Hi all,
I was wondering what NESTML's versioning scheme looks like, and what
versions of NEST each NESTML version supports! e.g. can I generate code for
multiple NEST versions with 1 NESTML version?
Best regards,
--
Robin De Schepper, MSc
Department of Brain and Behavioral Sciences
Unit of Neurophysiology
University of Pavia, Italy
Via Forlanini 6, 27100 Pavia - Italy
Tel: (+39) 038298-7607
http://www-5.unipv.it/dangelo/
Interested in network modelling?
Discover our framework <https://github.com/dbbs-lab/bsb>:
<https://github.com/dbbs-lab/bsb>
Good afternoon,
I have adapted the current nest izhikevich neuron model in C++ to obtain a
more general izhikevich neuron where more parameters can be set (for
example voltage shifts and the membrane capacitance), and the b-parameter
can change over time according to some condition, such that also thalamic
neurons can be simulated.
The new extension module works very well (with much thanks to all earlier
help regarding installing extension modules). So hopefully people can
eventually, with this model, obtain all the kinds of neurons that
Izhikevich describes. As soon as everything is cleaned up and finished, I
will upload the code to github. However, before I do that, I have two
questions:
1. For the new parameters I added to the existing izhikevich model, I could
only use parameter names that are in nest::names. However, for generality
and to make it easy to use, I thought it would be better to use the same
symbols that Izhikevich uses to describe his model. That way, people can
easily replicate all the different types of neurons that Izhikevich
describes. He uses these parameters:
[image: image.png]
Is it possible to include these parameters in the neuron model? Or is it
better to just replace them with other parameter names that are already in
the nest_names file?
2. The current izhikevich neuron model doesn't model realistic synapses.
The membrane potential just jumps on each spike arrival. I would like to
include different post-synaptic dynamics with different and preferably
multiple timescales (like the beta_multisynapse). Someone mentioned before
that a lot of the synaptic dynamics can be defined outside the neuron. So
can I use beta synapses with the izhikevich neuron as it is now? Or should
I somehow include these dynamics in the C++ file of my new module?
I hope the questions are clear. Please let me know if I should provide any
additional information.
Thanks in advance and have a very nice weekend!
Kind regards,
Nina
Dear experts,
To develop a spiking neuronal network model of the thalamus, I want to
adapt the Izhikevich neuron model to account for the behavior of
thalamocortical neurons. Before I do this, I wanted to test if it was
possible to install an extension module in my setup. Therefore I followed
these steps:
https://nest-extension-module.readthedocs.io/en/latest/extension_modules.ht…
to install this example nest-extension-module:
https://github.com/nest/nest-extension-module .
I am working with the tvb-multiscale docker container (
https://github.com/the-virtual-brain/tvb-multiscale/tree/master/tvb_multisc…)
in VScode on windows. I've been working with this succesfully and easily
managed to make thalamus models with the available aeIF neuron model of
NEST. I'm using a python 3.7.3 interpreter and NEST 3.
I've succesfully "made" the module with:
> docker@84fabd16af99:~/mmb$ cmake
> -Dwith-nest=/home/docker/env/neurosci/nest_build/bin/nest-config
> ../nest-extension-module-master
It gives me the message:
> You can now build and install 'mymodule' using
> make
> make install
> The library file libmymodule.so will be installed to
> /home/docker/env/neurosci/nest_build/lib/nest/
> Help files will be installed to
> /home/docker/env/neurosci/nest_build/share/doc/nest
> The module can be loaded into NEST using
> nest.Install('mymodule') (in PyNEST)
> (mymodule) Install (in SLI
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/docker/mmb
However, when I try to "make". I get a bunch of errors that I have added at
the end of this email. My colleague tried to install exactly the same
module in exactly the same way on his linux machine and it worked
perfectly. But somehow for me, I get these weird errors that I haven't
been able to resolve so far. Does anyone have an idea what the problem
might be? It would be greatly appreciated. If you need any additional
information please let me know.
Thank you in advance and have a nice day!
