Search found 35 matches

by aaronmil
Fri Oct 26, 2018 7:46 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 35
Views: 8231

Re: Installation problem Neuron

FWIW, I was able to get through make install without any errors by first exporting these environment variables: export CFLAGS='-Qunused-arguments -mmacosx-version-min=10.9 -stdlib=libc++' export CXXFLAGS='-Qunused-arguments -mmacosx-version-min=10.9 -stdlib=libc++' export LDFLAGS='-Qunused-arguments...
by aaronmil
Fri Oct 26, 2018 6:27 pm
Forum: OS X
Topic: Installation problem Neuron
Replies: 35
Views: 8231

Re: Installation problem Neuron

Hello all, I just updated my Mac OS to Mojava (10.14). It broke my NEURON install. Now, trying to re-install from the latest source is running up against problems related to deprecation of libstdc++ I use anaconda python2.7. I have updated the mac command line tools, and have the latest versions of ...
by aaronmil
Wed Jan 03, 2018 4:23 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

Michael, Thank you again for making some changes to ParallelContext. Here I'm sharing how I have exploited your tips to produce a Python module that implements apply(func, *args, **kwargs), sync and async versions of map(func, *sequences), and get(var_by_str_name) operations, using the ParallelConte...
by aaronmil
Thu Dec 28, 2017 3:01 am
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

It is not clear to me how to pass through key word arguments to callables even in pure python. Adendum: Ok. The following works. def f(a, b, c='what'): print(a) print(b) print(c) f(1,2,'hello') def call(callable, args, kwargs): callable(*args, **kwargs) call(f, (3, 4), {'c':'goodbye'}) But can one ...
by aaronmil
Thu Dec 21, 2017 2:06 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

hines wrote:
Thu Dec 21, 2017 1:29 pm
Made a slight change to the github repository so that the pc.submit() return value is the same as the return value of pc.userid().
Great, thank you!
by aaronmil
Thu Dec 21, 2017 2:04 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

ParallelContext.context has been fixed to execute on all pc.id_world() > 0. The fix is pushed to github. Thank you. With regard to your other suggestions, I will consider further. I start out with the prejudice that it is a bad idea to specify where a bulletin board submit should execute. The idea ...
by aaronmil
Tue Dec 19, 2017 8:32 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

Also, while I've got you, the unique id assigned to a submit call is not equal to the id returned upon job completion. It is its negative. from neuron import h pc = h.ParallelContext() def func(*args): return pc.runworker() submit_id = pc.submit(func, *args) while pc.working(): return_id = pc.userid...
by aaronmil
Tue Dec 19, 2017 6:28 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

Thank you, Michael. Is there any particular reason that you were enforcing that your new pccontext is not executed on the master? This module works just as well without the awkwardess of having to separately call the function on rank 0 manually: from neuron import h pc = h.ParallelContext() def _con...
by aaronmil
Fri Dec 15, 2017 2:56 pm
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

Hi, I have a question about using the ParallelContext interface. I am using Python. If I split a ParallelContext into subworlds, after pc.runworker() is called, pc.submit can be used to post jobs to the bulletin board, but there is no guarantee that all subworlds will end up executing a job. Instead...
by aaronmil
Fri Oct 27, 2017 2:31 am
Forum: Parallel NEURON
Topic: Passing parameters using pack/post, etc.
Replies: 18
Views: 14799

Re: Passing parameters using pack/post, etc.

I have a hoc and python example of the use of subworlds. Send a request to michael dot hines at yale dot edu and let me know if you want the python, hoc, or both versions of the example. Hi Michael, It would be very useful to see a python example of using subworlds to do parallel optimization of pa...
by aaronmil
Thu Apr 20, 2017 2:43 pm
Forum: UNIX/Linux
Topic: Running neuron with MPI using debian package
Replies: 1
Views: 7957

Re: Running neuron with MPI using debian package

Hi Roy,

#SBATCH -N is the number of nodes
#SBATCH -n is the number of processes

srun -n is the number of MPI ranks, which you have set to 1
by aaronmil
Mon Feb 06, 2017 8:06 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 10210

Re: Neuron as a Python Module Redux

Hi Rob, I'm having an awful time with a strange issue on my colleague's Windows 10 machine. We have 64-bit Anaconda2, and 64-bit NEURON 7.4 from the standard windows installer. We can run ipython, import neuron, and run simulations just fine - but only if we use the "ball and stick" specification of...
by aaronmil
Mon Apr 04, 2016 10:56 am
Forum: ModelDB and other online sources of models
Topic: modeldb inaccessible?
Replies: 1
Views: 9979

modeldb inaccessible?

or is it just me?
by aaronmil
Thu Sep 24, 2015 10:57 am
Forum: The GUI
Topic: Shape Plots for 1.5D Neurons
Replies: 1
Views: 5078

Shape Plots for 1.5D Neurons

I constructed my neuron morphology linearly with connect statements, without explicitly setting locations in 3D or even 2D space. Now when I view the morphology using a Shape Plot, it appears that 2D coordinates have been automatically assigned to each compartment, leading to a strange spiral shape ...
by aaronmil
Tue Jul 07, 2015 1:10 pm
Forum: Other questions
Topic: Plotting mtau and minf
Replies: 8
Views: 1327

Re: Plotting mtau and minf

GLOBALs are used in NMODL for two main reasons. One is for those parameters that are to have the same value across every instance of a particular ion channel or other mechanism. The other use is a way to reduce memory usage by "intermediate variables" such as gating state time constants and steady ...