v2.4.1

configure.ac.in

@@ -6,7 +6,7 @@
 #
 
 AC_PREREQ(2.52)
-AC_INIT([nest], [2.4.0], [nest_user@nest-initiative.org])
+AC_INIT([nest], [2.4.1], [nest_user@nest-initiative.org])
 
 # Prevent automatic rebuilding of Makefile.ins and configure if their
 # content or timestamp changes. Not doing this lead to failing builds
@@ -20,7 +20,7 @@ AM_MAINTAINER_MODE([disable])
 # releasetools/buildnest
 SLI_MAJOR=2
 SLI_MINOR=4
-SLI_PATCHLEVEL=0
+SLI_PATCHLEVEL=1
 
 SLI_PRGNAME="nest-$SLI_MAJOR.$SLI_MINOR.$SLI_PATCHLEVEL"
 SLI_VERSION=$SLI_MAJOR.$SLI_MINOR.$SLI_PATCHLEVEL

conngen/sli/conngen-interface.sli

@@ -65,7 +65,7 @@ def
 } def
 
 /CGConnect [/anytype] {
-  /Connect /synapse_model GetOption
+  /Connect /syn_spec GetOption /model get
   CGConnect_main
 } def
 

examples/nest/Potjans_2014/README.txt

@@ -23,9 +23,9 @@
 Cortical microcircuit simulation: SLI version
 
 This is an implementation of the multi-layer microcircuit model of early
-sensory cortex published by Potjans and Diesmann (2012) The cell-type specific
+sensory cortex published by Potjans and Diesmann (2014) The cell-type specific
 cortical microcircuit: relating structure and activity in a full-scale spiking
-network model. Cereb Cortex, online first. 
+network model. Cerebral Cortex: doi:10.1093/cercor/bhs358.
 
 
 Files:

models/iaf_chs_2007.h

@@ -76,7 +76,7 @@ namespace nest
  
      References:
      [1] Carandini M, Horton JC, Sincich LC (2007) Thalamic filtering of retinal
-     spike trains by postsynaptic summation. J Vis 7(14):20,1Ð11.
+     spike trains by postsynaptic summation. J Vis 7(14):20,1-11.
      [2] Rotter S & Diesmann M (1999) Exact simulation of time-invariant linear
      systems with applications to neuronal modeling. Biologial Cybernetics
      81:381-402.

pynest/nest/hl_api.py

@@ -420,6 +420,19 @@ def NumProcesses():
     sr("NumProcesses")
     return spp()
 
+@check_stack
+def SetNumRecProcesses(nrp):
+    """
+    Set the number of recording MPI processes to nrp. Usually,
+    spike detectors are distributed over all processes and record
+    from local neurons only. If a number of processes is dedicated to
+    spike detection, each spike detector is hosted on one of these
+    processes and records globally from all simulating processes.
+
+    """
+
+    sr("%d SetNumRecProcesses" % nrp)
+
 @check_stack
 def SetAcceptableLatency(port, latency):
     """

releasetools/buildnest.sh

@@ -54,7 +54,7 @@ if ( $#argv != 0 ) then
     exit 0
   endif
 else
-  set svndir="branches/nest-2.4/2.4.0"
+  set svndir="branches/nest-2.4/2.4.1"
   set branch=""
 endif
 
@@ -118,7 +118,7 @@ svn --quiet checkout $svn_id $nest_srcdir
 
 # add svn revision number to tarball name
 set svnver=`svnversion $nest_srcdir`
-set patchlevel = "0"
+set patchlevel = "1"
 
