Hi everyone, I'm working with Mario on the ArborIO project. I'm trying to make a synapse between two cells where one cell inhibits the other one at every spike. I've been trying to use
arbor.synapse('expsyn') but I cannot find a way. What I want is a small current input on the postsynaptic cell for each presynaptic spike, can any one point me in the right direction? Thanks!
What isn't working? Did you
place a synapse and try to form a connection that ends on it?
The unit tests might have to build a catalogue under MPI, can I assume that the unit tests always have mpi4py available so that I can Barrier? Otherwise I'd require some way to wait for one of the ranks to finish building the catalogue without
mpi4py and it seems a bit overkill for unit tests to start with file locking etc if we can just pip install mpi4py
The communicator that you use for the
context is not readable from Python and the mpi_comm has no interface
Even if they do that during setup/teardown, some nodes are going to have to wait an unknown time for the other node to build the catalogue
I fixed it by just using `mpi4py' though.
Yes, I guess the pattern is one of these:
- each proc makes their own w/ a unique name
- like 1. but after mv into one location (should be atomic)
- Master builds rest in Barrier
- Have two scripts, one for build cat, one for do tests. Might be my favourite, as we can use this for unit and unit-mpi
I went for (3):
def _build_cat(name, path):
from mpi4py.MPI import COMM_WORLD as comm
build_err = None
try:
if not comm.Get_rank():
subprocess.run(["build-catalogue", name, str(path)], check=True)
build_err = comm.bcast(build_err, root=0)
except Exception as e:
build_err = comm.bcast(e, root=0)
if build_err:
raise RuntimeError("Tests can't build catalogues")
return Path.cwd() / (name + "-catalogue.so")
@thorstenhater: here's the invite to the COMBINE slack, where there's a #neuroml channel: https://join.slack.com/t/combine-workspace/shared_invite/zt-wf7ndwqv-gkYW63umvtBdPBHgWscR3w
We've also got https://gitter.im/NeuroML/community set up, but we haven't officially moved to it yet
Last link, to the upcoming COMBINE meeting: https://combine-org.github.io/events/ (I think Padraig said he'll send out an e-mail about the NeuroML developer workshop too)
Hi @all, I'd like to bring your attention to the slightly improved Issue templates when you file one at https://github.com/arbor-sim/arbor/issues/new/choose
Issues are not just for bugs, we use them also for Feature Requests. When you do, make sure you add/remove the relevant labels. There are also two priority labels, which you can use to signal your urgency and desire for a timeline on addressing the issue. From now on, I'll be making sure you have a reply in a timely fashion.
Issues are not just for bugs, we use them also for Feature Requests. When you do, make sure you add/remove the relevant labels. There are also two priority labels, which you can use to signal your urgency and desire for a timeline on addressing the issue. From now on, I'll be making sure you have a reply in a timely fashion.
2 replies
Thanks @brenthuisman @thorstenhater, hope to see you there (more details at https://docs.neuroml.org/Events/202109-COMBINE.html). Would one of you (or @halfflat or @bcumming or @noraabiakar) be happy to give a 5 min intro to Arbor, and briefly mention the curretn/future plans for NeuroML support?
@brenthuisman let's hash out who goes where.
PSA: Once arbor-sim/arbor#1693 is merged all Python unit tests must follow the unittest naming conventions:
test_<my_test_file>.pyTest<MyTestCase>(unittest.TestCase):- With inside you can have multiple
test_<my_test_function>
It's important that test files start with test_, test cases start with Test and test functions with test_
doc/internals?
I think
options.py can also be burned now, right? Or is there still a use case for CLI args in the tests, not covered by theunittest CLI itself?
Hi @all, we have a "Projects" page up on the website. We'll gather interesting side-projects and put them up here. Target audience: PhDs or Postdocs looking for a (side-)project, or Master students looking for a thesis-project.
Have a look at: https://arbor-sim.org/projects/
Have a look at: https://arbor-sim.org/projects/
If you have an idea for such a project, do get in touch!