30 Nov
2021
30 Nov
'21
9:13 a.m.
Dear Maryada,
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 it’s 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 in 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:
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:
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
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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--
Thanks and Regards
*Maryada*
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