 # move to nest_srcdir
 cd $nest_srcdir

testsuite/regressiontests/ticket-881.sli

@@ -0,0 +1,102 @@
+/*
+ *  ticket-881.sli
+ *
+ *  This file is part of NEST.
+ *
+ *  Copyright (C) 2004 The NEST Initiative
+ *
+ *  NEST 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 2 of the License, or
+ *  (at your option) any later version.
+ *
+ *  NEST 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 NEST.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+/* BeginDocumentation
+
+Name: testsuite::ticket-881 - ConnectLayers creates too few connections under some conditions when running on multiple threads
+
+Synopsis: (ticket-881) run -> NEST exits if test fails
+
+Description:
+This tests creates a small layer, connects it all-to-all and checks if all expected connections have been created.
+
+This is a regression from nest-2.2.2 to 10kproject@r11284 (precise location unknown so far)
+Author: Hans Ekkehard Plesser
+*/
+
+
+(unittest) run
+/unittest using
+
+/topology lookup not { exit_test_gracefully } if
+using
+
+M_ERROR setverbosity
+
+/num_threads 4 def
+/node_pos [ [0.0 0.0] [0.0 0.0] [0.0 0.0] [0.0 0.0] ] def
+/num_nodes node_pos length def
+
+/num_expected num_nodes dup mul def   % all to all
+
+% Test 1: pairwise convergent
+{
+  ResetKernel
+  0 << /local_num_threads num_threads >> SetStatus
+
+  << /elements /iaf_neuron /positions node_pos >> CreateLayer
+  dup
+  << /connection_type (convergent) >> ConnectLayers
+
+  << >> GetConnections length num_expected eq 
+} assert_or_die
+
+% Test 2: pairwise divergent
+{
+  ResetKernel
+  0 << /local_num_threads num_threads >> SetStatus
+
+  << /elements /iaf_neuron /positions node_pos >> CreateLayer
+  dup
+  << /connection_type (divergent) >> ConnectLayers
+
+  << >> GetConnections length num_expected eq 
+} assert_or_die
+
+% Test 3: fixed fan-in
+{
+  ResetKernel
+  0 << /local_num_threads num_threads >> SetStatus
+
+  << /elements /iaf_neuron /positions node_pos >> CreateLayer
+  dup
+  << /connection_type (convergent) /number_of_connections num_nodes >> ConnectLayers
+
+  << >> GetConnections length num_expected eq 
+} assert_or_die
+
+% Test 4: fixed fan-out
+{
+  ResetKernel
+  0 << /local_num_threads num_threads >> SetStatus
+
+  << /elements /iaf_neuron /positions node_pos >> CreateLayer
+  dup
+  << /connection_type (divergent) /number_of_connections num_nodes >> ConnectLayers
+
+  << >> GetConnections length num_expected eq 
+} assert_or_die
+
+
+
+endusing
+endusing

topology/connection_creator_impl.h

@@ -266,7 +266,7 @@ namespace nest
             if (rng->drand() < kernel_->value(target.compute_displacement(iter->first, target_pos), rng)) {
 	      double w, d;
               get_parameters_(target.compute_displacement(iter->first, target_pos), rng, w, d);
-              connect_(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+              net_.connect(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             }
 
           }
@@ -281,7 +281,7 @@ namespace nest
               continue;
 	    double w, d;
             get_parameters_(target.compute_displacement(iter->first,target_pos), rng, w, d);
-	    connect_(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+	    net_.connect(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
           }
 
         }
@@ -315,7 +315,7 @@ namespace nest
             if (rng->drand() < kernel_->value(target.compute_displacement(iter->first,target_pos), rng)) {
 	      double w,d;
               get_parameters_(target.compute_displacement(iter->first,target_pos), rng, w, d);
-              connect_(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+              net_.connect(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             }
           }
 
@@ -327,7 +327,7 @@ namespace nest
               continue;
 	    double w,d;
             get_parameters_(target.compute_displacement(iter->first,target_pos), rng, w, d);
-              connect_(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+              net_.connect(iter->second, target_id, *tgt_it, target_thread, w, d, synapse_model_);
           }
 
         }
@@ -422,7 +422,7 @@ namespace nest
             }
 	    double w,d;
             get_parameters_(source.compute_displacement(target_pos,positions[random_id].first), rng, w,d);
-	    connect_(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+	    net_.connect(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             is_selected[random_id] = true;
           }
 
@@ -451,7 +451,7 @@ namespace nest
             index source_id = positions[random_id].second;
 	    double w,d;
             get_parameters_(source.compute_displacement(target_pos,positions[random_id].first), rng, w,d);
-	    connect_(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+	    net_.connect(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             is_selected[random_id] = true;
           }
 
