Update AutoPas to Combined Tuning

cmake/modules/autopas.cmake

@@ -23,8 +23,8 @@ if (ENABLE_AUTOPAS)
     set(AUTOPAS_USE_VECTORIZATION ${USE_VECTORIZATION} CACHE BOOL "Set via USE_VECTORIZATION" FORCE)
     set(AUTOPAS_VECTOR_INSTRUCTIONS ${VECTOR_INSTRUCTIONS} CACHE STRING "Set via VECTOR_INSTRUCTIONS_OPTIONS" FORCE)
 
-    # Merge of fixSpacialLocksResize 2023-05-08; This includes the rewrites of remainder traversal and iterators.
-    set(AUTOPAS_TAG e47c9257bb8d0c6ab680d02823b1e8749b25369a CACHE STRING "AutoPas Git tag or commit id to use")
+    # Merge of 798 (improve SoA loading); includes 787 combined tuning
+    set(AUTOPAS_TAG d338e23 CACHE STRING "AutoPas Git tag or commit id to use")
 
     FetchContent_Declare(
             autopasfetch
@@ -41,7 +41,8 @@ if (ENABLE_AUTOPAS)
         add_subdirectory(${autopasfetch_SOURCE_DIR} ${autopasfetch_BINARY_DIR} EXCLUDE_FROM_ALL)
     endif ()
 
-    set(AUTOPAS_LIB "autopas")
+    # Linking the md lib also links AutoPas
+    set(AUTOPAS_LIB "molecularDynamicsLibrary")
 else ()
     message(STATUS "Not using AutoPas.")
     set(AUTOPAS_LIB "")

examples/Adsorption/Generator/adsorption_autopas_tuning.xml

@@ -87,7 +87,7 @@
         <allowedTraversals>c01, c04, c08, c18, sli</allowedTraversals>
         <allowedContainers>linkedCells</allowedContainers>
         <selectorStrategy>fastestMedian</selectorStrategy>
-        <tuningStrategy>FullSearch</tuningStrategy><!--FullSearch, BayesianSearch, ...-->
+        <tuningStrategies>FullSearch</tuningStrategies><!--FullSearch, BayesianSearch, ...-->
         <dataLayouts>SoA</dataLayouts>
         <newton3>enabled</newton3>
         <tuningInterval>1000</tuningInterval>

examples/Argon/200K_18mol_l/config_autopas_allOptions.xml

@@ -44,16 +44,18 @@
       </parallelisation>
       -->
       <datastructure type="AutoPas">
+        <loglevel>off</loglevel><!--Level for the AutoPas logger-->
         <allowedTraversals>ds_sequential, lc_sliced, lc_sliced_balanced, lc_sliced_c02, lc_c01, lc_c01_combined_SoA, lc_c01_cuda, lc_c04, lc_c04_HCP, lc_c04_combined_SoA, lc_c08, lc_c18, vcc_cluster_iteration_cuda, vcl_cluster_iteration, vcl_c06, vcl_c01_balanced, vl_list_iteration, vlc_c01, vlc_c18, vlc_sliced, vlc_sliced_balanced, vlc_sliced_c02, vvl_as_built</allowedTraversals>
         <allowedContainers>DirectSum,LinkedCells, VerletLists, VerletListsCells, VerletClusterLists,VarVerletListsAsBuild,VerletClusterCells</allowedContainers>
         <selectorStrategy>fastestMean</selectorStrategy><!--fastestMedian,fastestAbs-->
-        <tuningStrategy>FullSearch</tuningStrategy><!--FullSearch, BayesianSearch, ...-->
+        <tuningStrategies>predictive,rulebased</tuningStrategies><!--Predictive, RuleBased, BayesianSearch, ...; Leave empty for full search-->
         <dataLayouts>AoS, SoA</dataLayouts>
         <newton3>enabled, disabled</newton3>
         <tuningAcquisitionFunction>lower-confidence-bound</tuningAcquisitionFunction> <!--only relevant for BayesianSearch-->
         <maxEvidence>20</maxEvidence>
         <tuningInterval>1000</tuningInterval>
         <tuningSamples>10</tuningSamples>
+        <ruleFile>AutoPas/examples/md-flexible/input/tuningRules.rule</ruleFile><!--check the AutoPas repo for examples-->
         <rebuildFrequency>10</rebuildFrequency>
         <skin>0.5</skin>
       </datastructure>

examples/Argon/200K_18mol_l/config_autopas_lc_ALL.xml

@@ -38,7 +38,9 @@
                 </loadBalancer>
             </parallelisation>
             <datastructure type="AutoPas">
+                <!-- <logLevel>info</logLevel> -->
                 <allowedContainers>linkedCells</allowedContainers>
+                <tuningStrategies>predictive,ruleBased</tuningStrategies>
                 <tuningInterval>10000</tuningInterval>
                 <tuningSamples>10</tuningSamples>
                 <rebuildFrequency>10</rebuildFrequency>

examples/all-options.xml

@@ -242,8 +242,8 @@
         <!-- specify what metric the selector should use to determine the optimal traversal -->
         <!-- possible values: fastetAbsolute, fastestMean, fastestMedian -->
         <selectorStrategy>fastestAbsolute</selectorStrategy>
-        <!-- set the auto tuning algorithm -->
-        <tuningStrategy>fullSearch</tuningStrategy>
+        <!-- set the tuning auto tuning pipeline -->
+        <tuningStrategies>fullSearch</tuningStrategies>
         <!-- Data layouts to be used: AoS, SoA -->
         <dataLayouts>SoA</dataLayouts>
         <!-- Allowed choices for newton 3 optimization: enabled, disabled -->

src/molecules/AutoPasSimpleMolecule.h

@@ -6,7 +6,7 @@
 
 #pragma once
 
-#include <autopas/molecularDynamics/MoleculeLJ.h>
+#include <molecularDynamicsLibrary/MoleculeLJ.h>
 #include <autopas/utils/SoAType.h>
 #include <autopas/utils/inBox.h>
 
@@ -336,4 +336,4 @@ class AutoPasSimpleMolecule final : public MoleculeInterface, public autopas::Pa
 	static Quaternion _quaternion;
 };
 
-std::ostream& operator<<( std::ostream& os, const AutoPasSimpleMolecule& m );
+std::ostream& operator<<( std::ostream& os, const AutoPasSimpleMolecule& m );