Kind regards,
Nina Doorn
Error message:
docker@84fabd16af99:~/mmb$ make
Scanning dependencies of target mymodule_module
[ 10%] Building CXX object src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o
In file included from
/home/docker/nest-extension-module-master/src/mymodule.cpp:30:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:92:1: error:
expected class-name before ‘{’ token
{
^
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:115:21:
error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’
using nest::Node::handle;
^~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:116:21:
error: type ‘nest::Node’ is not a base type for type ‘mynest::pif_psc_alpha’
using nest::Node::handles_test_event;
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:121:14:
error: ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&,
nest::port, nest::synindex, bool)’ marked ‘override’, but does not override
nest::port send_test_event( nest::Node&, nest::port, nest::synindex,
bool ) override;
^~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:129:8: error:
‘void mynest::pif_psc_alpha::handle(nest::SpikeEvent&)’ marked ‘override’,
but does not override
void handle( nest::SpikeEvent& ) override; //! accept spikes
^~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:130:8: error:
‘void mynest::pif_psc_alpha::handle(nest::CurrentEvent&)’ marked
‘override’, but does not override
void handle( nest::CurrentEvent& ) override; //! accept input
current
^~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:131:8: error:
‘void mynest::pif_psc_alpha::handle(nest::DataLoggingRequest&)’ marked
‘override’, but does not override
void handle( nest::DataLoggingRequest& ) override; //! allow recording
with multimeter
^~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:133:14:
error: ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’
marked ‘override’, but does not override
nest::port handles_test_event( nest::SpikeEvent&, nest::port ) override;
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:134:14:
error: ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’
marked ‘override’, but does not override
nest::port handles_test_event( nest::CurrentEvent&, nest::port )
override;
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:135:14:
error: ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&,
nest::port)’ marked ‘override’, but does not override
nest::port handles_test_event( nest::DataLoggingRequest&, nest::port )
override;
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:138:8: error:
‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’ marked
‘override’, but does not override
void get_status( DictionaryDatum& ) const override;
^~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:139:8: error:
‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’ marked
‘override’, but does not override
void set_status( const DictionaryDatum& ) override;
^~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:143:8: error:
‘void mynest::pif_psc_alpha::init_buffers_()’ marked ‘override’, but does
not override
void init_buffers_() override;
^~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:146:8: error:
‘void mynest::pif_psc_alpha::calibrate()’ marked ‘override’, but does not
override
void calibrate() override;
^~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:149:8: error:
‘void mynest::pif_psc_alpha::update(const nest::Time&, long int, long int)’
marked ‘override’, but does not override
void update( nest::Time const&, const long, const long ) override;
^~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘nest::port mynest::pif_psc_alpha::send_test_event(nest::Node&,
nest::port, nest::synindex, bool)’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:324:23:
error: no matching function for call to
‘nest::SpikeEvent::set_sender(mynest::pif_psc_alpha&)’
e.set_sender( *this );
^
In file included from
/home/docker/env/neurosci/nest_build/include/nest/connector_model.h:34,
from
/home/docker/env/neurosci/nest_build/include/nest/common_synapse_properties.h:27,
from
/home/docker/env/neurosci/nest_build/include/nest/connection.h:27,
from
/home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27,
from
/home/docker/nest-extension-module-master/src/mymodule.cpp:29:
/home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note:
candidate: ‘void nest::Event::set_sender(nest::Node&)’
Event::set_sender( Node& s )
^~~~~
/home/docker/env/neurosci/nest_build/include/nest/event.h:1288:1: note:
no known conversion for argument 1 from ‘mynest::pif_psc_alpha’ to
‘nest::Node&’
In file included from
/home/docker/nest-extension-module-master/src/mymodule.cpp:30:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::SpikeEvent&, nest::port)’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53:
error: ‘get_name’ was not declared in this scope
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:337:53: note:
suggested alternative: ‘get_V_m_’
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
get_V_m_
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::CurrentEvent&, nest::port)’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53:
error: ‘get_name’ was not declared in this scope
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:351:53: note:
suggested alternative: ‘get_V_m_’
