Hi Pooja,
Oh ok, thanks for the clarification. It does work.
Just a quick question then: is code co-generation supported by default
now? I thought we needed the {"neuron_synapse_pairs":
[["iaf_psc_exp_neuron", "stdp_synapse"]]} definition for that.
Thanks
On Wed, Mar 19, 2025 at 11:00 PM Babu, Pooja <
p.babu@fz-juelich.de> wrote:
Hi Pablo,
The error messages you see are due to a bug from our side. They are caused by an extra check we made on the synapse model, which is not necessary. We have fixed this now, and it will be available in the next release.
For now, you can ignore the messages because, according to your log, the code is generated and installed successfully.
Install the project...
-- Install configuration: ""
-- Installing: /tmp/nestml_target_iomfk96v/nestml_b572ebbec3644c89b7de9e463c4270f4_module.so
You can use the models generated in your simulation. Please let us know if you still observe any errors during the simulation.
Thank you,
Pooja
On 18. Mar 2025, at 03:52, Pablo Alejandro <pabloabur@gmail.com> wrote:
Hi Pooja
Not a problem. Thanks for helping.
I followed your recommendation and got the error message below. I got some warnings related to UCX, but I don't think this is the problem because the same code on a different ubuntu installation gives me the same nestml error messages.
Thanks
------------------------
[INFO] [2025.3.18 13:39:58 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it.
For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Mar 17 2025 15:10:53
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
[INFO] [2025.3.18 13:39:59 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it.
For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Mar 17 2025 15:10:53
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver
CMake Warning (dev) at CMakeLists.txt:95 (project):
cmake_minimum_required() should be called prior to this top-level project()
call. Please see the cmake-commands(7) manual for usage documentation of
both commands.
This warning is for project developers. Use -Wno-dev to suppress it.
-- The CXX compiler identification is GNU 11.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/remote/pablo.urbizagastegui/easybuild/software/GCCcore/11.2.0/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_b572ebbec3644c89b7de9e463c4270f4_module Configuration Summary
-------------------------------------------------------
C++ compiler : /home/remote/pablo.urbizagastegui/easybuild/software/GCCcore/11.2.0/bin/g++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -O2 -ftree-vectorize -march=native -fno-math-errno -std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto -O3 -DNDEBUG
NEST include dirs : -I/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest -I/home/remote/pablo.urbizagastegui/easybuild/software/libtool/2.4.6-GCCcore-11.2.0/include -I/home/remote/pablo.urbizagastegui/easybuild/software/libreadline/8.1-GCCcore-11.2.0/include -I/home/remote/pablo.urbizagastegui/easybuild/software/GSL/2.7-GCC-11.2.0/include -I/home/remote/pablo.urbizagastegui/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/include
NEST libraries flags : -L/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/lib64/nest -lnest -lsli /home/remote/pablo.urbizagastegui/easybuild/software/libtool/2.4.6-GCCcore-11.2.0/lib/libltdl.so /home/remote/pablo.urbizagastegui/easybuild/software/libreadline/8.1-GCCcore-11.2.0/lib/libreadline.so /home/remote/pablo.urbizagastegui/easybuild/software/ncurses/6.2-GCCcore-11.2.0/lib/libncurses.so /home/remote/pablo.urbizagastegui/easybuild/software/GSL/2.7-GCC-11.2.0/lib/libgsl.so /home/remote/pablo.urbizagastegui/easybuild/software/GSL/2.7-GCC-11.2.0/lib/libgslcblas.so /home/remote/pablo.urbizagastegui/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib/libmpi.so /home/remote/pablo.urbizagastegui/easybuild/software/GCCcore/11.2.0/lib64/libgomp.so /lib64/libpthread.so
-------------------------------------------------------
You can now build and install 'nestml_b572ebbec3644c89b7de9e463c4270f4_module' using
make
make install
The library file libnestml_b572ebbec3644c89b7de9e463c4270f4_module.so will be installed to
/tmp/nestml_target_iomfk96v
The module can be loaded into NEST using
(nestml_b572ebbec3644c89b7de9e463c4270f4_module) Install (in SLI)
nest.Install(nestml_b572ebbec3644c89b7de9e463c4270f4_module) (in PyNEST)
CMake Warning (dev) in CMakeLists.txt:
No cmake_minimum_required command is present. A line of code such as
cmake_minimum_required(VERSION 3.26)
should be added at the top of the file. The version specified may be lower
if you wish to support older CMake versions for this project. For more
information run "cmake --help-policy CMP0000".
