www.neuron.yale.edu

Thanks Michael. It sounds like this is partly developed on the Bluebrain work you've done already. The speedup is a bit unclear. Will an arbitrarily sized network speed up 10x with an ~500-1000core GPU? More practically, higher-end GPUs now have 3000-3500 cores - so will it be possible to assign eac...

Hi everyone

Is this project MIA? Last link I found dates back to 2014:

http://bitbucket.org/nrnhines/nrngpu

Just getting bit impatient with 1 node jobs sitting in cluster queues for many hrs.... Fantasizing about taking matters into my own hands :)

Thanks!
catubc

Michael So NEURON 7.4 seems to compile and run on my own workstation. I think there's something odd about the multiple versions of python used on the clusters. I assume that's what the "-2.7" in the error line stands for, i.e. some version of python. Give me a couple of days to work with t...

Dear All I'm working on installing 7.4-release on a cluster. Currently I'm having an issue that's probably very close to the end of the job. The error I get is: icpc: error #10236: File not found: 'build/temp.linux-x86_64-2.7/inithoc.o' Any suggestions? I thought maybe I'm not loading all the correc...

Dear All I'm running some code parallel context on a cluster and getting an odd warning. The code runs fine on my laptop and home workstation. The warning is this: *************************************************************************** 5 nrniv: PtrVector has no ptr_update callback 5 near line 0 ...

Thanks Ted, I'll take a quick look. I have never looked at this stuff...

Dear all I have a really simple question, I'm trying to save the synapse event times from a netcon object, but I keep getting an empty list. I'm wondering if this is a problem related to parallel context? It should be a simple issue... The python code is before, there's a NetStim setup to hold a ran...

Michael/Ted

Anyone make progress in this direction? I see there was one email in March/2014, but nothing since.

Does the code in the repository run? https://bitbucket.org/nrnhines/nrngpu/downloads

Thanks,
catubc

Hi everyone I've been trying for over 1 month to get NEURON to work on a cluster in Canada (Westgrid). I'm getting close but I still get errors like: dlopen failed - x86_64/.libs/libnrnmech.so: cannot read file data: Is a directory or /neuron/nrn-7.3/x86_64/lib/liboc.so.0: undefined symbol: __intel_...

Ted So it seems NEURON can run multithreaded system calls... The only issue is about a 25%-30% loss in efficiency (when comparing running the executables from NEURON vs. running them after NEURON terminates). I will work on this for a few days, but if you have any other suggestions, they are much ap...

Ted I've used the equivalent os.system call in python inside Michael's pysave_imembrane() function which as far as I researched is the only way for me to access the time value "t" in a parallel implementation. def pysave_imembrane(): #Hines' pybs.mod method calls this procedure at every ti...

Thanks Ted. I'll take a look at your code... it makes sense already. I'm assuming that the CPU cores will be offloaded on system call? That's my main concern as I'd like to be able to use NEURON on clusters and the lsa subroutines also are optimized for multithreading. catubc

Hi all. I've finally got my extracellular potential model to work properly, and now I'd like to be able to compute the potential every second or so of NEURON simulation. I'd like to be able to "pause" or somehow hang NEURON up every second of simulation and call another program (in FORTRAN...

Here's an update to anyone who's following this thread. I've been working on interpolating currents from nseg back to 3dpts and it's been quite a tricky endeavour. I'm getting close. Here's some videos of full 3d point current propagation, the online resolution is ok, but you can download them to se...

Thanks Ted, much appreciate the advice. I've used Gold et al 2007 for a few months now, I'll take another look to see if this problem is solved and certainly read up on your references. I am surprised that NEURON doesn't have an option for generating currents between sequential 3d morphology points....