Skip to content

Commit

Permalink
Merge pull request #1 from tammoippen/nest_3-fix211-connect_segfault
Browse files Browse the repository at this point in the history 
Remove old connection routines part 1
  • Loading branch information
@jakobj
jakobj committed Feb 11, 2016
2 parents 27d0331 + 53bb865 commit a767e2e
Show file tree
Hide file tree
Showing 16 changed files with 130 additions and 1,964 deletions.
498 changes: 0 additions & 498 deletions lib/sli/nest-init.sli
View file

Large diffs are not rendered by default.

772 changes: 82 additions & 690 deletions nestkernel/connection_builder_manager.cpp
View file

Large diffs are not rendered by default.

54 changes: 1 addition & 53 deletions nestkernel/connection_builder_manager.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -170,65 +170,13 @@ class ConnectionBuilderManager : public ManagerInterface
*/
bool connect( ArrayDatum& connectome );

void divergent_connect( index s,
const TokenArray& r,
const TokenArray& weights,
const TokenArray& delays,
index syn );
/**
* Connect one source node with many targets.
* The dictionary d contains arrays for all the connections of type syn.
* AKA DataConnect
*/

void divergent_connect( index s, DictionaryDatum d, index syn );

void random_divergent_connect( index s,
const TokenArray& r,
index n,
const TokenArray& w,
const TokenArray& d,
bool,
bool,
index syn );

void convergent_connect( const TokenArray& s,
index r,
const TokenArray& weights,
const TokenArray& delays,
index syn );

/**
* Specialized version of convegent_connect
* called by random_convergent_connect threaded
*/
void convergent_connect( const std::vector< index >& s_id,
index r,
const TokenArray& weight,
const TokenArray& delays,
index syn );

void random_convergent_connect( const TokenArray& s,
index t,
index n,
const TokenArray& w,
const TokenArray& d,
bool,
bool,
index syn );

/**
* Use openmp threaded parallelization to speed up connection.
* Parallelize over target list.
*/
void random_convergent_connect( TokenArray& s,
TokenArray& t,
TokenArray& n,
TokenArray& w,
TokenArray& d,
bool,
bool,
index syn );

// aka conndatum GetStatus
DictionaryDatum get_synapse_status( index gid, synindex syn, port p, thread tid );
// aka conndatum SetStatus
Expand Down
208 changes: 2 additions & 206 deletions nestkernel/nestmodule.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -927,200 +927,6 @@ NestModule::DataConnect_aFunction::execute( SLIInterpreter* i ) const
i->EStack.pop();
}

/* BeginDocumentation
Name: DivergentConnect - Connect node to a population of nodes.
Synopsis:
source [targets] DivergentConnect -> -
source [targets] /synmodel DivergentConnect -> -
source [targets] [weights] [delays] DivergentConnect -> -
source [targets] [weights] [delays] /synmodel DivergentConnect -> -
Parameters:
source - GID of source node
[targets] - array of (global IDs of) potential target nodes
[weights] - weights for the connections. List of the same size as targets or 1.
[delays] - delays for the connections. List of the same size as targets or 1.
/synmodel - The synapse model for the connection (see Options below)
Options:
If not given, the synapse model is taken from the Options dictionary
of the Connect command.
Description:
Connect a neuron with a set of target neurons.
Author:
Marc-Oliver Gewaltig
modified Ruediger Kupper, 20.3.2003
modified Jochen Eppler, 04.11.2005
SeeAlso: RandomDivergentConnect, ConvergentConnect
*/

void
NestModule::DivergentConnect_i_ia_a_a_lFunction::execute( SLIInterpreter* i ) const
{
i->assert_stack_load( 5 );

long source_adr = getValue< long >( i->OStack.pick( 4 ) );
TokenArray target_adr = getValue< TokenArray >( i->OStack.pick( 3 ) );

TokenArray weights = getValue< TokenArray >( i->OStack.pick( 2 ) );
TokenArray delays = getValue< TokenArray >( i->OStack.pick( 1 ) );

const Name synmodel_name = getValue< std::string >( i->OStack.pick( 0 ) );
const Token synmodel = kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
if ( synmodel.empty() )
throw UnknownSynapseType( synmodel_name.toString() );
const index synmodel_id = static_cast< index >( synmodel );

kernel().connection_builder_manager.divergent_connect(
source_adr, target_adr, weights, delays, synmodel_id );

i->OStack.pop( 5 );
i->EStack.pop();
}

// Documentation can be found in lib/sli/nest-init.sli near definition
// of the trie for RandomConvergentConnect.
void
NestModule::RDivergentConnect_i_i_ia_da_da_b_b_lFunction::execute( SLIInterpreter* i ) const
{
i->assert_stack_load( 8 );