This warning is for project developers. Use -Wno-dev to suppress it.
-- Configuring done (0.2s)
-- Generating done (0.0s)
-- Build files have been written to: /home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target
[ 25%] Building CXX object CMakeFiles/nestml_b572ebbec3644c89b7de9e463c4270f4_module_module.dir/nestml_b572ebbec3644c89b7de9e463c4270f4_module.o
In file included from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connection_manager_impl.h:33,
from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/nest_extension_interface.h:29,
from /home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/nestml_b572ebbec3644c89b7de9e463c4270f4_module.cpp:26:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:90:3: warning: no return statement in function returning non-void [-Wreturn-type]
90 | }
| ^
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::map<Name, std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> > >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:101:3: warning: no return statement in function returning non-void [-Wreturn-type]
101 | }
| ^
In file included from /home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/nestml_b572ebbec3644c89b7de9e463c4270f4_module.cpp:36:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml() [with targetidentifierT = nest::TargetIdentifierPtrRport]’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_model.h:164:25: required from ‘nest::GenericConnectorModel<ConnectionT>::GenericConnectorModel(std::string) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierPtrRport>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:62:5: required from ‘void nest::ModelManager::register_connection_model(const string&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/nest_impl.h:37:70: required from ‘void nest::register_connection_model(const string&) [with ConnectorModelT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:581:91: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:705:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
705 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘void nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::recompute_internal_variables() [with targetidentifierT = nest::TargetIdentifierPtrRport]’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:718:3: required from ‘nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml() [with targetidentifierT = nest::TargetIdentifierPtrRport]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_model.h:164:25: required from ‘nest::GenericConnectorModel<ConnectionT>::GenericConnectorModel(std::string) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierPtrRport>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:62:5: required from ‘void nest::ModelManager::register_connection_model(const string&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/nest_impl.h:37:70: required from ‘void nest::register_connection_model(const string&) [with ConnectorModelT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:581:91: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:693:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
693 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml() [with targetidentifierT = nest::TargetIdentifierIndex]’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_model.h:164:25: required from ‘nest::GenericConnectorModel<ConnectionT>::GenericConnectorModel(std::string) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:103:34: required from ‘void nest::ModelManager::register_specific_connection_model_(const string&) [with CompleteConnecionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:67:80: required from ‘void nest::ModelManager::register_connection_model(const string&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/nest_impl.h:37:70: required from ‘void nest::register_connection_model(const string&) [with ConnectorModelT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:581:91: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:705:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
705 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘void nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::recompute_internal_variables() [with targetidentifierT = nest::TargetIdentifierIndex]’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:718:3: required from ‘nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml() [with targetidentifierT = nest::TargetIdentifierIndex]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_model.h:164:25: required from ‘nest::GenericConnectorModel<ConnectionT>::GenericConnectorModel(std::string) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:103:34: required from ‘void nest::ModelManager::register_specific_connection_model_(const string&) [with CompleteConnecionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/model_manager_impl.h:67:80: required from ‘void nest::ModelManager::register_connection_model(const string&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/nest_impl.h:37:70: required from ‘void nest::register_connection_model(const string&) [with ConnectorModelT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml; std::string = std::__cxx11::basic_string<char>]’
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:581:91: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:693:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
693 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘bool nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::send(nest::Event&, size_t, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierPtrRport; size_t = long unsigned int]’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:391:22: required from ‘void nest::Connector<ConnectionT>::send_to_all(size_t, const std::vector<nest::ConnectorModel*>&, nest::Event&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierPtrRport>; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:383:3: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:459:22: warning: unused variable ‘minus_dt’ [-Wunused-variable]
459 | const double minus_dt = t_lastspike_ - ( start->t_ + __dendritic_delay );
| ^~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:488:14: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
488 | auto get_t = [t_hist_entry_ms](){ return t_hist_entry_ms; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:516:12: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
