Search found 104 matches

by shailesh
Thu Jan 12, 2017 8:53 am
Forum: UNIX/Linux
Topic: Issue Installing Neuron in Ubuntu 16.04 LTS
Replies: 6
Views: 13511

Re: Issue Installing Neuron in Ubuntu 16.04 LTS

Thanks JEGHC20 for posting those installation instructions. Really useful! Just to add to the potential pitfalls: > The above installation procedure failed (gave errors) when the system already had Anaconda. some of the errors were: collect2: error: ld returned 1 exit status Makefile:716: recipe for...
by shailesh
Mon Aug 17, 2015 12:52 am
Forum: Optimization
Topic: Problem in logging to savepath.fit
Replies: 4
Views: 7172

Re: Problem in logging to savepath.fit

Glad to know it came in handy! :)
by shailesh
Tue Jul 14, 2015 5:58 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

It's giving me: bash.exe"-3.1$ mpiexec -n 4 nrniv -mpi init.hoc CreateProcess failed, error 2 SMPD manager launch request failed with error 0x80070002. Error: unable to start the local smpd manager. I tried installing MPICH2 (wondering if that was the issue, as suggested somewhere online) by fo...
by shailesh
Mon Jul 13, 2015 4:50 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

Thanks! That works now (on Ubuntu). pc.nhost gives what is expected and also an improvement in the performance. How should I go about trying to do this on Windows? I read a few of the other posts here (suggesting commands involving bash, nrniv etc... https://www.neuron.yale.edu/phpBB/viewtopic.php?f...
by shailesh
Sun Jul 12, 2015 1:15 pm
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

I generally run NEURON on Windows 7, and so its mostly by just double-clicking the hoc file. While checking on Ubuntu the command was: nrngui init.hoc In both cases I got pc.nhost = 1. I suppose one does not really require the GUI when handling a simulation over multiple hosts, but I am not too fami...
by shailesh
Fri Jul 10, 2015 10:52 pm
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

I actually had read an earlier post by you on the forum regarding this and so did the 'Refresh' several times and reported the most frequent value. I suppose it is do with the OS as you suggested. Any suggestion regarding the earlier question: A part of the confusion stems from the fact that on my d...
by shailesh
Fri Jul 10, 2015 7:23 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

I may have some leads (and further issues) on the matter... My processor, Intel® Core™ i7-2600K, has 4 cores and supports 8 threads with hyper-threading. So the OS considers it as 8 CPUs (as verified in the 'Task Manager' in Windows and 'About This Computer' in Ubuntu. Further, on running a network ...
by shailesh
Thu Jul 09, 2015 11:12 pm
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

I did that and found something interesting: > On Windows 7 64-bit with NEURON v7.4 64-bit, I got "4 useful processors" > On Ubuntu 14.04 64-bit with NEURON v7.4 64-bit, I got "8 useful processors" My desktop has dual OS, and so the above was observed on exactly the same hardware....
by shailesh
Thu Jul 09, 2015 11:32 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

Thanks, thats good to know. Given this sccenario: Running a network model having 16 cells on the NeuroScience Gateway (NSG), with 2 nodes and 4 cores/node... giving me a total of 8 processors (nhost=8), with the cells distributed equally 2 per host. How could I make use of multi-threading here? As a...
by shailesh
Wed Jul 08, 2015 1:17 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 21690

Re: A ring network with multithreading

Came across this post and this bit interested me: Current versions of NEURON (including any of the alpha installers) can run multithreaded simulations of a model on a single host, or single threaded simulations of a model that is distributed over multiple hosts. It cannot run multithreaded simulatio...
by shailesh
Sat Apr 11, 2015 7:28 am
Forum: Modeling networks
Topic: single resistor as gap junction and connecting cells
Replies: 19
Views: 27732

Re: single resistor as gap junction and connecting cells

Thanks Michael, Ted for guiding me towards the solution! Using the LCB to generate the class really helped matters. I will elaborate a bit for the benefit of any future readers: On using the LCB to create the class (as described above), we get a HOC file having a procedure named 'refill()' which bas...
by shailesh
Wed Apr 08, 2015 2:22 am
Forum: Modeling networks
Topic: single resistor as gap junction and connecting cells
Replies: 19
Views: 27732

Re: single resistor as gap junction and connecting cells

Any thoughts on the above?
Note: I plan to connect the last and first internal nodes of adjacent sections (not the terminal nodes) and hence requiring 'gmat' in S/cm2 and not uS.
by shailesh
Wed Apr 01, 2015 11:45 am
Forum: Other questions
Topic: Regarding connection to ground under extracellular
Replies: 7
Views: 3541

Re: Regarding connection to ground under extracellular

Yes that indeed happens. If I change Ra/Re = 1, then identical responses are observed at both ends, and AP's are subsequently generated at the other segments from both ends. Viewing the circuit as a whole, I suppose it is natural to observe such a response. The two ends turn out to be symmetric, as ...
by shailesh
Wed Apr 01, 2015 6:17 am
Forum: Modeling networks
Topic: single resistor as gap junction and connecting cells
Replies: 19
Views: 27732

Re: single resistor as gap junction and connecting cells

Taking the above post a few steps further... I am trying to model two cells (for now, later more) such that their extracellular spaces are connected (ephaptic): http://s2.postimg.org/ju633bntl/image.png I plan to implement the extracellular link (Rlink) between two extracellular nodes in different s...
by shailesh
Sun Mar 22, 2015 11:41 am
Forum: Other questions
Topic: Regarding connection to ground under extracellular
Replies: 7
Views: 3541

Re: Regarding connection to ground under extracellular

Any suggestions on what could be wrong here?