13 Sep
2024
13 Sep
'24
10:38 a.m.
Ah, yes, that is indeed very informative. It indicates that the Boost C++ libraries are
missing. Would it be possible for you to add Boost to the conda environment?
Perhaps you could check the full installation instructions for NESTML on Anaconda at:
https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installa…
Hope this helps!
Charl
On Fri, Sep 13, 2024, at 09:41, Jona Scholz wrote:
Hi Charl,
The terminal logs are shown below. Is that the error message you were looking for?
Thanks for your help :)
Kind regards,
Jona
CMake Warning (dev) at CMakeLists.txt:93 (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/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-------------------------------------------------------
nestml_7f8d1ff3e3e8497da87659816759e61b_module Configuration Summary
-------------------------------------------------------
C++ compiler : /home/jona/miniconda3/envs/neuro/bin/x86_64-conda-linux-gnu-c++
Build static libs : OFF
C++ compiler flags : -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include
NEST compiler flags : -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona
-mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2
-ffunction-sections -pipe -isystem /home/jona/miniconda3/envs/neuro/include
-fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/nest-simulator_1724732927678/work=/usr/local/src/conda/nest-simulator-3.8
-fdebug-prefix-map=/home/jona/miniconda3/envs/neuro=/usr/local/src/conda-prefix -lrt
-std=c++17 -Wall -fopenmp -O2 -fdiagnostics-color=auto
NEST include dirs : -I/home/jona/miniconda3/envs/neuro/include/nest
-I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include
-I/home/jona/miniconda3/envs/neuro/include -I/home/jona/miniconda3/envs/neuro/include
NEST libraries flags : -L/home/jona/miniconda3/envs/neuro/lib/nest -lnest -lsli
/home/jona/miniconda3/envs/neuro/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so
-------------------------------------------------------
You can now build and install 'nestml_7f8d1ff3e3e8497da87659816759e61b_module'
using
make
make install
The library file libnestml_7f8d1ff3e3e8497da87659816759e61b_module.so will be installed
to
/tmp/nestml_target_t1m_k1tx
The module can be loaded into NEST using
(nestml_7f8d1ff3e3e8497da87659816759e61b_module) Install (in SLI)
nest.Install(nestml_7f8d1ff3e3e8497da87659816759e61b_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 3.30)
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 (3.7s)
-- Generating done (0.0s)
-- Build files have been written to: /home/jona/rstdp-gym/target
[ 66%] Building CXX object
CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o
[ 66%] Building CXX object
CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o
In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36,
from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35,
from
/home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36,
from
/home/jona/miniconda3/envs/neuro/include/nest/connection_manager_impl.h:26,
from
/home/jona/rstdp-gym/target/nestml_7f8d1ff3e3e8497da87659816759e61b_module.cpp:26:
/home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error:
boost/iterator/iterator_adaptor.hpp: No such file or directory
26 | #include <boost/iterator/iterator_adaptor.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from /home/jona/miniconda3/envs/neuro/include/nest/sort.h:36,
from /home/jona/miniconda3/envs/neuro/include/nest/connector_base.h:35,
from
/home/jona/miniconda3/envs/neuro/include/nest/connection_manager.h:36,
from /home/jona/miniconda3/envs/neuro/include/nest/kernel_manager.h:30,
from /home/jona/rstdp-gym/target/iaf_psc_alpha_neuron_nestml.cpp:33:
/home/jona/miniconda3/envs/neuro/include/nest/iterator_pair.h:26:10: fatal error:
boost/iterator/iterator_adaptor.hpp: No such file or directory
26 | #include <boost/iterator/iterator_adaptor.hpp>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[2]: ***
[CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:76:
CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/nestml_7f8d1ff3e3e8497da87659816759e61b_module.o]
Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: ***
[CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/build.make:90:
CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/iaf_psc_alpha_neuron_nestml.o]
Error 1
make[1]: *** [CMakeFiles/Makefile2:110:
CMakeFiles/nestml_7f8d1ff3e3e8497da87659816759e61b_module_module.dir/all] Error 2
make: *** [Makefile:156: all] Error 2
On Thu, Sep 12, 2024 at 12:17 PM Charl Linssen <nest-users(a)turingbirds.com> wrote:
__
Hi Jona,
Sorry about the error. It might be related to the conda environment; the issue seems to
be that there is an error during compilation, but the error message is not shown in these
logs. Could you check in your terminal (that you used to launch the Jupyter notebook
server) for the error messages from gcc?