long source_adr = getValue< long >( i->OStack.pick( 7 ) );
size_t n = getValue< long >( i->OStack.pick( 6 ) );
TokenArray target_adr = getValue< TokenArray >( i->OStack.pick( 5 ) );
TokenArray weights = getValue< TokenArray >( i->OStack.pick( 4 ) );
TokenArray delays = getValue< TokenArray >( i->OStack.pick( 3 ) );
bool allow_multapses = getValue< bool >( i->OStack.pick( 2 ) );
bool allow_autapses = getValue< bool >( i->OStack.pick( 1 ) );

const Name synmodel_name = getValue< std::string >( i->OStack.pick( 0 ) );
const Token synmodel = kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
if ( synmodel.empty() )
throw UnknownSynapseType( synmodel_name.toString() );
const index synmodel_id = static_cast< index >( synmodel );

kernel().connection_builder_manager.random_divergent_connect(
source_adr, target_adr, n, weights, delays, allow_multapses, allow_autapses, synmodel_id );

i->OStack.pop( 8 );
i->EStack.pop();
}


/* BeginDocumentation
Name: ConvergentConnect - Connect population of nodes to a single node.
Synopsis:
[sources] target /synmodel ConvergentConnect -> -
[sources] target /synmodel ConvergentConnect -> -
[sources] target [weights] [delays] /synmodel ConvergentConnect -> -
Parameters:
[source] - GID of source nodes
target - array of (global IDs of) potential target nodes
[weights] - weights for the connections. List of the same size as sources or 1.
[delays] - delays for the connections. List of the same size as sources or 1.
/synmodel - The synapse model for the connection (see Options below)
Options:
If not given, the synapse model is taken from the Options dictionary
of the Connect command.
Description:
Connect a set of source neurons to a single neuron.
Author:
Ruediger Kupper, via copy-paste-and-modify from Oliver's DivergentConnect.
Modified Ruediger Kupper, 20.03.2003
Modified Jochen Martin Eppler, 03.03.2009
SeeAlso: RandomConvergentConnect, DivergentConnect
*/

void
NestModule::ConvergentConnect_ia_i_a_a_lFunction::execute( SLIInterpreter* i ) const
{
i->assert_stack_load( 5 );

TokenArray source_adr = getValue< TokenArray >( i->OStack.pick( 4 ) );
long target_adr = getValue< long >( i->OStack.pick( 3 ) );

TokenArray weights = getValue< TokenArray >( i->OStack.pick( 2 ) );
TokenArray delays = getValue< TokenArray >( i->OStack.pick( 1 ) );

const Name synmodel_name = getValue< std::string >( i->OStack.pick( 0 ) );
const Token synmodel = kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
if ( synmodel.empty() )
throw UnknownSynapseType( synmodel_name.toString() );
const index synmodel_id = static_cast< index >( synmodel );

kernel().connection_builder_manager.convergent_connect(
source_adr, target_adr, weights, delays, synmodel_id );

i->OStack.pop( 5 );
i->EStack.pop();
}


// Documentation can be found in lib/sli/nest-init.sli near definition
// of the trie for RandomConvergentConnect.
void
NestModule::RConvergentConnect_ia_i_i_da_da_b_b_lFunction::execute( SLIInterpreter* i ) const
{
i->assert_stack_load( 8 );

TokenArray source_adr = getValue< TokenArray >( i->OStack.pick( 7 ) );
long target_adr = getValue< long >( i->OStack.pick( 6 ) );
size_t n = getValue< long >( i->OStack.pick( 5 ) );
TokenArray weights = getValue< TokenArray >( i->OStack.pick( 4 ) );
TokenArray delays = getValue< TokenArray >( i->OStack.pick( 3 ) );
bool allow_multapses = getValue< bool >( i->OStack.pick( 2 ) );
bool allow_autapses = getValue< bool >( i->OStack.pick( 1 ) );

const Name synmodel_name = getValue< std::string >( i->OStack.pick( 0 ) );
const Token synmodel = kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
if ( synmodel.empty() )
throw UnknownSynapseType( synmodel_name.toString() );
const index synmodel_id = static_cast< index >( synmodel );

kernel().connection_builder_manager.random_convergent_connect(
source_adr, target_adr, n, weights, delays, allow_multapses, allow_autapses, synmodel_id );

i->OStack.pop( 8 );
i->EStack.pop();
}

// Documentation can be found in lib/sli/nest-init.sli near definition
// of the trie for RandomConvergentConnect.
void
NestModule::RConvergentConnect_ia_ia_ia_daa_daa_b_b_lFunction::execute( SLIInterpreter* i ) const
{
i->assert_stack_load( 8 );

