Search found 21 matches

by catubc
Sat Jul 23, 2016 4:05 pm
Forum: Parallel NEURON
Topic: NEURON on GPUs?
Replies: 3
Views: 5422

Re: NEURON on GPUs?

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...
by catubc
Wed Jul 06, 2016 12:18 am
Forum: Parallel NEURON
Topic: NEURON on GPUs?
Replies: 3
Views: 5422

NEURON on GPUs?

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
by catubc
Tue Jun 16, 2015 1:15 am
Forum: UNIX/Linux
Topic: Neuron 7.4 installation on cluster - missing "inithoc.o"
Replies: 3
Views: 5587

Re: Neuron 7.4 installation on cluster - missing "inithoc.o"

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 tech people...
by catubc
Fri Jun 12, 2015 5:58 pm
Forum: UNIX/Linux
Topic: Neuron 7.4 installation on cluster - missing "inithoc.o"
Replies: 3
Views: 5587

Neuron 7.4 installation on cluster - missing "inithoc.o"

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...
by catubc
Wed May 27, 2015 11:31 am
Forum: Parallel NEURON
Topic: Pointer Vector warning - python NEURON running on clusters
Replies: 1
Views: 5183

Pointer Vector warning - python NEURON running on clusters

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 ...
by catubc
Mon May 18, 2015 10:10 pm
Forum: Parallel NEURON
Topic: Recording synapse times for random input - parallel context
Replies: 2
Views: 5187

Re: Recording synapse times for random input - parallel cont

Thanks Ted, I'll take a quick look. I have never looked at this stuff...
by catubc
Wed May 13, 2015 2:07 pm
Forum: Parallel NEURON
Topic: Recording synapse times for random input - parallel context
Replies: 2
Views: 5187

Recording synapse times for random input - parallel context

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...
by catubc
Wed Dec 17, 2014 10:58 pm
Forum: Parallel NEURON
Topic: NEURON on GPUs?
Replies: 1
Views: 5015

NEURON on GPUs?

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
by catubc
Fri Aug 22, 2014 11:46 am
Forum: Parallel NEURON
Topic: Installing NEURON on cluster
Replies: 1
Views: 7080

Installing NEURON on cluster

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_...
by catubc
Sat Jul 26, 2014 1:41 am
Forum: Parallel NEURON
Topic: Pause/Stop NEURON simulation to call run another program
Replies: 5
Views: 7469

Re: Pause/Stop NEURON simulation to call run another program

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...
by catubc
Fri Jul 25, 2014 1:51 am
Forum: Parallel NEURON
Topic: Pause/Stop NEURON simulation to call run another program
Replies: 5
Views: 7469

Re: Pause/Stop NEURON simulation to call run another program

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 time step fo...
by catubc
Tue Jul 22, 2014 12:55 am
Forum: Parallel NEURON
Topic: Pause/Stop NEURON simulation to call run another program
Replies: 5
Views: 7469

Re: Pause/Stop NEURON simulation to call run another program

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
by catubc
Mon Jul 21, 2014 10:41 pm
Forum: Parallel NEURON
Topic: Pause/Stop NEURON simulation to call run another program
Replies: 5
Views: 7469

Pause/Stop NEURON simulation to call run another program

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 or perhap...
by catubc
Wed Jun 18, 2014 12:44 am
Forum: Other questions
Topic: Interpxyz.hoc interpolated segments not connecting
Replies: 5
Views: 1147

Re: Interpxyz.hoc interpolated segments not connecting

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...
by catubc
Fri Jun 13, 2014 11:30 pm
Forum: Other questions
Topic: Interpxyz.hoc interpolated segments not connecting
Replies: 5
Views: 1147

Re: Interpxyz.hoc interpolated segments not connecting

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....