Merge branch 'master' of github.com:nest/nest-simulator into new_regi…

…stration

.github/workflows/codeql.yml

@@ -51,7 +51,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@47b3d888fe66b639e431abf22ebca059152f1eea # v3.24.5
+        uses: github/codeql-action/init@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -61,7 +61,7 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@47b3d888fe66b639e431abf22ebca059152f1eea # v3.24.5
+        uses: github/codeql-action/autobuild@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -74,6 +74,6 @@ jobs:
       #   ./location_of_script_within_repo/buildscript.sh
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@47b3d888fe66b639e431abf22ebca059152f1eea # v3.24.5
+        uses: github/codeql-action/analyze@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
         with:
           category: "/language:${{matrix.language}}"

.github/workflows/scorecards.yml

@@ -71,6 +71,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@47b3d888fe66b639e431abf22ebca059152f1eea # v3.24.5
+        uses: github/codeql-action/upload-sarif@3ab4101902695724f9365a384f86c1074d94e18c # v3.24.7
         with:
           sarif_file: results.sarif

doc/htmldoc/static/css/custom.css

@@ -204,8 +204,12 @@ div[role="main"] .md-source {
   color: var(--nest-orange);
 	background-color: #ffffff8a;
 	border-radius: 5px;
-	padding: 6px;
 }
+/* Add padding around buttons on index page */
+#welcome-to-the-nest-simulator-documentation [data-md-color-primary="orange"] .md-typeset a {
+   padding: 6px;
+}
+
 .md-typeset details {
    background-color: white;
 }

lib/sli/nest-init.sli

@@ -413,7 +413,7 @@ def
 
 /CreateParameter trie
 [/dictionarytype] /CreateParameter_D load addtotrie
-[/doubletype] /CreateParameter_D load addtotrie
+[/doubletype] { /val Set << /constant << /value val >> >> CreateParameter_D } addtotrie
 def
 
 /GetValue [/parametertype]

nestkernel/connection_manager.cpp

@@ -93,9 +93,9 @@ nest::ConnectionManager::~ConnectionManager()
 }
 
 void
-nest::ConnectionManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+nest::ConnectionManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     // Add connection rules
     register_conn_builder< OneToOneBuilder >( "one_to_one" );
@@ -153,7 +153,7 @@ nest::ConnectionManager::initialize( const bool adjust_number_of_threads_or_rng_
 }
 
 void
-nest::ConnectionManager::finalize( const bool adjust_number_of_threads_or_rng_seed_only )
+nest::ConnectionManager::finalize( const bool adjust_number_of_threads_or_rng_only )
 {
   source_table_.finalize();
   target_table_.finalize();
@@ -163,7 +163,7 @@ nest::ConnectionManager::finalize( const bool adjust_number_of_threads_or_rng_se
   std::vector< std::vector< std::vector< size_t > > >().swap( secondary_recv_buffer_pos_ );
   compressed_spike_data_.clear();
 
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     for ( auto cbf : connbuilder_factories_ )
     {
@@ -902,13 +902,13 @@ nest::ConnectionManager::connect_( Node& source,
   {
 #pragma omp atomic write
     has_primary_connections_ = true;
-    check_primary_connections_[ tid ].set_true();
+    check_primary_connections_.set_true( tid );
   }
   else if ( check_secondary_connections_[ tid ].is_false() and not is_primary )
   {
 #pragma omp atomic write
     secondary_connections_exist_ = true;
-    check_secondary_connections_[ tid ].set_true();
+    check_secondary_connections_.set_true( tid );
   }
 }
 

nestkernel/event_delivery_manager.cpp

@@ -76,9 +76,9 @@ EventDeliveryManager::~EventDeliveryManager()
 }
 
 void
-EventDeliveryManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+EventDeliveryManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     init_moduli();
     reset_timers_for_preparation();
@@ -790,7 +790,7 @@ EventDeliveryManager::gather_target_data( const size_t tid )
   assert( not kernel().connection_manager.is_source_table_cleared() );
 
   // assume all threads have some work to do
-  gather_completed_checker_[ tid ].set_false();
+  gather_completed_checker_.set_false( tid );
   assert( gather_completed_checker_.all_false() );
 
   const AssignedRanks assigned_ranks = kernel().vp_manager.get_assigned_ranks( tid );
@@ -802,7 +802,7 @@ EventDeliveryManager::gather_target_data( const size_t tid )
   {
     // assume this is the last gather round and change to false
     // otherwise
-    gather_completed_checker_[ tid ].set_true();
+    gather_completed_checker_.set_true( tid );
 
