150,15 +153,26 @@ class tools::Logger {
      * @param i_indentation definition of the indentation (used in all messages, except welcome, start and finish).
      */
     Logger( const int i_processRank = 0,
-            const std::string i_programName = "SWE teaching code",
-            const std::string i_welcomeMessage = "Welcome to the",
+            const std::string i_programName = "SWE",
+            const std::string i_welcomeMessage = "Welcome to",
+            const std::string i_copyRights =  "\n\nSWE Copyright (C) 2012\n"
+                                              "  Technische Universitaet Muenchen\n"
+                                              "  Department of Informatics\n"
+                                              "  Chair of Scientific Computing\n"
+                                              "  http://www5.in.tum.de/SWE\n"
+                                              "\n"
+                                              "SWE comes with ABSOLUTELY NO WARRANTY.\n"
+                                              "SWE is free software, and you are welcome to redistribute it\n"
+                                              "under certain conditions.\n"
+                                              "Details can be found in the file \'gpl.txt\'.",
             const std::string i_finishMessage = "finished successfully.",
             const std::string i_midDelimiter = "\n------------------------------------------------------------------\n",
-            const std::string i_largeDelimiter = "\n****************************************\n",
+            const std::string i_largeDelimiter = "\n*************************************************************\n",
             const std::string i_indentation = "\t" ):
             processRank(i_processRank),
             programName(i_programName),
             welcomeMessage(i_welcomeMessage),
+            copyRights(i_copyRights),
             finishMessage(i_finishMessage),
             midDelimiter(i_midDelimiter),
             largeDelimiter(i_largeDelimiter),
@@ -190,6 +204,7 @@ class tools::Logger {
         std::cout << largeDelimiter
                   << welcomeMessage << " "
                   << programName
+                  << copyRights
                   << largeDelimiter;
       }
     }

src/tools/help.hh

@@ -151,6 +151,25 @@ inline std::string generateFileName(std::string baseName, int timeStep) {
 	return FileName.str();
 };
 
+/**
+ * Generates an output file name for a multiple SWE_Block version based on the ordering of the blocks.
+ *
+ * @param i_baseName base name of the output.
+ * @param i_blockPositionX position of the SWE_Block in x-direction.
+ * @param i_blockPositionY position of the SWE_Block in y-direction.
+ * @param i_fileExtension file extension of the output file.
+ * @return
+ */
+inline std::string generateFileName( std::string i_baseName,
+                                     int i_blockPositionX, int i_blockPositionY,
+                                     std::string i_fileExtension=".nc" ) {
+
+  std::ostringstream l_fileName;
+
+  l_fileName << i_baseName << "_" << i_blockPositionX << i_blockPositionY << i_fileExtension;
+  return l_fileName.str();
+};
+
 /**
  * generate output filename for the multiple-SWE_Block version
  * (for serial and parallel (OpenMP and MPI) versions that use