Hello Pedro.
thank you for reporting the issues.
It's great that you now have a working setup.
I took a look at nestml conda-forge package and removed PyGSL as a hard
dependency of it. However, this causes nestml to display the following
warnings:
WARNING:root:PyGSL is not available. The stiffness test will be skipped.
WARNING:root:Error when importing: No module named ‘pygsl’
If needed, you can now reinstall the PyGSL package, which will make the
warnings disappear.
A complete environment with pygsl can be installed as follows:
mamba install nestml nest-simulator pygsl
Best
Steffen
Am 19.02.26 um 16:50 schrieb Pedro R. Pinheiro:
> Hello Charl and Pooja. Thank you for the quick response and the insights
> provided.
>
> Pooja, by following the instructions, I cloned the NEST repo and created a
> micromamba environment using the environment.yml file provided in the NEST
> github. The installation and testing were smooth. By running
> generate_target I got the error " /usr/bin/ld: cannot find -ltinfo: No such
> file or directory ", which I could correct by installing the following
> packages in my ubuntu distro:
>
> sudo apt install libncurses5-dev libncursesw5-dev
>
> NESTML seems to work fine now. Can I assume the setup was done properly?
>
> Best,
> Pedro.
>
> Em qui., 19 de fev. de 2026 às 07:04, Pooja Babu <p.babu@fz-juelich.de>
> escreveu:
>
>> Hi Pedro,
>>
>> To add to Charl's response, the error with libpthread.so is an existing
>> issue when NEST is installed using conda-forge:
>> https://github.com/nest/nestml/issues/1256.
>> Could you try installing NEST from source in the same mamba environment
>> and try again? The installation instructions can be found here:
>> https://nest-simulator.readthedocs.io/en/stable/installation/developer.html#dev-install
>>
>> Hope this helps!
>>
>> Regards,
>> Pooja
>> On 2/19/26 10:31 AM, Charl Linssen wrote:
>>
>> Dear Pedro,
>>
>> Thank you for writing in! Let me address your questions one by one.
>>
>> 1 -- PyGSL is only an optional dependency; the warning can be safely
>> ignored. I'm actually not sure where the PyGSL dependency comes from; it's
>> not in the requirements.txt of ODE-toolbox, NESTML or NEST as far as I can
>> see.
>>
>> 2 -- I think this is fine, but perhaps a conda/mamba expert can say more
>> about this. (I am not a mamba user myself.)
>>
>> 3 -- The ``generate_target()`` function is the basic, primary function.
>> The ``NESTCodeGeneratorUtils.generate_code_for()`` function is an
>> additional convenience function, that will create temporary paths for the
>> generated code, which is especially useful in a Jupyter notebook where the
>> same cell (that invokes the code generation) may be run over and over again.
>>
>> Hope this helps, please don't hesitate to get back in touch if you should
>> run into any further issues or questions.
>>
>> Yours,
>> Charl
>>
>>
>> On Wed, Feb 18, 2026, at 15:37, Pedro R. Pinheiro wrote:
>>
>> Hi everyone. I have a couple of questions pertaining to NESTML and would
>> appreciate some support. I use NEST via WSL with Ubuntu 24.04.3 LTS.
>> More specifically, I use the micromamba extension on VS Code to manage
>> virtual environments and install python packages via conda-forge.
>>
>> 1) When using NEST 3.9 I get an error saying that PyGSL is incompatible
>> and the simulator returns me a warning saying the stiffness test will be
>> skipped.
>>
>> [image: image.png]
>>
>> WARNING:root:PyGSL is not available. The stiffness test will be skipped.
>> WARNING:root:Error when importing: No module named 'pygsl
>>
>> I didn't have this problem before, when I used NEST 3.8.
>>
>> My installation steps currently are essentially:
>>
>> micromamba install -c conda-forge nest-simulator=3.9 ipython cxx-compiler
>> cmake make swig pkg-config
>> pip install nestml
>>
>> When I try to install pygsl via micromamba the only version I can attempt
>> is 2.6.2. Installing pygsl via pip also gives an error even if I have swig
>> and pkg-config installed.
>>
>> 2) When generating a target using generate_target, I get the following
>> error message:
>>
>> /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so:
>> No such file or directory
>>
>> I realised that while I do not have libpthread.so under that path I do
>> have libpthread.so.0 and creating a symlink directing the former to the
>> latter solves the problem. Is this acceptable?
>>
>> ln -s
>> /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so.0
>> /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so
>>
>> 3) I would like to know if using NESTCodeGeneratorUtils*.*generate_code_for
>> is better or equivalent to using generate_target.
>>
>> That's it for now. Thank you in advance for your help.
>>
>> Best,
>> Pedro.
>> _______________________________________________
>> NEST Users mailing list -- users@nest-simulator.org
>> To unsubscribe send an email to users-leave@nest-simulator.org
>>
>>
>>
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>>
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>>
>
>
> _______________________________________________
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> To unsubscribe send an email to users-leave@nest-simulator.org
--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data-labs/sdl-neuroscience
---------------------------------------------------------------------------------------------