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
get_V_m_
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘nest::port
mynest::pif_psc_alpha::handles_test_event(nest::DataLoggingRequest&,
nest::port)’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53:
error: ‘get_name’ was not declared in this scope
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:366:53: note:
suggested alternative: ‘get_V_m_’
throw nest::UnknownReceptorType( receptor_type, get_name() );
^~~~~~~~
get_V_m_
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘void mynest::pif_psc_alpha::get_status(DictionaryDatum&) const’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:380:3: error:
‘ArchivingNode’ has not been declared
ArchivingNode::get_status( d );
^~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h: In member
function ‘void mynest::pif_psc_alpha::set_status(const DictionaryDatum&)’:
/home/docker/nest-extension-module-master/src/pif_psc_alpha.h:397:3: error:
‘ArchivingNode’ has not been declared
ArchivingNode::set_status( d );
^~~~~~~~~~~~~
In file included from
/home/docker/env/neurosci/nest_build/include/nest/connection_manager_impl.h:33,
from
/home/docker/nest-extension-module-master/src/mymodule.cpp:38:
/home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:
In instantiation of ‘nest::ConnBuilder*
nest::ConnBuilderFactory<ConnBuilderType>::create(nest::NodeCollectionPTR,
nest::NodeCollectionPTR, const DictionaryDatum&, const DictionaryDatum&)
const [with ConnBuilderType = mynest::StepPatternBuilder;
nest::NodeCollectionPTR = std::shared_ptr<nest::NodeCollection>;
DictionaryDatum = lockPTRDatum<Dictionary, (&
SLIInterpreter::Dictionarytype)>]’:
/home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:67:3:
required from here
/home/docker/env/neurosci/nest_build/include/nest/conn_builder_factory.h:72:12:
error: no matching function for call to
‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR&,
nest::NodeCollectionPTR&, const DictionaryDatum&, const DictionaryDatum&)’
return new ConnBuilderType( sources, targets, conn_spec, syn_spec );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from
/home/docker/nest-extension-module-master/src/mymodule.cpp:31:
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3:
note: candidate:
‘mynest::StepPatternBuilder::StepPatternBuilder(nest::NodeCollectionPTR,
nest::NodeCollectionPTR, const DictionaryDatum&, const
std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>
>&)’
StepPatternBuilder( const nest::NodeCollectionPTR sources,
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:35:3:
note: no known conversion for argument 4 from ‘const DictionaryDatum’
{aka ‘const lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)>’}
to ‘const std::vector<lockPTRDatum<Dictionary, (&
SLIInterpreter::Dictionarytype)> >&’
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7:
note: candidate: ‘mynest::StepPatternBuilder::StepPatternBuilder(const
mynest::StepPatternBuilder&)’
class StepPatternBuilder : public nest::ConnBuilder
^~~~~~~~~~~~~~~~~~
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7:
note: candidate expects 1 argument, 4 provided
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7:
note: candidate:
‘mynest::StepPatternBuilder::StepPatternBuilder(mynest::StepPatternBuilder&&)’
/home/docker/nest-extension-module-master/src/step_pattern_builder.h:32:7:
note: candidate expects 1 argument, 4 provided
In file included from
/home/docker/env/neurosci/nest_build/include/nest/model_manager.h:31,
from
/home/docker/env/neurosci/nest_build/include/nest/kernel_manager.h:31,
from
/home/docker/env/neurosci/nest_build/include/nest/connector_base_impl.h:26,
from
/home/docker/env/neurosci/nest_build/include/nest/connection.h:29,
from
/home/docker/nest-extension-module-master/src/drop_odd_spike_connection.h:27,
from
/home/docker/nest-extension-module-master/src/mymodule.cpp:29:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘bool nest::GenericModel<ElementT>::has_proxies() [with
ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:174:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:176:17:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘has_proxies’
return proto_.has_proxies();
~~~~~~~^~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘bool nest::GenericModel<ElementT>::one_node_per_process()
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:181:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:183:17:
error: ‘class mynest::pif_psc_alpha’ has no member named
‘one_node_per_process’
return proto_.one_node_per_process();
~~~~~~~^~~~~~~~~~~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘bool nest::GenericModel<ElementT>::is_off_grid() [with
ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:188:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:190:17:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘is_off_grid’
return proto_.is_off_grid();
~~~~~~~^~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void nest::GenericModel<ElementT>::calibrate_time(const
nest::TimeConverter&) [with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:195:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:197:10:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘calibrate_time’;
did you mean ‘calibrate’?
