Search found 48 matches

by jackfolla
Mon Feb 14, 2011 10:31 am
Forum: Parallel NEURON
Topic: "point process not located in a section" with multisplit
Replies: 12
Views: 6083

Re: "point process not located in a section" with multisplit

Dear hines, with if (syn.has_loc()) {...} I solve the problem of the error, but I don't solve the problem that I can't access to point of process that not is located in a section. Now my code is: proc stimul_syn() { local r,s localobj nc,syn,src,name nclist1=new List() nclist2=new List() for r=0, $1...
by jackfolla
Fri Feb 11, 2011 5:57 am
Forum: UNIX/Linux
Topic: Add patch code to Neuron on Ubuntu
Replies: 6
Views: 4140

Re: Add patch code to Neuron on Ubuntu

Dear hines, I just checked on my old PC: Inserting a printf("Hello world") instruction into "function nrn_dbl_truncate_precision()", it prints many times, for each iteration, the string "Hello world". Instead, on MacBook this does not occur. So in fadvance.c into "...
by jackfolla
Thu Feb 10, 2011 1:28 pm
Forum: UNIX/Linux
Topic: Add patch code to Neuron on Ubuntu
Replies: 6
Views: 4140

Re: Add patch code to Neuron on Ubuntu

Dear hines, the versions on the two machines are the same. I tried (on MacBook Pro) to insert printf in "nrn_dbl_truncate_precision()", but it does not print anything. At this time, I don't have the opportunity to try the same thing on the other PC (because I'm not at home). I'll try later...
by jackfolla
Wed Feb 09, 2011 6:16 pm
Forum: UNIX/Linux
Topic: Add patch code to Neuron on Ubuntu
Replies: 6
Views: 4140

Re: Add patch code to Neuron on Ubuntu

Right, I forgot this last step. Now, there are this two situations: 1) On my old PC (dual-core 32 bit, with Ubuntu 9.04), the test "hhchain.hoc" returns this output: 22.0516626398788453 22.0516626399454623 mantissa precision 53 bits, result diff 6.66169e-11 22.0516626398788453 22.051662639...
by jackfolla
Tue Feb 08, 2011 7:10 am
Forum: UNIX/Linux
Topic: Add patch code to Neuron on Ubuntu
Replies: 6
Views: 4140

Add patch code to Neuron on Ubuntu

Dear all, I want apply a patch code to Neuron on my Ubuntu v. 10.10. This patch modifies 3 files: "fadvance.c" (in "/home/MY_NAME/neuron/nrn-7.1/src/nrnoc"), "hoc_init.hoc" and "math.c" (both in "/home/MY_NAME/neuron/nrn-7.1/src/oc"). In "/home/...
by jackfolla
Fri Feb 04, 2011 6:09 pm
Forum: Parallel NEURON
Topic: spikerecord() and spikeout() in single cell MULTISPLIT
Replies: 2
Views: 2297

Re: spikerecord() and spikeout() in single cell MULTISPLIT

Dear Hines, thanks a lot. I have an other question: formerly you sent me a patch (roundoff.patch) for roundoff error in multisplit case, and a test program (hhchain.hoc). Now I want to apply this patch. I used (on Ubuntu Linux 10.10) "patch -p1 < roundoff.patch" (in /home/my_user_name/neur...
by jackfolla
Fri Feb 04, 2011 6:58 am
Forum: Parallel NEURON
Topic: spikerecord() and spikeout() in single cell MULTISPLIT
Replies: 2
Views: 2297

spikerecord() and spikeout() in single cell MULTISPLIT

Dear all, I have the following problem: I want to record and print the spike train of the single cell that I multisplitted. Using the following code: objref tvec, idvec proc spikerecord() {local i localobj nc, nil tvec = new Vector() if (section_exists("soma", 0)) { soma nc=new NetCon(&...
by jackfolla
Wed Jan 19, 2011 12:18 pm
Forum: Parallel NEURON
Topic: "point process not located in a section" with multisplit
Replies: 12
Views: 6083

"point process not located in a section" with multisplit

Dear all, I have the following problem: I applying to a single-cell model the Multisplit parallelization. I know that one of the key steps is to put in the code function "section_exists()" to manage the access to the sections assigned to different hosts. My approach is to run the code and ...
by jackfolla
Mon Jan 03, 2011 7:48 am
Forum: Parallel NEURON
Topic: Multisplit simulations of a network (multiple neurons)
Replies: 1
Views: 2498

Multisplit simulations of a network (multiple neurons)

Dear All, I would be interested in understanding how to make Multisplit simulations of a network (obviously with multiple neurons). In the article "Fully Implicit Parallel Simulation of Single Neurons", paragraph "Network simulations" (page 14), there is a mention of this techniq...
by jackfolla
Thu Dec 02, 2010 6:59 am
Forum: Parallel NEURON
Topic: exp() out of range with parallel network
Replies: 3
Views: 3825

Re: exp() out of range with parallel network

Dear Ted, the network consists of neurons Ca1-Ca3. Using only Ca1 neurons, the error does not occur (even with multiple processors): consequently, I deduced that the warnings are generated by a few mistakes in the template (or file .mod) for the neuron Ca3. For now I put on stand-by this issue. Now,...
by jackfolla
Mon Nov 29, 2010 11:53 am
Forum: Parallel NEURON
Topic: exp() out of range with parallel network
Replies: 3
Views: 3825

exp() out of range with parallel network

Dear all, I have parallelized a network of neurons. When I call my parallel version with 1 proc, I have the same results than the serial version. time cell 11.2 1 11.2 2 11.2 3 11.2 4 12.925 0 But, when I call my parallel version with more procs, the following warnings occur: exp(715.745) out of ran...
by jackfolla
Mon Sep 27, 2010 10:30 am
Forum: Parallel NEURON
Topic: Multisplit simulation of a single neuron
Replies: 26
Views: 14174

Re: Multisplit simulation of a single neuron

Dear Hines,
in my new version of software roundoff errors involve also spikes times beetwen serial version and multisplit version.

These times differ increasingly with the progress of the run.

If it is possible, I send you this new version.

Thanks.
by jackfolla
Sat Sep 25, 2010 1:10 pm
Forum: Parallel NEURON
Topic: Multisplit simulation of a single neuron
Replies: 26
Views: 14174

Re: Multisplit simulation of a single neuron

Dear Hines, I solved the problem of spikes. I modify: current=u*0.2 if (section_exists("soma", 0)) insert_IClamp(tstop,current,u) with initial_current=0.2 insert_IClamp(tstop,initial_current) ... proc batchrun(){ ... if (section_exists("soma", 0) && u>1) clamp.amp = u*0.2...
by jackfolla
Fri Sep 24, 2010 4:30 pm
Forum: Parallel NEURON
Topic: Multisplit simulation of a single neuron
Replies: 26
Views: 14174

Re: Multisplit simulation of a single neuron

Dear Hines,
I send you a mail with my multisplit version.

With -np 1 it runs correctly.
With -np 2 it not runs correctly (tvec empty).

Maybe, there are any problems with sections.

I'm trying to solve...
by jackfolla
Fri Sep 24, 2010 3:15 pm
Forum: Parallel NEURON
Topic: Multisplit simulation of a single neuron
Replies: 26
Views: 14174

Re: Multisplit simulation of a single neuron

Dear Hines, I'll try your suggestion. I have another question: I would like to create a family of runs (simulations), where for each of which simulations the parameter "del" of IClamp is changed. In practice: proc insert_IClamp() { access soma if ($3==1) clamp = new IClamp(0.5) clamp.del =...