Updated 2D seismic plane waves convergence benchmark.

bench/seismic/wp/plane_waves_2d/configs/gen_configs.js

@@ -35,27 +35,42 @@ var l_parts = [1, 13];
 for( var l_cl = 0; l_cl < l_cls.length; l_cl++ ) {
   for( var l_ty = 0; l_ty < l_base.length; l_ty++ ) {
     for( var l_pa = 0; l_pa < l_parts.length; l_pa++  ) {
-      console.log( 'generating config for char length / type / part:', l_cls[l_cl], '/', l_base[l_ty], '/', l_parts[l_pa] );
+      for( var l_ro = 0; l_ro < 2; l_ro++ ) {
+        var l_id = l_base[l_ty] + '_cl_'  + l_cls[l_cl] + '_pa_' + l_parts[l_pa];
+        // create reorder-only mesh for parallel configs
+        if( l_base[l_ty] == 'gts' && l_parts[l_pa] != 1 && l_ro == 1 ) {
+          l_id = l_id + '_reorder_only';
+        }
+        else if( l_ro == 1 ) {
+          continue;
+        }
+
+        console.log( 'generating config for char length / type / part / reorder only:', l_cls[l_cl], '/', l_base[l_ty], '/', l_parts[l_pa] ), '/', l_ro;
 
 
-      var l_meshBase =  'meshes/gen/edge_v/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa];
-      var l_meshExt = '.msh';
-      var l_config = 'gen/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml';
+        var l_meshBase = 'meshes/gen/edge_v/' + l_id;
+        var l_meshExt = '.msh';
+        var l_config = 'gen/' + l_id + '.xml';
 
-      l_fs.outputFile(
-        l_config,
-        nunjucks.render(
-          'config.njk', {
-            i_meshBase: l_meshBase,
-            i_meshExt: l_meshExt,
-            i_errorXml: 'errors/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml'
+        l_fs.outputFile(
+          l_config,
+          nunjucks.render(
+            'config.njk', {
+              i_meshBase: l_meshBase,
+              i_meshExt: l_meshExt,
+              i_waveField: 'wave_field/' + l_id + '/wf',
+              i_receivers: 'receivers/' + l_id,
+              i_errorXml: 'errors/' + l_id + '.xml'
+            }
+          ),
+          function(l_err) {
+            if(l_err) return console.log( l_err );
           }
-        ),
-        function(l_err) {
-          if(l_err) return console.log( l_err );
-        }
-      )
+        )
+      }
     }
+
+
   }
 }
 console.log( 'done' )

bench/seismic/wp/plane_waves_2d/meshes/README.rst

 Meshes for the 2D Plane Waves Setups
 ====================================
 
+The "reorder_only" GTS-versions went through the same reordering as the parallel versions but only have a single partition.
+
 Used commands:
 
 .. code-block:: bash

bench/seismic/wp/plane_waves_2d/meshes/edge_v.njk

@@ -25,9 +25,11 @@
 <edge_v>
   <mesh>
     <periodic>106</periodic>
+    <reorder_only>{{i_reorderOnly}}</reorder_only>
 {%- if i_nParts > 1 %}
     <n_partitions>{{i_nParts}}</n_partitions>
 {%- endif %}
+    <write_element_annotations>1</write_element_annotations>
     <files>
       <in>{{i_meshIn}}</in>
       <out>
@@ -38,7 +40,7 @@
   </mesh>
 
   <time>
-    <n_groups>6</n_groups>
+    <n_groups>{{i_nTimeGroups}}</n_groups>
 {%- if i_nParts == 1 %}
     <files>
       <out_time_steps>{{i_statsOut}}</out_time_steps>

bench/seismic/wp/plane_waves_2d/meshes/gen_configs.js

@@ -49,23 +49,45 @@ for( var l_cl = 0; l_cl < l_cls.length; l_cl++ ) {
     )
   }
 