proto_.calibrate_time( tc );
~~~~~~~^~~~~~~~~~~~~~
calibrate
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void
nest::GenericModel<ElementT>::sends_secondary_event(nest::GapJunctionEvent&)
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:209:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:17:
error: ‘class mynest::pif_psc_alpha’ has no member named
‘sends_secondary_event’; did you mean ‘send_test_event’?
return proto_.sends_secondary_event( ge );
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
send_test_event
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:211:43:
error: return-statement with a value, in function returning ‘void’
[-fpermissive]
return proto_.sends_secondary_event( ge );
^
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void
nest::GenericModel<ElementT>::sends_secondary_event(nest::InstantaneousRateConnectionEvent&)
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:216:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:17:
error: ‘class mynest::pif_psc_alpha’ has no member named
‘sends_secondary_event’; did you mean ‘send_test_event’?
return proto_.sends_secondary_event( re );
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
send_test_event
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:218:43:
error: return-statement with a value, in function returning ‘void’
[-fpermissive]
return proto_.sends_secondary_event( re );
^
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void
nest::GenericModel<ElementT>::sends_secondary_event(nest::DiffusionConnectionEvent&)
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:223:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:17:
error: ‘class mynest::pif_psc_alpha’ has no member named
‘sends_secondary_event’; did you mean ‘send_test_event’?
return proto_.sends_secondary_event( de );
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
send_test_event
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:225:43:
error: return-statement with a value, in function returning ‘void’
[-fpermissive]
return proto_.sends_secondary_event( de );
^
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void
nest::GenericModel<ElementT>::sends_secondary_event(nest::DelayedRateConnectionEvent&)
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:230:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:17:
error: ‘class mynest::pif_psc_alpha’ has no member named
‘sends_secondary_event’; did you mean ‘send_test_event’?
return proto_.sends_secondary_event( re );
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
send_test_event
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:232:43:
error: return-statement with a value, in function returning ‘void’
[-fpermissive]
return proto_.sends_secondary_event( re );
^
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘nest::SignalType
nest::GenericModel<ElementT>::sends_signal() const [with ElementT =
mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:237:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:239:17:
error: ‘const class mynest::pif_psc_alpha’ has no member named
‘sends_signal’
return proto_.sends_signal();
~~~~~~~^~~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘const nest::Node&
nest::GenericModel<ElementT>::get_prototype() const [with ElementT =
mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:267:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:269:10:
error: invalid initialization of reference of type ‘const nest::Node&’ from
expression of type ‘const mynest::pif_psc_alpha’
return proto_;
^~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘void nest::GenericModel<ElementT>::set_model_id(int)
[with ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:274:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:276:10:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘set_model_id’
proto_.set_model_id( i );
~~~~~~~^~~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘int nest::GenericModel<ElementT>::get_model_id() [with
ElementT = mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:281:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:283:17:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_model_id’
return proto_.get_model_id();
~~~~~~~^~~~~~~~~~~~
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘DictionaryDatum
nest::GenericModel<ElementT>::get_status_() [with ElementT =
mynest::pif_psc_alpha; DictionaryDatum = lockPTRDatum<Dictionary, (&
SLIInterpreter::Dictionarytype)>]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:251:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:253:30:
error: ‘class mynest::pif_psc_alpha’ has no member named ‘get_status_base’;
did you mean ‘get_status’?