 #pragma omp master
     {
@@ -819,7 +819,7 @@ EventDeliveryManager::gather_target_data( const size_t tid )
       assigned_ranks, kernel().mpi_manager.get_send_recv_count_target_data_per_rank() );
 
     const bool gather_completed = collocate_target_data_buffers_( tid, assigned_ranks, send_buffer_position );
-    gather_completed_checker_[ tid ].logical_and( gather_completed );
+    gather_completed_checker_.logical_and( tid, gather_completed );
 
     if ( gather_completed_checker_.all_true() )
     {
@@ -842,7 +842,7 @@ EventDeliveryManager::gather_target_data( const size_t tid )
 #pragma omp barrier
 
     const bool distribute_completed = distribute_target_data_buffers_( tid );
-    gather_completed_checker_[ tid ].logical_and( distribute_completed );
+    gather_completed_checker_.logical_and( tid, distribute_completed );
 
     // resize mpi buffers, if necessary and allowed
     if ( gather_completed_checker_.any_false() and kernel().mpi_manager.adaptive_target_buffers() )
@@ -864,7 +864,7 @@ EventDeliveryManager::gather_target_data_compressed( const size_t tid )
   assert( not kernel().connection_manager.is_source_table_cleared() );
 
   // assume all threads have some work to do
-  gather_completed_checker_[ tid ].set_false();
+  gather_completed_checker_.set_false( tid );
   assert( gather_completed_checker_.all_false() );
 
   const AssignedRanks assigned_ranks = kernel().vp_manager.get_assigned_ranks( tid );
@@ -874,7 +874,7 @@ EventDeliveryManager::gather_target_data_compressed( const size_t tid )
   while ( gather_completed_checker_.any_false() )
   {
     // assume this is the last gather round and change to false otherwise
-    gather_completed_checker_[ tid ].set_true();
+    gather_completed_checker_.set_true( tid );
 
 #pragma omp master
     {
@@ -891,7 +891,7 @@ EventDeliveryManager::gather_target_data_compressed( const size_t tid )
     const bool gather_completed =
       collocate_target_data_buffers_compressed_( tid, assigned_ranks, send_buffer_position );
 
-    gather_completed_checker_[ tid ].logical_and( gather_completed );
+    gather_completed_checker_.logical_and( tid, gather_completed );
 
     if ( gather_completed_checker_.all_true() )
     {
@@ -916,7 +916,7 @@ EventDeliveryManager::gather_target_data_compressed( const size_t tid )
     // all data it is responsible for to buffers. Now combine with information on whether other ranks
     // have sent all their data. Note: All threads will return the same value for distribute_completed.
     const bool distribute_completed = distribute_target_data_buffers_( tid );
-    gather_completed_checker_[ tid ].logical_and( distribute_completed );
+    gather_completed_checker_.logical_and( tid, distribute_completed );
 
     // resize mpi buffers, if necessary and allowed
     if ( gather_completed_checker_.any_false() and kernel().mpi_manager.adaptive_target_buffers() )

nestkernel/io_manager.cpp

@@ -68,9 +68,9 @@ IOManager::~IOManager()
 }
 
 void
-IOManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+IOManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     // Register backends again, since finalize cleans up
     // so backends from external modules are unloaded
@@ -114,7 +114,7 @@ IOManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
 }
 
 void
-IOManager::finalize( const bool adjust_number_of_threads_or_rng_seed_only )
+IOManager::finalize( const bool adjust_number_of_threads_or_rng_only )
 {
   for ( const auto& it : recording_backends_ )
   {
@@ -125,7 +125,7 @@ IOManager::finalize( const bool adjust_number_of_threads_or_rng_seed_only )
     it.second->finalize();
   }
 
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     for ( const auto& it : recording_backends_ )
     {

nestkernel/kernel_manager.cpp

@@ -88,7 +88,7 @@ nest::KernelManager::initialize()
 {
   for ( auto& manager : managers )
   {
-    manager->initialize( /* adjust_number_of_threads_only */ false );
+    manager->initialize( /* adjust_number_of_threads_or_rng_only */ false );
   }
 
   ++fingerprint_;
@@ -122,7 +122,7 @@ nest::KernelManager::finalize()
 
   for ( auto&& m_it = managers.rbegin(); m_it != managers.rend(); ++m_it )
   {
-    ( *m_it )->finalize( /* adjust_number_of_threads_only */ false );
+    ( *m_it )->finalize( /* adjust_number_of_threads_or_rng_only */ false );
   }
   initialized_ = false;
 }
@@ -147,15 +147,15 @@ nest::KernelManager::change_number_of_threads( size_t new_num_threads )
   // Finalize in reverse order of initialization with old thread number set
   for ( auto mgr_it = managers.rbegin(); mgr_it != managers.rend(); ++mgr_it )
   {
-    ( *mgr_it )->finalize( /* adjust_number_of_threads_or_rng_seed_only */ true );
+    ( *mgr_it )->finalize( /* adjust_number_of_threads_or_rng_only */ true );
   }
 
   vp_manager.set_num_threads( new_num_threads );
 
