Search found 45 matches
- 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...
- 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.
Thank you.
I'll try this approach.Currently the easiest way to do this is with mod files describing pump mechanism.
- 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...
- 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 ...
- 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...
- 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...
- 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
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
- 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_...
- 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.
It is great.
Thank you
Best
Stefano
With this option and saveMat, the saving time was reduced over 100 times. From minutes/hours to a few seconds.- if you only need the traces, you can reduce the save time by setting cfg.saveDataInclude = ['simData']
It is great.
Thank you
Best
Stefano
- 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...
- 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=...
- 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
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
- 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...
- 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/...
- 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 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
That was the cause of the issue.The question then is why libreadline is available on the login node but not (one of) the compute nodes.
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