TokenArray source_adr = getValue< TokenArray >( i->OStack.pick( 7 ) );
TokenArray target_adr = getValue< TokenArray >( i->OStack.pick( 6 ) );
TokenArray n = getValue< TokenArray >( i->OStack.pick( 5 ) );
TokenArray weights = getValue< TokenArray >( i->OStack.pick( 4 ) );
TokenArray delays = getValue< TokenArray >( i->OStack.pick( 3 ) );
bool allow_multapses = getValue< bool >( i->OStack.pick( 2 ) );
bool allow_autapses = getValue< bool >( i->OStack.pick( 1 ) );

const Name synmodel_name = getValue< std::string >( i->OStack.pick( 0 ) );
const Token synmodel = kernel().model_manager.get_synapsedict()->lookup( synmodel_name );
if ( synmodel.empty() )
throw UnknownSynapseType( synmodel_name.toString() );
const index synmodel_id = static_cast< index >( synmodel );

kernel().connection_builder_manager.random_convergent_connect(
source_adr, target_adr, n, weights, delays, allow_multapses, allow_autapses, synmodel_id );

i->OStack.pop( 8 );
i->EStack.pop();
}


/* BeginDocumentation
Name: MemoryInfo - Report current memory usage.
Description:
Expand Down Expand Up @@ -1599,7 +1405,7 @@ NestModule::MPIAbort_iFunction::execute( SLIInterpreter* i ) const
gid - global id of the node
Description:
This function is helpful in the implementation of parallelized wiring
routines that create idential random structures independent of the
routines that create identical random structures independent of the
number of machines and threads participating in the simulation. The
function is used in SLI libraries, e.g. in the implementation of
RandomConvergentConnect. There is probably no need to directly use
Expand All @@ -1608,7 +1414,7 @@ NestModule::MPIAbort_iFunction::execute( SLIInterpreter* i ) const
In NEST each node (e.g. neuron) is assigned to a virtual process and
each virtual process maintains its own random number generator. In a
simulation run the virtual processes are equally distributed over the
participating machines and threads as speciefied by the user. In NEST
participating machines and threads as specified by the user. In NEST
2.0 virtual processes are identified with threads. Thus, with the
option /total_num_virtual_procs of [0] set to n, there are in total
always n threads (virtual processes) independent of the number of
Expand Down Expand Up @@ -1913,16 +1719,6 @@ NestModule::init( SLIInterpreter* i )
i->createcommand( "DataConnect_i_D_s", &dataconnect_i_D_sfunction );
i->createcommand( "DataConnect_a", &dataconnect_afunction );

i->createcommand( "DivergentConnect_i_ia_a_a_l", &divergentconnect_i_ia_a_a_lfunction );
i->createcommand(
"RandomDivergentConnect_i_i_ia_da_da_b_b_l", &rdivergentconnect_i_i_ia_da_da_b_b_lfunction );

i->createcommand( "ConvergentConnect_ia_i_a_a_l", &convergentconnect_ia_i_a_a_lfunction );
i->createcommand(
"RandomConvergentConnect_ia_i_i_da_da_b_b_l", &rconvergentconnect_ia_i_i_da_da_b_b_lfunction );
i->createcommand( "RandomConvergentConnect_ia_ia_ia_daa_daa_b_b_l",
&rconvergentconnect_ia_ia_ia_daa_daa_b_b_lfunction );

i->createcommand( "ResetNetwork", &resetnetworkfunction );
i->createcommand( "ResetKernel", &resetkernelfunction );

Expand Down
30 changes: 0 additions & 30 deletions nestkernel/nestmodule.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -291,36 +291,6 @@ class NestModule : public SLIModule
void execute( SLIInterpreter* ) const;
} connect_g_g_D_Dfunction;

class DivergentConnect_i_ia_a_a_lFunction : public SLIFunction
{
public:
void execute( SLIInterpreter* ) const;
} divergentconnect_i_ia_a_a_lfunction;

class RDivergentConnect_i_i_ia_da_da_b_b_lFunction : public SLIFunction
{
public:
void execute( SLIInterpreter* ) const;
} rdivergentconnect_i_i_ia_da_da_b_b_lfunction;

class ConvergentConnect_ia_i_a_a_lFunction : public SLIFunction
{
public:
void execute( SLIInterpreter* ) const;
} convergentconnect_ia_i_a_a_lfunction;

class RConvergentConnect_ia_i_i_da_da_b_b_lFunction : public SLIFunction
{
public:
void execute( SLIInterpreter* ) const;
} rconvergentconnect_ia_i_i_da_da_b_b_lfunction;

class RConvergentConnect_ia_ia_ia_daa_daa_b_b_lFunction : public SLIFunction
{
public:
void execute( SLIInterpreter* ) const;
} rconvergentconnect_ia_ia_ia_daa_daa_b_b_lfunction;

class ResetKernelFunction : public SLIFunction
{
public:
Expand Down
Loading

0 comments on commit a767e2e

Please sign in to comment.