   // Initialize in original order with new number of threads set
   for ( auto& manager : managers )
   {
-    manager->initialize( /* adjust_number_of_threads_or_rng_seed_only */ true );
+    manager->initialize( /* adjust_number_of_threads_or_rng_only */ true );
   }
 
   // Finalizing deleted all register components. Now that all infrastructure

nestkernel/logging_manager.cpp

@@ -42,9 +42,9 @@ nest::LoggingManager::LoggingManager()
 }
 
 void
-nest::LoggingManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+nest::LoggingManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     dict_miss_is_error_ = true;
   }

nestkernel/manager_interface.h

@@ -68,12 +68,13 @@ class ManagerInterface
    * is responsible for calling the initialization routines on the
    * specific managers in correct order.
    *
-   * @param adjust_number_of_threads_only  Pass true if calling from kernel_manager::change_number_of_threads() to limit
-   * operations to those necessary for thread adjustment.
+   * @param adjust_number_of_threads_or_rng_only  Pass true if calling from kernel_manager::change_number_of_threads()
+   * or RandomManager::get_status() to limit operations to those necessary for thread adjustment or switch or re-seeding
+   * of RNG.
    *
    * @see finalize()
    */
-  virtual void initialize( const bool adjust_number_of_threads_only ) = 0;
+  virtual void initialize( const bool adjust_number_of_threads_or_rng_only ) = 0;
 
   /**
    * Take down manager after operation.
@@ -88,12 +89,12 @@ class ManagerInterface
    * specific managers in correct order, i.e., the opposite order of
    * initialize() calls.
    *
-   * @param adjust_number_of_threads_only  Pass true if calling from kernel_manager::change_number_of_threads() to limit
-   * operations to those necessary for thread adjustment.
+   * @param adjust_number_of_threads_or_rng_only  Pass true if calling from kernel_manager::change_number_of_threads()
+   * to limit operations to those necessary for thread adjustment.
    *
    * @see initialize()
    */
-  virtual void finalize( const bool adjust_number_of_threads_only ) = 0;
+  virtual void finalize( const bool adjust_number_of_threads_or_rng_only ) = 0;
 
   /**
    * Set the status of the manager

nestkernel/module_manager.cpp

@@ -61,7 +61,7 @@ ModuleManager::ModuleManager()
 
 ModuleManager::~ModuleManager()
 {
-  finalize( /* adjust_number_of_threads_or_rng_seed_only */ false ); // closes dynamically loaded modules
+  finalize( /* adjust_number_of_threads_or_rng_only */ false ); // closes dynamically loaded modules
   lt_dlexit();
 }
 
@@ -71,9 +71,9 @@ ModuleManager::initialize( const bool )
 }
 
 void
-ModuleManager::finalize( const bool adjust_number_of_threads_or_rng_seed_only )
+ModuleManager::finalize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( adjust_number_of_threads_or_rng_seed_only )
+  if ( adjust_number_of_threads_or_rng_only )
   {
     return;
   }

nestkernel/module_manager.h

@@ -53,7 +53,7 @@ class ModuleManager : public ManagerInterface
   void initialize( const bool ) override;
 
   //! Unload modules but only on full ResetKernel(), not when just changing then number of threads
-  void finalize( const bool adjust_number_of_threads_only ) override;
+  void finalize( const bool adjust_number_of_threads_or_rng_only ) override;
 
   //! To be called after change of number of threads to re-register components provided by modules
   void reinitialize_dynamic_modules();

nestkernel/mpi_manager.cpp

@@ -178,9 +178,9 @@ nest::MPIManager::init_mpi( int* argc, char** argv[] )
 #endif /* #ifdef HAVE_MPI */
 
 void
-nest::MPIManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+nest::MPIManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( adjust_number_of_threads_or_rng_seed_only )
+  if ( adjust_number_of_threads_or_rng_only )
   {
     return;
   }

nestkernel/music_manager.cpp

@@ -48,9 +48,9 @@ MUSICManager::MUSICManager()
 }
 
 void
-MUSICManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+MUSICManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
-  if ( adjust_number_of_threads_or_rng_seed_only )
+  if ( adjust_number_of_threads_or_rng_only )
   {
     return;
   }

nestkernel/node_manager.cpp

@@ -68,15 +68,15 @@ NodeManager::~NodeManager()
 }
 
 void
-NodeManager::initialize( const bool adjust_number_of_threads_or_rng_seed_only )
+NodeManager::initialize( const bool adjust_number_of_threads_or_rng_only )
 {
   // explicitly force construction of wfr_nodes_vec_ to ensure consistent state
   wfr_network_size_ = 0;
   local_nodes_.resize( kernel().vp_manager.get_num_threads() );
   num_thread_local_devices_.resize( kernel().vp_manager.get_num_threads(), 0 );
   ensure_valid_thread_local_ids();
 
-  if ( not adjust_number_of_threads_or_rng_seed_only )
+  if ( not adjust_number_of_threads_or_rng_only )
   {
     sw_construction_create_.reset();
   }