@@ -520,7 +520,7 @@ namespace nest
             Position<D> source_pos = (*positions)[random_id].first;
 	    double w,d;
             get_parameters_(source.compute_displacement(target_pos,source_pos), rng, w,d);
-	    connect_(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+	    net_.connect(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             is_selected[random_id] = true;
           }
 
@@ -549,7 +549,7 @@ namespace nest
             Position<D> source_pos = (*positions)[random_id].first;
 	    double w,d;
             get_parameters_(source.compute_displacement(target_pos,source_pos), rng, w,d);
-	    connect_(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
+	    net_.connect(source_id, target_id, *tgt_it, target_thread, w, d, synapse_model_);
             is_selected[random_id] = true;
           }
 
@@ -627,7 +627,7 @@ namespace nest
 	Node* target_ptr = net_.get_node(target_id);
 	double w,d;
         get_parameters_(target_displ, net_.get_grng(), w,d);
-        connect_(source_id, target_id, target_ptr, target_ptr->get_thread(), w, d, synapse_model_);
+        net_.connect(source_id, target_id, target_ptr, target_ptr->get_thread(), w, d, synapse_model_);
         is_selected[random_id] = true;
       }
 

topology/doc/Topology_UserManual.tex

@@ -81,7 +81,7 @@
 Håkon Enger\\[1ex]
 \normalsize Department of Mathematical Sciences and Technology\\\normalsize Norwegian University of Life Sciences\\
 \normalsize 1432 Ås, Norway}
-\date{NEST 2.2 (r9977 or later)\\[8cm]
+\date{NEST 2.2 and 2.4 (r9977 or later)\\[8cm]
 \centerline{\includegraphics{nest-initiative-logo}}}
 
 
@@ -106,14 +106,15 @@
   For NEST 2.2, Håkon Enger rewrote most of the Topology library code,
   thereby improving performance considerably.
 
-  This User Manual describes the NEST 2.2 version of the NEST Topology
-  Library. Please see Chapter~\ref{sec:changes} for a summary of changes.
+  This User Manual describes the NEST 2.2 and 2.4 versions of the NEST Topology
+  Library. Please see Chapter~\ref{sec:changes} for a summary of
+  changes to 2.2. There are no changes in Topology from 2.2 to 2.4.
 
   We plan further improvements to the Topology Module in the future, 
   which may include changes to the API to remove some of the remaining
   inconsistencies and provide a cleaner user interface.
 
-  \vspace*{\fill}{\centerline{\footnotesize{Copyright \copyright{} 2010 The NEST Initiative}}}
+  \vspace*{\fill}{\centerline{\footnotesize{Copyright \copyright{} 2004 The NEST Initiative}}}
 \end{abstract}
 
 \tableofcontents
@@ -138,7 +139,7 @@ \chapter{Introduction}\label{sec:intro}
 for details; where appropriate, that documentation also points to
 relevant SLI documentation.
 
-This manual describes the Topology Module included with NEST~2.2, code
+This manual describes the Topology Module included with NEST~2.2 and~2.4, code
 revision 9977 or later.  This version differs from older ones in some
 important aspects as detailed in Section~\ref{sec:changes}. In our
 experience, though, most scripts using the Topology Module can be

topology/doc/make_manual.sh

@@ -17,10 +17,10 @@ rm -f ${fname}.{aux,bbl,blg,idx,ilg,ins,lof,log,lot,pdf,synctex.gz,toc}
 rm -f user_manual_figures/*
 rm -f user_namual_scripts/*.log
 
-# Run scripts
+# Run scripts / -u ensures unbuffered output 
 cd user_manual_scripts
-${PYTHON} layers.py      > layers.log
-${PYTHON} connections.py > connections.log
+${PYTHON} -u layers.py      > layers.log
+${PYTHON} -u connections.py > connections.log
 cd ..
 
 # Do the LaTeX Dance
@@ -31,4 +31,4 @@ ${LATEX}  ${fname}
 ${LATEX}  ${fname}
 
 # remove temporary files
-rm -f ${fname}.{aux,bbl,blg,idx,ilg,ind,ins,lof,log,lot,synctex.gz,toc}
+rm -f ${fname}.{aux,bbl,blg,idx,ilg,ind,ins,lof,log,lot,synctex.gz,toc}