DictionaryDatum d = proto_.get_status_base();
~~~~~~~^~~~~~~~~~~~~~~
get_status
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h: In
instantiation of ‘nest::Node*
nest::GenericModel<ElementT>::allocate_(void*) [with ElementT =
mynest::pif_psc_alpha]’:
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:159:1:
required from here
/home/docker/env/neurosci/nest_build/include/nest/genericmodel.h:161:9:
error: cannot convert ‘mynest::pif_psc_alpha*’ to ‘nest::Node*’ in
initialization
Node* n = new ( adr ) ElementT( proto_ );
^
make[2]: *** [src/CMakeFiles/mymodule_module.dir/build.make:63:
src/CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:125:
src/CMakeFiles/mymodule_module.dir/all] Error 2
make: *** [Makefile:152: all] Error 2
Dear Sir, Dear Madam,
I am currently trying to install NEST in order to be able to use it within
an IDE, like Spyder. For the moment I am only able to do the following:
open Terminal
python3
import nest
This works when I use it in the terminal of the computer, but when I open
Spyder and execute the following:
import nest
neuron=nest.Create("iaf_psc_alpha")
neuron.get()
I get the following error message in the IPython console:
runfile('/Users/julienballbe/NEST/untitled0.py',
wdir='/Users/julienballbe/NEST')
Traceback (most recent call last):
File "/Users/julienballbe/NEST/untitled0.py", line 11, in <module>
neuron=nest.Create("iaf_psc_alpha")
AttributeError: module 'nest' has no attribute 'Create'
I am using a Macbook pro M1Max, MacOS 12.0, Spyder 5.1.5, Python 3.9.7.
I followed the instruction for building nest on your website (
https://nest-simulator.readthedocs.io/en/latest/installation/mac_install.ht…)
and used your recommendation for M1 macs (
https://nest-simulator.readthedocs.io/en/latest/installation/conda_tips.html
).
I build Nest following your instruction, the only error I got was when I
ran :
(nest-simulator-dev) julienballbe@pclnrs241 NEST % make installcheck
NEST Testsuite Results
----------------------------------------------------------------------
Phase Tests Skipped Failures Errors Time
----------------------------------------------------------------------
01 basetests 6 0 0 0 2.0
02 selftests 8 0 0 0 1.0
03 unittests 179 0 0 0 47.0
04 regressiontests 94 2 0 0 55.0
07 pynesttests 93 0 0 93 2.0
07 pynesttests nc 0 0 0 0 0.0
08 cpptests 30 0 0 0 0.0
----------------------------------------------------------------------
Total 410 2 0 93 107.0
----------------------------------------------------------------------
THE NEST TESTSUITE DISCOVERED PROBLEMS
The following tests failed
| .share.nest.testsuite.pytests.test_NodeCollection
| .share.nest.testsuite.pytests.test_aeif_lsodar
| .share.nest.testsuite.pytests.test_changing_tic_base
| .share.nest.testsuite.pytests.test_clopath_synapse
| .share.nest.testsuite.pytests.test_connect_all_to_all
| .share.nest.testsuite.pytests.test_connect_array_fixed_indegree
| .share.nest.testsuite.pytests.test_connect_array_fixed_outdegree
| .share.nest.testsuite.pytests.test_connect_arrays
| .share.nest.testsuite.pytests.test_connect_conngen
| .share.nest.testsuite.pytests.test_connect_fixed_indegree
| .share.nest.testsuite.pytests.test_connect_fixed_outdegree
| .share.nest.testsuite.pytests.test_connect_fixed_total_number
| .share.nest.testsuite.pytests.test_connect_one_to_one
| .share.nest.testsuite.pytests.test_connect_pairwise_bernoulli
|
.share.nest.testsuite.pytests.test_connect_symmetric_pairwise_bernoulli
| .share.nest.testsuite.pytests.test_create
| .share.nest.testsuite.pytests.test_current_recording_generators
| .share.nest.testsuite.pytests.test_erfc_neuron
| .share.nest.testsuite.pytests.test_errors
| .share.nest.testsuite.pytests.test_events
| .share.nest.testsuite.pytests.test_facetshw_stdp
| .share.nest.testsuite.pytests.test_get_set
| .share.nest.testsuite.pytests.test_getconnections
| .share.nest.testsuite.pytests.test_getnodes
| .share.nest.testsuite.pytests.test_glif_cond
| .share.nest.testsuite.pytests.test_glif_psc
| .share.nest.testsuite.pytests.test_helper_functions
| .share.nest.testsuite.pytests.test_jonke_synapse
| .share.nest.testsuite.pytests.test_json