-for( var l_ty = 0; l_ty < l_base.length; l_ty++ ) {
-  for( var l_pa = 0; l_pa < l_parts.length; l_pa++ ) {
-      console.log( 'generating EDGE-V config for char length / nParts:', l_cls[l_cl], '/', l_parts[l_pa] )
-      l_fs.outputFile(
-        'gen/configs/edge_v/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml',
-        nunjucks.render(
-          'edge_v.njk', {
-            i_meshIn:  'gen/gmsh/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.msh',
-            i_nParts: l_parts[l_pa],
-            i_meshOut: 'gen/edge_v/' + l_base[l_ty] + '_cl_'  + l_cls[l_cl] + '_pa_' + l_parts[l_pa],
-            i_statsOut: 'gen/stats/edge_v_'  + l_cls[l_cl] + '.csv',
-          }
-        ),
-        function(l_err) {
-          if(l_err) return console.log( l_err );
+  for( var l_ty = 0; l_ty < l_base.length; l_ty++ ) {
+    for( var l_pa = 0; l_pa < l_parts.length; l_pa++ ) {
+      for( var l_ro = 0; l_ro < 2; l_ro++ ) {
+        var l_id = l_base[l_ty] + '_cl_'  + l_cls[l_cl] + '_pa_' + l_parts[l_pa];
+        // create reorder-only mesh for parallel configs
+        if( l_base[l_ty] == 'gts' && l_parts[l_pa] != 1 && l_ro == 1 ) {
+          l_id = l_id + '_reorder_only';
+        }
+        else if( l_ro == 1 ) {
+          continue;
         }
-      )
+
+        console.log( 'generating EDGE-V config for char length / nParts / reorder only:', l_cls[l_cl], '/', l_parts[l_pa], '/', l_ro )
+
+        var l_configOut = 'gen/configs/edge_v/' + l_id + '.xml';
+        var l_nTimeGroups = 1;
+        if( l_base[l_ty] == 'lts' ) {
+          l_nTimeGroups = 5;
+        }
+        var l_meshOut = 'gen/edge_v/' + l_id;
+        var l_statsOut = 'gen/stats/edge_v_'  + l_id + '.csv';
+
+        l_fs.outputFile(
+          l_configOut,
+          nunjucks.render(
+            'edge_v.njk', {
+              i_meshIn:  'gen/gmsh/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.msh',
+              i_nParts: l_parts[l_pa],
+              i_nTimeGroups: l_nTimeGroups,
+              i_reorderOnly: l_ro,
+              i_meshOut: l_meshOut,
+              i_statsOut: l_statsOut,
+            }
+          ),
+          function(l_err) {
+            if(l_err) return console.log( l_err );
+          }
+        )
+      }
     }
   }
 }

bench/seismic/wp/plane_waves_2d/meshes/generate.sh

@@ -42,6 +42,12 @@ do
     do
       echo "$(date) running EDGE-V for char length ${l_cl} for nParts ${l_pa}"
       edge_v -x gen/configs/edge_v/${l_ty}_cl_${l_cl}_pa_${l_pa}.xml 2>&1 > gen/logs/${l_ty}_cl_${l_cl}_pa_${l_pa}_edge_v.log
+
+      if [[ l_pa -gt 1 && ${l_ty} == 'gts' ]]
+      then
+        echo "$(date) running EDGE-V for char length ${l_cl} for nParts ${l_pa} (reorder only)"
+        edge_v -x gen/configs/edge_v/${l_ty}_cl_${l_cl}_pa_${l_pa}_reorder_only.xml 2>&1 > gen/logs/${l_ty}_cl_${l_cl}_pa_${l_pa}_reorder_only_edge_v.log
+      fi
     done
   done
 done

bench/seismic/wp/plane_waves_2d/runs/README.rst

+Runs of the 2D Plane Waves Setups
+=================================
+
+Used commands:
+
+.. code-block:: bash
+
+  ./run_all.sh -e $(pwd)/edge

bench/seismic/wp/plane_waves_2d/runs/run_all.sh

@@ -71,6 +71,12 @@ do
       else
         echo "$(date) running EDGE for ${l_ty}, char length ${l_cl} and for nParts ${l_pa}"
         mpiexec --oversubscribe -n ${l_pa} ${EDGE_PATH} -x configs/gen/${l_ty}_cl_${l_cl}_pa_${l_pa}.xml 2>&1 > logs/edge_${l_ty}_cl_${l_cl}_pa_${l_pa}.log
+
+        if [[ ${l_ty} == 'gts' ]]
+        then
+          echo "$(date) running EDGE for ${l_ty}, char length ${l_cl} and for nParts ${l_pa} (reorder only)"
+          ${EDGE_PATH} -x configs/gen/${l_ty}_cl_${l_cl}_pa_${l_pa}_reorder_only.xml 2>&1 > logs/edge_${l_ty}_cl_${l_cl}_pa_${l_pa}_reorder_only.log
+        fi
       fi
     done
   done

bench/seismic/wp/plane_waves_3d/configs/README.rst

+Configs for the 3D Plane Waves Setups
+=====================================
+
+Used commands:
+
+.. code-block:: bash
+
+  ./gen_configs.js

bench/seismic/wp/plane_waves_3d/configs/config.njk

@@ -5,6 +5,7 @@
   @author Alexander Breuer (breuer AT mytum.de)
 