516 | auto get_t = [__t_spike](){ return __t_spike; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:556:12: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
556 | auto get_t = [__t_spike](){ return __t_spike; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:413:18: warning: unused variable ‘__timestep’ [-Wunused-variable]
413 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:415:10: warning: variable ‘get_thread’ set but not used [-Wunused-but-set-variable]
415 | auto get_thread = [tid]()
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘bool nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::send(nest::Event&, size_t, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierIndex; size_t = long unsigned int]’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:391:22: required from ‘void nest::Connector<ConnectionT>::send_to_all(size_t, const std::vector<nest::ConnectorModel*>&, nest::Event&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:383:3: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:459:22: warning: unused variable ‘minus_dt’ [-Wunused-variable]
459 | const double minus_dt = t_lastspike_ - ( start->t_ + __dendritic_delay );
| ^~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:488:14: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
488 | auto get_t = [t_hist_entry_ms](){ return t_hist_entry_ms; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:516:12: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
516 | auto get_t = [__t_spike](){ return __t_spike; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:556:12: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
556 | auto get_t = [__t_spike](){ return __t_spike; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:413:18: warning: unused variable ‘__timestep’ [-Wunused-variable]
413 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:415:10: warning: variable ‘get_thread’ set but not used [-Wunused-but-set-variable]
415 | auto get_thread = [tid]()
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘void nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::update_internal_state_(double, double, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierPtrRport]’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:483:9: required from ‘bool nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::send(nest::Event&, size_t, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierPtrRport; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:391:22: required from ‘void nest::Connector<ConnectionT>::send_to_all(size_t, const std::vector<nest::ConnectorModel*>&, nest::Event&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierPtrRport>; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:383:3: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:767:18: warning: unused variable ‘__timestep’ [-Wunused-variable]
767 | const double __timestep = timestep; // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:768:10: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
768 | auto get_t = [t_start](){ return t_start; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h: In instantiation of ‘void nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::update_internal_state_(double, double, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierIndex]’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:483:9: required from ‘bool nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<targetidentifierT>::send(nest::Event&, size_t, const nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestmlCommonSynapseProperties&) [with targetidentifierT = nest::TargetIdentifierIndex; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:391:22: required from ‘void nest::Connector<ConnectionT>::send_to_all(size_t, const std::vector<nest::ConnectorModel*>&, nest::Event&) [with ConnectionT = nest::stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml<nest::TargetIdentifierIndex>; size_t = long unsigned int]’
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connector_base.h:383:3: required from here
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:767:18: warning: unused variable ‘__timestep’ [-Wunused-variable]
767 | const double __timestep = timestep; // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml.h:768:10: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
768 | auto get_t = [t_start](){ return t_start; }; // do not remove, this is in case the predefined time variable ``t`` is used in the NESTML model
| ^~~~~
[ 50%] Building CXX object CMakeFiles/nestml_b572ebbec3644c89b7de9e463c4270f4_module_module.dir/iaf_psc_delta_neuron_nestml.o
In file included from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connection_manager_impl.h:33,
from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/event_delivery_manager_impl.h:29,
from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/universal_data_logger_impl.h:29,
from /home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:35:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:90:3: warning: no return statement in function returning non-void [-Wreturn-type]
90 | }
| ^
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::map<Name, std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> > >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:101:3: warning: no return statement in function returning non-void [-Wreturn-type]
101 | }
| ^
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp: In member function ‘void iaf_psc_delta_neuron_nestml::init_state_internal_()’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:175:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
175 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp: In member function ‘void iaf_psc_delta_neuron_nestml::recompute_internal_variables(bool)’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:218:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
218 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp: In member function ‘virtual void iaf_psc_delta_neuron_nestml::update(const nest::Time&, long int, long int)’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:272:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
272 | for (long i = 0; i < NUM_SPIKE_RECEPTORS; ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:263:10: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
