30 Nov
2021
30 Nov
'21
11:54 a.m.
Dear Jochen,
Thanks for taking the time for this. I tested 4th option from your
suggestions as that is the cleanest way to import my work without further
impacting my analysis script. Everything seems to work as expected.
I am not sure if this change is documented or is an intuitive change.
However, it would be nice to have it on the comparison page.
Thanks for your help!
On Tue, Nov 30, 2021 at 9:36 AM Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
wrote:
Dear Maryada,
[Re-sending with properly rendered Markdown. Sorry for the noise]
I re-tested my code and realized that I didn't set overwrite_files to
False properly, so you are right, I received the error.
Good.
However, since I am importing my code from NEST 2.xx version to v3.1 and
all my previous implementation also have similar two-phase simulations,
this was not the case earlier. To my understanding, unless you call
*ResetKernel*, it is a single simulation and should not overwrite the
current file as is the case when recording in memory.
The behavior has indeed been as you describe with NEST 2.x. However, it
was changed with NEST 3.0.
In the 2.x series of NEST, all recording devices had a flag
close_after_simulate, which defaulted to False. As this flag resulted in
a high bookkeeping complexity internally and was confusing to many users,
it has been removed in favor of the clearer semantics that each call to
Simulate() produces its own file.
I ran your script (with syntax changes) on my laptop which only has nest
2.20 version and the attached data file contains recording for the whole
run and not just the last subpart of simulation. I would understand if the
functionality is changed in the latest version, however, I was wondering if
there is a possible work-around. I surely cannot manually store all the
data given that I also record from a multimeter and these are
memory-consuming simulations.
If you want to run repetitive simulations *and* get all your data (either
in separate files or a single file) with NEST 3.x, you have several
possibilities:
1.
You change the kernel property data_path inbetween calls to Simulate().
This would let NEST put the data for *all* recorders in different
directories. You can use os.mkdir to create the directories from
within your simulation script:
import nest, os# Create nodes# Connect nodes
os.mkdir("path_for_sim1")
nest.data_path = "path_for_sim1"
nest.Simulate(1000)
os.mkdir("path_for_sim2")
nest.data_path = "path_for_sim2"
nest.Simulate(2000)
2.
You can move your files to somewhere safe using os.rename(), instead
of setting data_path.
3.
You can set a different data_prefix between calls to Simulate() (i.e.,
nest.data_prefix
= "sim1_", nest.data_prefix = "sim2_", …). That way you wouldn’t
have
to create directories, but your data files would instead be prefixed as to
your choice.
4.
You can use Prepare(), Run(), Cleanup() instead of Simulate() as
explained in the Guide on running simulations
<https://nest-simulator.readthedocs.io/en/latest/guides/running_simulations.html#split-a-simulation-into-multiple-intervals>.
For each call to Run(), the recorders would actually append to the
files, as those are only closed in Cleanup() (and re-opened in
Prepare()). In fact, Simulate() is actually just a wrapper around the
three aforementioned functions.
Cheers,
Jochen!
On Mon, Nov 29, 2021 at 10:24 PM Jochen Martin Eppler <
j.eppler(a)fz-juelich.de> wrote:
--
Thanks and Regards
*Maryada*
Dear Maryada,
I have just played a bit with your example (see attachment for a slightly
extended and reformatted version) and as far as I can see, NEST behaves
exactly as expected (and documented).
Please let me explain:
-
When using the recording backend ascii
<https://nest-simulator.readthedocs.io/en/v3.1/models/recording_backend_ascii.html>
with the kernel attribute overwrite_files
<https://nest-simulator.readthedocs.io/en/v3.1/ref_material/pynest_apis.html#nest.NestModule.overwrite_files>
set to True, you have to move files away at the location in your
script saying do something, otherwise the data files get overwritten
by each new call to Simulate() and you consequently get to see only
the results from the last run (which is what you report).
-
If you set overwrite_files to False, and did not move the file away,
you will get an error upon repeated calls to Simulate(), as the file
to be created by the backend already exists.
-
When using the recording backend memory
<https://nest-simulator.readthedocs.io/en/v3.1/models/recording_backend_memory.html>,
overwrite_files is not even considered, as that does not actually
write files.
-
Data just accumulates in the recording backend memory until it is
explicitly cleared by running Input_SD.n_events = 0.
See the linked backend documentation pages for more information.
I hope this helps to clear up things.
Cheers,
Jochen!
On 29.11.21 18:32, Maryada Maryada wrote:
Dear NEST users,
I am trying to debug my network and I found that my spike_recorder with
*ascii* option isn't working as expected.
I am simulating a network for a few milliseconds (say 1000. ms) and then
do some structure changes and then re-run for another phase of a few ms
(say 4000. ms)
In the compact version, I am trying to see how this sample code would
work.
import nest
nest.ResetKernel()
nest.SetKernelStatus({
"overwrite_files": True,
"data_path": './Debug-Log',
"data_prefix": 'DEBUG-SPIKE-REC',
})
noise_device = nest.Create("poisson_generator",params={'start':
0.,'rate'
: 100.})
sd_params = {
"record_to": 'ascii',
"label": "Input_spike_recorder"
}
Input_SD = nest.Create("spike_recorder",1, params=sd_params)
nest.Connect(noise_device,Input_SD)
nest.Simulate(100.)
# do something here
nest.Simulate(100.)
*Issue:* I only get the data recorded from 100th millisecond but for
memory, I get all the data from 0-200 ms.
This behavior is consistent for both overwrite_files as True and False.
In the previous version (v2.20) I also used the same approach and had no
issues. Is there a newer way to do such a simulation paradigm?
I didn't find anything on this on the comparison page of NESTv2.x and
NESTv3.x
Am I missing something? It's really important for my work, I hope I could
find a solution.
--
Thanks and Regards
*Maryada*
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--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
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52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
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Prof. Dr. Frauke Melchior
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--
Thanks and Regards
*Maryada*
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
_______________________________________________
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To unsubscribe send an email to users-leave(a)nest-simulator.org