   @section LICENSE
+  Copyright (c) 2021, Friedrich Schiller University Jena
   Copyright (c) 2019, Alexander Breuer
   Copyright (c) 2016, Regents of the University of California
   All rights reserved.
@@ -25,9 +26,10 @@
 <edge>
   <cfr>
     <mesh>
-      <files>
-        <in>{{i_meshIn}}</in>
-      </files>
+      <in>
+        <base>{{i_meshBase}}</base>
+        <extension>{{i_meshExt}}</extension>
+      </in>
       <boundary>
         <periodic>106</periodic>
       </boundary>

bench/seismic/wp/plane_waves_3d/configs/gen_configs.js

@@ -5,6 +5,7 @@
  * @author Alexander Breuer (breuer AT mytum.de)
  *
  * @section LICENSE
+ * Copyright (c) 2021, Friedrich Schiller University Jena
  * Copyright (c) 2019, Alexander Breuer
  * All rights reserved.
  *
@@ -28,32 +29,33 @@ var l_fs = require('fs-extra');
 
 // minimum edge lengths
 var l_cls = [25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1];
-var l_base = ['lts', 'gts_on_lts', 'gts'];
+var l_base = ['lts', 'gts'];
+var l_parts = [1, 8];
 
 for( var l_cl = 0; l_cl < l_cls.length; l_cl++ ) {
-	for( var l_ty = 0; l_ty < l_base.length; l_ty++ ) {
-		console.log( 'generating config for char length:', l_cls[l_cl] )
+  for( var l_ty = 0; l_ty < l_base.length; l_ty++ ) {
+    for( var l_pa = 0; l_pa < l_parts.length; l_pa++  ) {
+      console.log( 'generating config for char length / type / part:', l_cls[l_cl], '/', l_base[l_ty], '/', l_parts[l_pa] );
 
-		var l_path = 'meshes/gen/ascii/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.msh';
-		if( l_base[l_ty] == 'lts' ) {
-			l_path =  'meshes/gen/hdf5/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.h5m'
-		}
-		else if( l_base[l_ty] == 'gts_on_lts' ) {
-			l_path =  'meshes/gen/ascii/lts_' + l_cls[l_cl] + '.msh'
-		}
 
-		l_fs.outputFile(
-			'gen/configs/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.xml',
-			nunjucks.render(
-				'config.njk', {
-					i_meshIn: l_path,
-					i_errorXml: 'errors/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.xml'
-				}
-			),
-			function(l_err) {
-				if(l_err) return console.log( l_err );
-			}
-		)
-	}
+      var l_meshBase =  'meshes/gen/edge_v/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa];
+      var l_meshExt = '.msh';
+      var l_config = 'gen/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml';
+
+      l_fs.outputFile(
+        l_config,
+        nunjucks.render(
+          'config.njk', {
+            i_meshBase: l_meshBase,
+            i_meshExt: l_meshExt,
+            i_errorXml: 'errors/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml'
+          }
+        ),
+        function(l_err) {
+          if(l_err) return console.log( l_err );
+        }
+      )
+    }
+  }
 }
 console.log( 'done' )

bench/seismic/wp/plane_waves_3d/meshes/README.rst

+Meshes for the 3D Plane Waves Setups
+====================================
+
+Used commands:
+
+.. code-block:: bash
+
+  ./generate.sh

bench/seismic/wp/plane_waves_3d/meshes/edge_v.njk

@@ -5,6 +5,7 @@
   @author Alexander Breuer (breuer AT mytum.de)
 
   @section LICENSE
+  Copyright (c) 2021, Friedrich Schiller University Jena
   Copyright (c) 2019, Alexander Breuer
   All rights reserved.
 
@@ -24,18 +25,12 @@
 <edge_v>
   <mesh>
     <periodic>106</periodic>
-{%- if i_nParts > 1 %}
     <n_partitions>{{i_nParts}}</n_partitions>
-{%- endif %}
     <files>
       <in>{{i_meshIn}}</in>
-      <out>{{i_meshOut}}.h5m</out>
-{%- if i_nParts > 1 %}
-      <out_by_partition>
+      <out>
         <base>{{i_meshOut}}</base>
-        <extension>.h5m</extension>
-      </out_by_partition>
-{%- endif %}
+        <extension>.msh</extension></out>
     </files>
   </mesh>
 

bench/seismic/wp/plane_waves_3d/meshes/gen_configs.js

@@ -5,6 +5,7 @@
  * @author Alexander Breuer (breuer AT mytum.de)
  *
  * @section LICENSE
+ * Copyright (c) 2021, Friedrich Schiller University Jena
  * Copyright (c) 2019, Alexander Breuer
  * All rights reserved.
  *
@@ -46,24 +47,24 @@ for( var l_cl = 0; l_cl < l_cls.length; l_cl++ ) {
         if(l_err) return console.log( l_err );
       }
     )
-  }
 
