Multisplit single cell with many synapses
Posted: Mon Feb 04, 2013 2:54 am
Hello,
1. I've made a multi-compartmental single-cell model neuron that runs without error with multisplit over 6 processors (on a single Microsoft Windows/Intel computer).
2. I've added many (e.g. 2000) Exp2Syn point processes to this single cell, distributed across most of the segments, with each synapse driven by a dedicated NetCon and NetStim pair. I intend to drive each synapse independently; the parameters of each NetStim instance will be set before the start of each run. This simulation runs fine without parallelization.
3. I'd like to run this synaptic simulation parallelized over all local processor cores, as in (1) above. My initial attempts - simply selecting the same ParallelComputing GUI settings as in (1) - resulted in an error "usable mindelay is 0". I have not yet carefully investigated this error, but found one forum post that talks about NetCon with multisplit: http://www.neuron.yale.edu/phpbb/viewto ... t=15#p5763
I figure I should take a step back and try to understand any relevant fundamentals ...
A. What are the considerations necessary when adding synapses (NetStim->NetCon->Exp2Syn) to a multisplit single-cell model?
B. Is there a particular published model or other material that would be a good reference?
I've read what I could find on parallelization, much of which seems to pertain to distributing workloads across clusters of machines, and/or to situations where multiple cells exist. Unfortunately, I was not yet able to understand how my situation maps onto those cases. Perhaps additional readings of those papers will get me there. In the meantime, any pointers would be much appreciated.
Thank you.
1. I've made a multi-compartmental single-cell model neuron that runs without error with multisplit over 6 processors (on a single Microsoft Windows/Intel computer).
2. I've added many (e.g. 2000) Exp2Syn point processes to this single cell, distributed across most of the segments, with each synapse driven by a dedicated NetCon and NetStim pair. I intend to drive each synapse independently; the parameters of each NetStim instance will be set before the start of each run. This simulation runs fine without parallelization.
3. I'd like to run this synaptic simulation parallelized over all local processor cores, as in (1) above. My initial attempts - simply selecting the same ParallelComputing GUI settings as in (1) - resulted in an error "usable mindelay is 0". I have not yet carefully investigated this error, but found one forum post that talks about NetCon with multisplit: http://www.neuron.yale.edu/phpbb/viewto ... t=15#p5763
I figure I should take a step back and try to understand any relevant fundamentals ...
A. What are the considerations necessary when adding synapses (NetStim->NetCon->Exp2Syn) to a multisplit single-cell model?
B. Is there a particular published model or other material that would be a good reference?
I've read what I could find on parallelization, much of which seems to pertain to distributing workloads across clusters of machines, and/or to situations where multiple cells exist. Unfortunately, I was not yet able to understand how my situation maps onto those cases. Perhaps additional readings of those papers will get me there. In the meantime, any pointers would be much appreciated.
Thank you.