| .share.nest.testsuite.pytests.test_labeled_synapses
| .share.nest.testsuite.pytests.test_mc_neuron
| .share.nest.testsuite.pytests.test_multiple_synapses
| .share.nest.testsuite.pytests.test_nodeParametrization
| .share.nest.testsuite.pytests.test_onetooneconnect
| .share.nest.testsuite.pytests.test_parameter
| .share.nest.testsuite.pytests.test_parrot_neuron
| .share.nest.testsuite.pytests.test_parrot_neuron_ps
| .share.nest.testsuite.pytests.test_poisson_generator_rate_change
| .share.nest.testsuite.pytests.test_pp_psc_delta
| .share.nest.testsuite.pytests.test_pp_psc_delta_stdp
| .share.nest.testsuite.pytests.test_quantal_stp_synapse
| .share.nest.testsuite.pytests.test_random123
| .share.nest.testsuite.pytests.test_random_parameter
| .share.nest.testsuite.pytests.test_rate_copy_model
| .share.nest.testsuite.pytests.test_rate_instantaneous_and_delayed
| .share.nest.testsuite.pytests.test_rate_neuron
| .share.nest.testsuite.pytests.test_rate_neuron_communication
| .share.nest.testsuite.pytests.test_recording_backend_ascii
| .share.nest.testsuite.pytests.test_recording_backend_memory
| .share.nest.testsuite.pytests.test_recording_backends
| .share.nest.testsuite.pytests.test_refractory
| .share.nest.testsuite.pytests.test_regression_issue-1034
| .share.nest.testsuite.pytests.test_regression_issue-1409
| .share.nest.testsuite.pytests.test_regression_issue-2069
| .share.nest.testsuite.pytests.test_regression_issue-2125
| .share.nest.testsuite.pytests.test_siegert_neuron
| .share.nest.testsuite.pytests.test_split_simulation
| .share.nest.testsuite.pytests.test_stack
| .share.nest.testsuite.pytests.test_status
| .share.nest.testsuite.pytests.test_stdp_multiplicity
| .share.nest.testsuite.pytests.test_stdp_nn_synapses
| .share.nest.testsuite.pytests.test_stdp_synapse
| .share.nest.testsuite.pytests.test_stdp_triplet_synapse
| .share.nest.testsuite.pytests.test_step_rate_generator
| .share.nest.testsuite.pytests.test_synapsecollection
| .share.nest.testsuite.pytests.test_threads
| .share.nest.testsuite.pytests.test_tsodyks2_synapse
| .share.nest.testsuite.pytests.test_urbanczik_synapse
| .share.nest.testsuite.pytests.test_visualization
| .share.nest.testsuite.pytests.test_vogels_sprekeler_synapse
| .share.nest.testsuite.pytests.test_weight_recorder
| .share.nest.testsuite.pytests.test_weights_as_lists
| .share.nest.testsuite.pytests.test_sp.test_conn_builder
| .share.nest.testsuite.pytests.test_sp.test_disconnect
| .share.nest.testsuite.pytests.test_sp.test_disconnect_multiple
| .share.nest.testsuite.pytests.test_sp.test_enable_multithread
| .share.nest.testsuite.pytests.test_sp.test_growth_curves
| .share.nest.testsuite.pytests.test_sp.test_sp_manager
| .share.nest.testsuite.pytests.test_sp.test_synaptic_elements
| .share.nest.testsuite.pytests.test_sp.test_update_synaptic_elements
|
.share.nest.testsuite.pytests.test_spatial.test_SynapseCollection_distance
| .share.nest.testsuite.pytests.test_spatial.test_basics
| .share.nest.testsuite.pytests.test_spatial.test_connect_layers
| .share.nest.testsuite.pytests.test_spatial.test_connect_sliced
|
.share.nest.testsuite.pytests.test_spatial.test_connection_with_elliptical_mask
| .share.nest.testsuite.pytests.test_spatial.test_create_spatial
| .share.nest.testsuite.pytests.test_spatial.test_dumping
| .share.nest.testsuite.pytests.test_spatial.test_layerNodeCollection
|
.share.nest.testsuite.pytests.test_spatial.test_layer_GetStatus_SetStatus
| .share.nest.testsuite.pytests.test_spatial.test_plotting
| .share.nest.testsuite.pytests.test_spatial.test_rotated_rect_mask
|
.share.nest.testsuite.pytests.test_spatial.test_selection_function_and_elliptical_mask
| .share.nest.testsuite.pytests.test_spatial.test_spatial_distributions
Please report test failures by creating an issue at
https://github.com/nest/nest_simulator/issues
----------------------------------------------------------------------
make[3]: *** [CMakeFiles/installcheck] Error 1
make[2]: *** [CMakeFiles/installcheck.dir/all] Error 2
make[1]: *** [CMakeFiles/installcheck.dir/rule] Error 2
make: *** [installcheck] Error 2
Can you please help me with this?
