Search found 45 matches

by bremen
Sat Feb 16, 2019 5:01 pm
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 11004

Re: diffusion intracellular->extracellular->intracellular

Hi. After some more testing i have some questions: 1) I have recorded a vector, pointed to the outside name of the substance "self.soma(0.5)._ref_xo", to record the concentration in the ecs. The resulting graph is congruent with my expectation since it records only a part of the entire dif...
by bremen
Tue Feb 12, 2019 8:22 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 11004

Re: diffusion intracellular->extracellular->intracellular

Hi.
Thank you.
Currently the easiest way to do this is with mod files describing pump mechanism.
I'll try this approach.
by bremen
Sun Feb 10, 2019 10:32 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 11004

Re: diffusion intracellular->extracellular->intracellular

Hi. I was able to solve most of the workflow but I'm missing something in the "MultiCompartmentReaction". I'm trying to release the substance X, correctly generated in the internal region of cell_1, to the ecs. With the MultiCompartmentReaction wrote in this way: rxd.MultiCompartmentReacti...
by bremen
Thu Feb 07, 2019 11:25 am
Forum: Reaction-diffusion in NEURON
Topic: diffusion intracellular->extracellular->intracellular
Replies: 7
Views: 11004

diffusion intracellular->extracellular->intracellular

Hi. After reading the 2018 paper, i was wondering if is feasible, with rxd.extracellular, to reproduce the following situation: A substance X is internally produced by cell_1. It is pumped outside the membrane into the extracellular space. Here it diffuses until it reaches cell_2. It is then uptake ...
by bremen
Sat Jun 23, 2018 5:09 am
Forum: UNIX/Linux
Topic: Make error on Piz Daint cluster
Replies: 0
Views: 11281

Make error on Piz Daint cluster

Hi. I'm trying to compile NEURON on Piz Daint (Cray) but i have encountered an error during the make. export MPICC=cc ./configure --prefix=`pwd` --without-x --with-paranrn --without-nmodl --without-memacs CC=cc CXX=CC With this configure i obtain and "undefined reference to symbol '__tls_get_ad...
by bremen
Sat May 12, 2018 12:07 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 46196

Re: Spike source and target sections

Hi. I have changed the previous code with something simpler but there is still something odd. Let assume to connect 10 B_cell to 1 C_cell on the same section ['soma'] with 10 synPerConn. netParams.connParams['B_pop_2_C_pop] = {'preConds': {'pop': 'B_pop'}, 'postConds': {'pop': 'C_pop'}, 'sec': ['som...
by bremen
Sat Apr 28, 2018 4:05 pm
Forum: NetPyNE
Topic: VERSION RELEASES
Replies: 28
Views: 51737

Re: VERSION RELEASES

Hi Salva.

I think there is an issue with pip --upgrade to 0.7.8. It says that the latest available is the 0.7.7

Cheers
Stefano
by bremen
Sat Apr 28, 2018 3:51 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 46196

Re: Spike source and target sections

Hi Salva. I have a doubt about this for cycle. pop_C = 10 for p in range(0,len(pop_C)): netParams.connParams['Pop_B->Pop_C'+str(p)] = {'preConds': {'pop': 'Pop_B'}, 'postConds': {'pop': 'Pop_C'}, 'weight': 1, 'sec': location[p], 'delay': 0.1, 'loc': 0.5, 'synsPerConn' : 30, 'connList': [Pop_B_2_Pop_...
by bremen
Sat Apr 28, 2018 3:15 pm
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 15017

Re: Slow speed to save sim results

Hi Salva.
- if you only need the traces, you can reduce the save time by setting cfg.saveDataInclude = ['simData']
With this option and saveMat, the saving time was reduced over 100 times. From minutes/hours to a few seconds.
It is great.

Thank you

Best
Stefano
by bremen
Sat Apr 21, 2018 10:32 am
Forum: NetPyNE
Topic: Slow speed to save sim results
Replies: 2
Views: 15017

Slow speed to save sim results

Hi Salvador. I'm saving the voltage traces of about 200 neurons, into a mat file, and the time to save them can be up to 3 time the total run time of the simulation. The file is saved at the same rate (about 2-3MB/s) on clusters and on workstations with SSD drives, and it is independent on the numbe...
by bremen
Sun Mar 25, 2018 7:34 am
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 46196

Re: Spike source and target sections

Hi Salvador. I'm checking that everything, so far, is correct but, looking at the complete output, i saw something strange: Created connection preGid=0, postGid=1, sec= dend_0 , loc=0.7421, synMech=CF_AMPA, weight=1, delay=1.00, threshold=10 Created connection preGid=0, postGid=1, sec= dend_0 , loc=...
by bremen
Sun Mar 25, 2018 6:21 am
Forum: NetPyNE
Topic: Field names are restricted to 31 characters
Replies: 2
Views: 16612

Re: Field names are restricted to 31 characters

Hi Salvador.
Yes that was the cause.
I have reduces the length of the names, involved in the connection description, and the mat file was saved without problems.

Cheers
Stefano
by bremen
Sat Mar 24, 2018 1:36 pm
Forum: NetPyNE
Topic: Field names are restricted to 31 characters
Replies: 2
Views: 16612

Field names are restricted to 31 characters

Hi. I restarted working on my net but, after the first simulation, the code crashed during the creation of the Mat file with the following: "ValueError: Field names are restricted to 31 characters" I have in fact used more than 31 characters in the "netParams.connParams" connecti...
by bremen
Sun Mar 11, 2018 6:11 am
Forum: UNIX/Linux
Topic: Invalid syntax in "hclass3.py to hclass3.pyc"
Replies: 1
Views: 9186

Invalid syntax in "hclass3.py to hclass3.pyc"

Hi. I'm doing new installations of the latest NEURON code, from the git repository, and there is a SyntaxError which i haven't seen in previous builds. It does compile till the end and everything seems running as usual. byte-compiling /nrn/lib/python/neuron/hclass3.py to hclass3.pyc File "/nrn/...
by bremen
Tue Feb 20, 2018 2:23 pm
Forum: UNIX/Linux
Topic: Error in MOD compilation with a Slurm script
Replies: 3
Views: 9918

Re: Error in MOD compilation with a Slurm script

Hi.
The question then is why libreadline is available on the login node but not (one of) the compute nodes.
That was the cause of the issue.
The admin of the cluster installed libreadline, on the compute nodes, and i was able to compile the MODs and run the simulations.

Thank you
Stefano