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.
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.
- 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.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.
- 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
- 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
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#...
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.
- 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.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.
- 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
- 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
NEST Users mailing list --users@nest-simulator.org To unsubscribe send an email tousers-leave@nest-simulator.org
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#...
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.
- 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.
- 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
- 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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
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#...
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.
- 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.
- 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
- 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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Dear Steffen,
Thank you for your response. I tried the mamba command you pointed out but it only runs without errors if nest 3.8 is installed. If I explicitly specify 3.9 it returns the same error that I mentioned in the first email.
pygsl [2.3.4|2.5.1|2.6.2|2.6.4] would require │ └─ gsl >=2.7,<2.8.0a0 *, which conflicts with any installable versions previously reported;
Best, Pedro.
Em sex., 20 de fev. de 2026 às 06:56, Steffen Graber s.graber@fz-juelich.de escreveu:
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#...
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.
- 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.
- 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
- 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
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
NEST Users mailing list -- users@nest-simulator.org 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-...
-
Charl Linssen -
Pedro R. Pinheiro -
Pooja Babu -
Steffen Graber