I stay at your disposal for any further information.
Thank you for your help,
Best feelings,
Julien Ballbé
--
*Julien BALLBÉ Y SABATÉ*
*Étudiant en thèse - PhD student*
*Neurophysiology of Visual Computation*
Centre Giovanni Borelli - CNRS UMR 9010
Université de Paris
45 rue des Saint-Pères, 75006 Paris, France
Tel: +33 6 79 03 40 35
Hi there NEST community,
I am trying to build an interface between [NEST reduced cell models (Izhikevich/AdExp) and NeuronUnit](https://github.com/russelljjarvis/NESTNeuronUnit).
For example here is one such [interface](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/nes… )
I find that if I run a single current injection experiment using the interface I get an expected number of spikes, but if I keep re-using the same interface in more and more experiments I get the same or similar number of spikes even with different current injection values. Its as if the initial conditions of the model are not re-setting properly.
I wonder if there are any ideas of things I could check.
This [simple file works okay](https://github.com/russelljjarvis/NESTNeuronUnit/blob/master/test_int…, but it only has one simulation run.
Russell Jarvis (he,him)
PhD Neuroscience
[Personal Website](https://russelljjarvis.github.io/home/)
I acknowledge the Dja Dja Wurrung and Taungurung Owners and Custodians of the lands on which I live and work and pay my respect to Elders past, present and future.
phone: 61444576301
email: russelljarvis(a)protonmail.com
Sent with [ProtonMail](https://protonmail.com/) Secure Email.
Dear NEST users,
In the past version, for debugging purposes I used to get information of my
source and target using the GetStatus function.
However, with NEST 3.0, I couldn't find a way to do so, mainly because I
have to pass either a SynpaseCollection or NeuronCollection as a function
argument to GetStatus. Is it possible to fetch node collection from neuron
id? Or any easier way to get source and target properties.
I referred document at link
https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.…
I have attached the python file for the same.
--
Thanks,
*Maryada*
Dear NEST users,
In the past version, for debugging purposes, I used to get information of
my source and target using the GetStatus function.
However, with NEST 3.0, I couldn't find a way to do so, mainly because I
have to pass either a SynpaseCollection or NeuronCollection as a function
argument to GetStatus. Is it possible to fetch node collection from neuron
id? Or any easier way to get the source and target properties.
I referred document at link
https://nest-simulator.readthedocs.io/en/v3.1/guides/connection_management.…
I have attached the python file for the same.
--
Thanks and Regards
*Maryada*
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today
Monday 8 November, 11.30-12.30 CET (UTC+1).
Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section.
As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams.
Agenda
* Welcome
* Review of NEST User Mailing List
* Project team round
* In-depth discussion
The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-11-08-Open-NEST-Developer-…
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
Log-in information
------------------
We use a virtual conference room provided by DFN (Deutsches Forschungsnetz).
You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available.
Web client
* Visit https://conf.dfn.de/webapp/conference/97938800
* Enter your name and allow your browser to use camera and microphone
* The conference does not need a PIN to join, just click join and you're in.
In case you see a dfnconf logo and the phrase "Auf den Meetingveranstalter warten", just be patient, the meeting host needs to join first (a voice will tell you).
VC system/software
How to log in with a video conferencing system, depends on you VC system or software.
- Using the H.323 protocol (eg Polycom): vc.dfn.net##97938800 or 194.95.240.2##97938800
- Using the SIP protocol:97938800@vc.dfn.de
- By telephone: +49-30-200-97938800
For those who do not have a video conference system or suitable
software, Polycom provides a pretty good free app for iOS and Android,
so you can join from your tablet (Polycom RealPresence Mobile, available
from AppStore/PlayStore). Note that firewalls may interfere with
videoconferencing in various and sometimes confusing ways.
For more technical information on logging in from various VC systems,
please see
http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4