263 | auto get_t = [origin, lag](){ return nest::Time( nest::Time::step( origin.get_steps() + lag + 1) ).get_ms(); };
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml.cpp:257:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
257 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
[ 75%] Building CXX object CMakeFiles/nestml_b572ebbec3644c89b7de9e463c4270f4_module_module.dir/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.o
In file included from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/connection_manager_impl.h:33,
from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/event_delivery_manager_impl.h:29,
from /home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/universal_data_logger_impl.h:29,
from /home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:35:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:90:3: warning: no return statement in function returning non-void [-Wreturn-type]
90 | }
| ^
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h: In member function ‘nest::ConnBuilder* nest::ConnBuilderFactory<ConnBuilderType, is_tripartite>::create(nest::NodeCollectionPTR, nest::NodeCollectionPTR, nest::NodeCollectionPTR, const DictionaryDatum&, const std::map<Name, std::vector<lockPTRDatum<Dictionary, (& SLIInterpreter::Dictionarytype)> > >&) const’:
/home/remote/pablo.urbizagastegui/easybuild/software/nest/3.8-foss-2021b/include/nest/conn_builder_factory.h:101:3: warning: no return statement in function returning non-void [-Wreturn-type]
101 | }
| ^
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp: In member function ‘void iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml::init_state_internal_()’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:185:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
185 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp: In member function ‘void iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml::recompute_internal_variables(bool)’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:237:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
237 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp: In member function ‘virtual void iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml::update(const nest::Time&, long int, long int)’:
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:293:24: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
293 | for (long i = 0; i < NUM_SPIKE_RECEPTORS; ++i)
| ~~^~~~~~~~~~~~~~~~~~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:284:10: warning: variable ‘get_t’ set but not used [-Wunused-but-set-variable]
284 | auto get_t = [origin, lag](){ return nest::Time( nest::Time::step( origin.get_steps() + lag + 1) ).get_ms(); };
| ^~~~~
/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/target/iaf_psc_delta_neuron_nestml__with_stdp_synapse_nestml.cpp:278:16: warning: unused variable ‘__timestep’ [-Wunused-variable]
278 | const double __timestep = nest::Time::get_resolution().get_ms(); // do not remove, this is necessary for the timestep() function
| ^~~~~~~~~~
[100%] Linking CXX shared module nestml_b572ebbec3644c89b7de9e463c4270f4_module.so
[100%] Built target nestml_b572ebbec3644c89b7de9e463c4270f4_module_module
[100%] Built target nestml_b572ebbec3644c89b7de9e463c4270f4_module_module
Install the project...
-- Install configuration: ""
-- Installing: /tmp/nestml_target_iomfk96v/nestml_b572ebbec3644c89b7de9e463c4270f4_module.so
[18,stdp_synapse_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[43,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[44,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [2:0;47:0]]: Variable 'post_trace__for_stdp_synapse_nestml' not defined!
[48,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [40:83;40:83]]: Variable post_trace__for_stdp_synapse_nestml could not be resolved!
[49,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [40:27;40:94]]: The type of the expression (left-hand side = 'w / Wmax'; binary operator = ' - '; right-hand side = '(alpha * lambda * (w / Wmax) ** mu_minus * post_trace__for_stdp_synapse_nestml)') could not be derived: left-hand side has type 'real' whereas right-hand side has type 'error'!
[50,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [40:18;40:95]]: Type of 'Wmax * (w / Wmax - (alpha * lambda * (w / Wmax) ** mu_minus * post_trace__for_stdp_synapse_nestml))' could not be derived!
[51,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[52,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [2:0;47:0]]: Variable 'post_trace__for_stdp_synapse_nestml' not defined!
[56,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, ERROR, [40:18;40:95]]: Type of 'Wmax * (w / Wmax - (alpha * lambda * (w / Wmax) ** mu_minus * post_trace__for_stdp_synapse_nestml))' could not be derived!
[1742265598.987054] [xcs-node-01:583058:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1742265598.987061] [xcs-node-01:583058:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory.
[1742265606.167279] [xcs-node-01:583058:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1742265606.167288] [xcs-node-01:583058:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory.
[1742265606.471417] [xcs-node-01:583058:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1742265606.471426] [xcs-node-01:583058:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory.
[1742265616.606287] [xcs-node-01:583058:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1742265616.606297] [xcs-node-01:583058:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory.
On Tue, Mar 18, 2025 at 5:15 AM Babu, Pooja <p.babu@fz-juelich.de> wrote:
Hi Pablo,
Apologies for not getting back to you sooner, as I was on holiday.
I got a bit confused earlier and suggested uncommenting the “neuron_synapse_pair,” but indeed, that is not necessary as it is already handled by the NESTCodeGeneratorUtils.generate_code_for() function.
module_name, neuron_model_name, synapse_model_name = \
NESTCodeGeneratorUtils.generate_code_for("models/neurons/iaf_psc_delta_neuron.nestml",
nestml_stdp_model,
post_ports=["post_spikes"],
logging_level="WARNING",
codegen_opts={"delay_variable”: {"stdp_synapse": "d"},
"weight_variable”: {"stdp_synapse": "w"}})
The above function works fine. If this is still not working for you, please share the error log.