Cheers,
Charl
On Wed, Sep 11, 2024, at 22:06, Jona Scholz wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
Dear Charl and Anno,
Thank you for your replies.
I hadn't heard about neurons that don't reset and will have to look into it more.
Thank you :)
I can't seem to run the SFA neuron tutorial linked in Charl's reply. It fails in
the first call to NESTCodeGeneratorUtils.generate_code_for(...) with an error found below.
I have tried it on two Ubuntu systems using NestML versions 8.0.0-rc1 and 8.0.0-rc2 with
the iaf_psc_alpha_neuron.nestml model from the NestML master branch. It is probably just
some technical problem on my end and I'm sure I will be able to resolve it soon.
Nonetheless, if anyone spots something obvious in the error message below, please let me
know.
Thanks for your help and have a great day!
Kind regards,
Jona
The error message:
---------------------------------------------------------------------------
CalledProcessError Traceback (most recent call last) File
~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174,
in NESTBuilder.build(self) * 173
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:173>
current_stage **=** **"**build**"** *--> 174
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:174>
subprocess.check_call(make_all_cmd, stderr=stderr, stdout=stdout, shell=shell, * 175
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:175>
cwd**=**str**(os**.**path**.**join(target_path))) ** 176
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:176>
current_stage **=** **"**install**"** File
*~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369, in check_call(*popenargs,
**kwargs) * 368
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:368>
cmd **=** popenargs[**0**] *--> 369
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:369>
raise CalledProcessError(retcode, cmd) * 370
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/subprocess.py:370>
**return* 0 CalledProcessError: Command '['make', '-j8',
'all']' returned non-zero exit status 2. During handling of the above
exception, another exception occurred: GeneratedCodeBuildException Traceback (most recent
call last) Cell In[2], line 3 * 1 **# generate and build code* * 2 module_name_no_sfa,
neuron_model_name_no_sfa **=** \ *----> 3
NESTCodeGeneratorUtils.generate_code_for("iaf_psc_alpha_neuron.nestml") File
~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136,
in NESTCodeGeneratorUtils.generate_code_for(cls, nestml_neuron_model,
nestml_synapse_model, module_name, target_path, post_ports, mod_ports, codegen_opts,
logging_level) * 133
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:133>
uniq_id **=** **str**(uuid**.**uuid4()**.**hex) ** 134
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:134>
module_name **=** **"**nestml_**"** **+** uniq_id **+**
**"**_module**"** *--> 136
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:136>
generate_nest_target(input_path=input_fns, * 137
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:137>
install_path**=**install_path, ** 138
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:138>
logging_level**=**logging_level, ** 139
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:139>
module_name**=**module_name, ** 140
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:140>
target_path**=**target_path, ** 141
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:141>
suffix**=**"**_nestml**"**, ** 142
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:142>
codegen_opts**=**_codegen_opts) ** 144
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:144>
**if* nestml_synapse_model: * 145
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_code_generator_utils.py:145>
**return* module_name, mangled_neuron_name, mangled_synapse_name File
~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270,
in generate_nest_target(input_path, target_path, install_path, logging_level, module_name,
store_log, suffix, dev, codegen_opts) * 243
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:243>
**def* generate_nest_target(input_path: Union[str, Sequence[str]], target_path:
Optional[str] = None, * 244
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:244>
install_path: Optional[**str**] **=** **None*, logging_level="ERROR", * 245
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:245>
module_name**=**None*, store_log: bool = False, suffix: str = "", * 246
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:246>
dev: **bool** **=** **False*, codegen_opts: Optional[Mapping[str, Any]] = None): * 247
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:247>
** **r**"""Generate and build code for NEST Simulator.* * 248
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:248>
** 249
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:249>
** Parameters* (...) * 268
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:268>
** A dictionary containing additional options for the target code generator.* * 269
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:269>
** """* --> 270
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:270>
generate_target(input_path, target_platform="NEST", target_path=target_path,
