Search found 26 matches

by bremen
Sat Jun 23, 2018 5:09 am
Forum: UNIX/Linux
Topic: Make error on Piz Daint cluster
Replies: 0
Views: 70

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_addr@@G...
by bremen
Sat May 12, 2018 12:07 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 4858

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: 13
Views: 7743

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: 4858

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: 138

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: 138

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: 4858

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: 133

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: 133

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" connections names. Can be th...
by bremen
Sun Mar 11, 2018 6:11 am
Forum: UNIX/Linux
Topic: Invalid syntax in "hclass3.py to hclass3.pyc"
Replies: 1
Views: 257

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/lib/p...
by bremen
Tue Feb 20, 2018 2:23 pm
Forum: UNIX/Linux
Topic: Error in MOD compilation with a Slurm script
Replies: 3
Views: 342

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
by bremen
Thu Feb 15, 2018 4:20 pm
Forum: UNIX/Linux
Topic: Error in MOD compilation with a Slurm script
Replies: 3
Views: 342

Error in MOD compilation with a Slurm script

Hi. On a cluster I have a custom installation of NEURON 7.5 (October build) compiled with a Python 2.7.12 module, installed on the machine. The problem arise in the way I try to compile the MOD files: 1) if I manually load the python module, the path to NEURON and start the virtual environment, cont...
by bremen
Thu Dec 14, 2017 7:57 am
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1583

Re: Netpyne on clusters

It worked.
Thank you.
by bremen
Tue Dec 12, 2017 3:33 pm
Forum: NetPyNE
Topic: Spike source and target sections
Replies: 17
Views: 4858

Re: Spike source and target sections

section labels that consist of a list are automatically converted to that format (ie. 'name_index') since netpyne requires section names to be strings. This was the missing key element. In my main model, i have full control on the name of each dendritic section which, coincidentally, was the same u...
by bremen
Tue Dec 12, 2017 2:30 pm
Forum: NetPyNE
Topic: Netpyne on clusters
Replies: 4
Views: 1583

Re: Netpyne on clusters

Seems like there is some issue with matplotlib -- can you import it by itself outside of netpyne? -bash-4.2$ python Python 2.7.12 (default, Aug 8 2016, 09:48:40) [GCC 4.8.5 20150623 (Red Hat 4.8.5-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import matplo...