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: 9643

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: 4782

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: 12509

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 followi...
by shailesh
Mon Jul 13, 2015 4:50 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 12509

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: 12509

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: 12509

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: 12509

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: 12509

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. My processor is Int...
by shailesh
Thu Jul 09, 2015 11:32 am
Forum: Parallel NEURON
Topic: A ring network with multithreading
Replies: 26
Views: 12509

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: 12509

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: 20877

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: 20877

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: 1963

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: 20877

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: 1963

Re: Regarding connection to ground under extracellular

Any suggestions on what could be wrong here?