Regards,
Pooja
On 11. Mar 2025, at 04:05, Pablo Alejandro <pabloabur@gmail.com> wrote:
I tried the same thing on another installation (ubuntu, with apt and pip install) and got the same error message. How can I test whether this is not an installation issue? There is no error if I comment the "neuron_synapse_pair" entry.
Thanks
On Fri, Mar 7, 2025 at 9:41 AM Pablo Alejandro <pabloabur@gmail.com> wrote:
Hi Pooja, Thank you for your guidance. I removed the comments but I got a different error message: [INFO] [2025.3.7 9:35:8 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it.
For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Mar 5 2025 14:24:10
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named 'pygsl'
[INFO] [2025.3.7 9:35:9 /home/remote/pablo.urbizagastegui/easybuild/build/nest/3.8/foss-2021b/nest-simulator/nestkernel/vp_manager.cpp:74 @ VPManager::initialize()] : OMP_NUM_THREADS is set in your environment, but NEST ignores it.
For details, see the Guide to parallel computing in the NEST Documentation.
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.8.0
Built: Mar 5 2025 14:24:10
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "V_m" as it is solved by propagator solver
WARNING:root:Not preserving expression for variable "refr_t" as it is solved by propagator solver
[18,stdp_synapse_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[36,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[40,stdp_synapse_nestml__with_iaf_psc_delta_neuron_nestml, WARNING, [8:8;8:17]]: Variable 'd' has the same name as a physical unit!
[1741300508.992276] [xcs-node-01:414339:0] ib_md.c:1225 UCX WARN IB: ibv_fork_init() was disabled or failed, yet a fork() has been issued.
[1741300508.992283] [xcs-node-01:414339:0] ib_md.c:1226 UCX WARN IB: data corruption might occur when using registered memory.
Traceback (most recent call last):
File "/home/remote/pablo.urbizagastegui/git/nest-simulator/pynest/examples/Potjans_2014/test.py", line 58, in <module>
NESTCodeGeneratorUtils.generate_code_for("iaf_psc_delta_neuron.nestml",
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator_utils.py", line 138, in generate_code_for
generate_nest_target(input_path=input_fns,
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 291, in generate_nest_target
generate_target(input_path, target_platform="NEST", target_path=target_path, logging_level=logging_level,
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 215, in generate_target
return process()
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 514, in process
generate_code(code_generator, models)
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/frontend/pynestml_frontend.py", line 459, in generate_code
code_generators.generate_code(models)
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 288, in generate_code
self.generate_synapses(synapses)
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/code_generator.py", line 174, in generate_synapses
self.generate_synapse_code(synapse)
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 271, in generate_synapse_code
super().generate_synapse_code(synapse)
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/code_generator.py", line 225, in generate_synapse_code
template_namespace=self._get_synapse_model_namespace(synapse),
File "/home/remote/pablo.urbizagastegui/easybuild/software/nestml/8.0.0-foss-2021b/lib/python3.9/site-packages/pynestml/codegeneration/nest_code_generator.py", line 575, in _get_synapse_model_namespace
assert len(namespace["pre_ports"]) <= 1, "Synapses only support one spiking input port"
AssertionError: Synapses only support one spiking input port
On Thu, Mar 6, 2025 at 7:01 PM Babu, Pooja <p.babu@fz-juelich.de> wrote:
Hi Pablo,
Thank you for writing in!
The following lines in the script “test.py” are commented:
codegen_opts={#"neuron_synapse_pairs”:
# [{"neuron": "iaf_psc_delta_neuron”,
# "synapse": "stdp_synapse"}],
… }
Could you uncomment them and run the script again?
Regards,
Pooja
On 6. Mar 2025, at 05:53, Pablo Alejandro <pabloabur@gmail.com> wrote:
Hi everyone,
I am currently working with nest/nestml that was installed with EasyBuild (i.e. a tool to manage software in HPC systems). Nest was installed with OpenMPI support (see nest_easybuild.eb attached) and it seems to be working fine. Nestml is failing when I try the stdp tutorial (see error log slurm-782.out and test.py script attached). I also attached the installation steps for nestml (nestml_easybuild.eb) and the slurm script (run_job_simple.sh) to this email.
Could someone please assist me with further debugging this? This looks like an installation problem, but I get no errors if I'm using no synapse models.
Thanks
--
Pablo Alejandro
<run_job_simple.sh><nestml_easybuild.eb><test.py><nest_easybuild.eb><slurm-782.out>_______________________________________________
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