NEST Users March 2025

users@nest-simulator.org

4 participants
3 discussions

NESTML - Error when generating code in an EasyBuild installation
by Pablo Alejandro 06 Mar '25

06 Mar '25

Hi everyone, I am currently working with nest/nestml that was installed with EasyBuild <https://docs.easybuild.io/> (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 <https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows…> (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

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First LTP interaction in STDP and synaptic time delay in STDP
by iiro.ahokainen＠tuni.fi 06 Mar '25

06 Mar '25

I'm a bit confused with NEST's STDP models. I'm not sure if the issues that I have found are design choices or unintended bugs. To debug stdp models, I added print statements in the stdp_synapse.h file: double minus_dt; while ( start != finish ) { minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ); std::cout<<"minus_dt: "<<minus_dt<<std::endl; std::cout<<"postspike time: "<<start->t_<<std::endl; ++start; // get_history() should make sure that // start->t_ > t_lastspike - dendritic_delay, i.e. minus_dt < 0 assert( minus_dt < -1.0 * kernel().connection_manager.get_stdp_eps() ); weight_ = facilitate_( weight_, Kplus_ * std::exp( minus_dt / tau_plus_ ) ); } I created two parrot neurons and fed spike times to the first neuron. I set the syn_delay to 0.3 ms. I found two issues: 1. If the spike train consists of only one spike, no STDP updates are performed. I would expect one positive update since the postsynaptic spike arrives 0.3 ms after the presynaptic spike. 2. minus_dt=-0.6 instead of -0.3. The spike separation is 0.3 ms, however for the STDP calculation, one uses 0.6 ms which confuses me. Indeed, simulating with presynaptic spike train [10., 20.] leads to weight change 1.0->35.5443 (lamba=1, mu_plus=mu_minus=0, otherwise defaults). Analytically, the same can be achieved by calculating (1/100 + np.exp(-0.6/20) - np.exp(-9.4/20))*100 = np.float64(35.54432652658074) This confirms that indeed minus_dt=-0.6 ms and that the first LTP STDP interaction is neglected. Are these known issues or new findings? I tested with NEST 3.3 and 3.8 and both had the same issues. I do not understand the point of having dendritic_delay in minus_dt = t_lastspike_ - ( start->t_ + dendritic_delay ), as it is already included in the start->t_ (?).

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Exponential Euler Support in NESTML
by justin.r.davis＠essie.ufl.edu 05 Mar '25

05 Mar '25

I've got a version of the HH model (via a NESTML file) which seems to be requiring an exponential Euler solver (ie the one commonly used for e^x dependent biologic systems) to most efficiently solve the equations*. From my reading of the NESTML code generator tools source, only rk45 and forward-Euler are supported. The difference between Euler and Exponential Euler doesn't seem that significant, so I wanted to see if I could get the exponential version implemented....however, what's become unclear to me is whether or not this is a limitation of NEST, NESTML or the underlying solvers and how I'd go about getting a different solver implemented. Are there any guides around on how one would implement a new solver and/or information which would help me figure this out. thx. jrd *=forward Euler does work for some (might work with even smaller timestep) cases, but it requires a time step of 0.01ms. I'm comparing with a Brian2 version of the model running with a 0.1ms time step with it's natively supported exponential Euler solver which is what is making me look into other solvers for my NESTML-based code.

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NEST Users March 2025