logging_level=logging_level, * 271
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:271>
module_name**=**module_name, store_log**=**store_log, suffix**=**suffix,
install_path**=**install_path, ** 272
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:272>
dev**=**dev, codegen_opts**=**codegen_opts) File
*~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193,
in generate_target(input_path, target_platform, target_path, install_path, logging_level,
module_name, store_log, suffix, dev, codegen_opts) * 165
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:165>
**r**"""Generate and build code for the given target platform.* * 166
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:166>
** 167
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:167>
**Parameters* (...) * 188
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:188>
** A dictionary containing additional options for the target code generator.* * 189
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:189>
**"""* * 191
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:191>
configure_front_end(input_path, target_platform, target_path, install_path, logging_level,
** 192
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:192>
module_name, store_log, suffix, dev, codegen_opts) *--> 193
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:193>
if not process() == 0: * 194
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:194>
**raise* Exception("Error(s) occurred while processing the model") File
~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482,
in process() * 480
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:480>
**# perform build* * 481
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:481>
**if* _builder is not None: --> 482
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:482>
_builder.build() * 484
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:484>
**if* FrontendConfiguration.store_log: * 485
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/frontend/pynestml_frontend.py:485>
store_log_to_file() File
*~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:181,
in NESTBuilder.build(self) * 177
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:177>
subprocess**.**check_call(make_install_cmd, stderr**=**stderr, stdout**=**stdout,
shell**=**shell, ** 178
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:178>
cwd**=**str**(os**.**path**.**join(target_path))) ** 180
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:180>
**except* subprocess.CalledProcessError as e: --> 181
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raise GeneratedCodeBuildException(stages_exception[current_stage]) * 183
<https://vscode-remote+wsl-002bubuntu.vscode-resource.vscode-cdn.net/home/jona/rstdp-gym/~/miniconda3/envs/neuro/lib/python3.10/site-packages/pynestml/codegeneration/nest_builder.py:183>
**finally*: * 184
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**if* self._options["redirect"]:
On Tue, Sep 10, 2024 at 9:33 AM Anno Kurth <a.kurth(a)fz-juelich.de> wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org Hi Jona,
you might also be interested in the leaky integrate-and-fire model with
adaptive threshold
[https://nest-simulator.readthedocs.io/en/latest/models/mat2_psc_exp.html].
Here, the voltage is not reset after a threshold crossing, though.
Best
Anno
On 10.09.24 09:15, Charl Linssen wrote:
> Hi Jona,
>
> Thanks for writing in! Could the NESTML model(s) used in the tutorial at
https://nestml.readthedocs.io/en/latest/tutorials/spike_frequency_adaptatio…
be what you're looking for? In general, it's easy to take a NESTML model (see
https://nestml.readthedocs.io/en/latest/models_library/index.html) and add a threshold
adaptation mechanism to it. Please let us know how you fare! (Please make sure you're
using the latest NESTML, v8.0.0-rc1 or the GitHub master version.)
>
> With kind regards,
> Charl
>
> On Tue, Sep 10, 2024, at 08:09, jona.m.scholz(a)gmail.com wrote:
>> Hello everyone,
>>
>> just a quick question in case anybody knows: is there a LIF model that
>> has an adaptive spike threshold in NEST?
>>
>> I know there's the GLIF model which can have a threshold, but it seems
>> to bring other deviations from the conventional LIF model that I want
>> to avoid. There's also the adaptive exponential integrate and fire
>> model, but again I don't want the exponential part.
>>
>> It's not a problem if no such model exists in NEST, I am only asking so
>> I don't reimplement an existing model.
>>
>> Any feedback would be appreciated.
>>
>> Kind regards,
>> Jona
>> _______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Anno Kurth
Institute for Advanced Simulation (IAS-6)
Computational and Systems Neuroscience
Jülich Research Centre
Jülich, Germany
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
_______________________________________________
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To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
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To unsubscribe send an email to users-leave(a)nest-simulator.org