-  for( var l_pa = 0; l_pa < l_parts.length; l_pa++ ) {
-    console.log( 'generating EDGE-V config for char length / nParts:', l_cls[l_cl], '/', l_parts[l_pa] )
-    l_fs.outputFile(
-      'gen/configs/edge_v/lts_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml',
-      nunjucks.render(
-        'edge_v.njk', {
-          i_meshIn:  'gen/ascii/lts_' + l_cls[l_cl] + '.msh',
-          i_nParts: l_parts[l_pa],
-          i_meshOut: 'gen/hdf5/lts_cl_'  + l_cls[l_cl] + '_pa_' + l_parts[l_pa],
-          i_statsOut: 'gen/stats/edge_v_'  + l_cls[l_cl] + '.csv',
+    for( var l_pa = 0; l_pa < l_parts.length; l_pa++ ) {
+      console.log( 'generating EDGE-V config for char length / nParts:', l_cls[l_cl], '/', l_parts[l_pa] )
+      l_fs.outputFile(
+        'gen/configs/edge_v/' + l_base[l_ty] + '_cl_' + l_cls[l_cl] + '_pa_' + l_parts[l_pa] + '.xml',
+        nunjucks.render(
+          'edge_v.njk', {
+            i_meshIn:  'gen/gmsh/' + l_base[l_ty] + '_' + l_cls[l_cl] + '.msh',
+            i_nParts: l_parts[l_pa],
+            i_meshOut: 'gen/edge_v/' + l_base[l_ty] + '_cl_'  + l_cls[l_cl] + '_pa_' + l_parts[l_pa],
+            i_statsOut: 'gen/stats/edge_v_'  + l_cls[l_cl] + '.csv',
+          }
+        ),
+        function(l_err) {
+          if(l_err) return console.log( l_err );
         }
-      ),
-      function(l_err) {
-        if(l_err) return console.log( l_err );
-      }
-    )
+      )
+    }
   }
 }
 console.log( 'done' )

bench/seismic/wp/plane_waves_3d/meshes/generate.sh

@@ -5,6 +5,7 @@
 # @author Alexander Breuer (breuer AT mytum.de)
 #
 # @section LICENSE
+# Copyright (c) 2021, Friedrich Schiller University Jena
 # Copyright (c) 2019, Alexander Breuer
 # All rights reserved.
 #
@@ -26,7 +27,7 @@ echo "gmsh-version:"
 gmsh --version
 
 rm -r gen 2> /dev/null
-mkdir -p gen/ascii gen/hdf5 gen/logs
+mkdir -p gen/gmsh gen/edge_v gen/logs
 
 ./gen_configs.js
 
@@ -35,12 +36,12 @@ do
   for l_ty in gts lts
   do
     echo "$(date) running gmsh char length ${l_cl} for type ${l_ty}"
-    gmsh -3 -format msh2 gen/configs/gmsh/${l_ty}_${l_cl}.geo -o gen/ascii/${l_ty}_${l_cl}.msh 2>&1 > gen/logs/${l_ty}_${l_cl}.msh.log
-  done
+    gmsh -3 -format msh2 gen/configs/gmsh/${l_ty}_${l_cl}.geo -o gen/gmsh/${l_ty}_${l_cl}.msh > gen/logs/gmsh_${l_ty}_${l_cl}.log 2>&1
 
-  for l_pa in 1 8
-  do
-    echo "$(date) running EDGE-V for char length ${l_cl} for nParts ${l_pa}"
-    edge_v -x gen/configs/edge_v/lts_cl_${l_cl}_pa_${l_pa}.xml 2>&1 > gen/logs/lts_cl_${l_cl}_pa_${pa}.h5m.log
+    for l_pa in 1 8
+    do
+      echo "$(date) running EDGE-V for char length ${l_cl} for nParts ${l_pa}"
+      edge_v -x gen/configs/edge_v/${l_ty}_cl_${l_cl}_pa_${l_pa}.xml > gen/logs/edge_v_${l_ty}_cl_${l_cl}_pa_${l_pa}.log 2>&1
+    done
   done
 done