Hi Jochen, 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. 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.

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.

On Mon, Nov 29, 2021 at 10:24 PM Jochen Martin Eppler < j.eppler@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:

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*

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

​

-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653

---

Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation

---

---

Forschungszentrum Juelich GmbH 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), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior

---

---

---

NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org

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@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:

...

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*


_______________________________________________
NEST Users mailing list --users@nest-simulator.org
To unsubscribe send an email tousers-leave@nest-simulator.org

​

-- 
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation



------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
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),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht,
Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org

-- Thanks and Regards

*Maryada*

---

NEST Users mailing list --users@nest-simulator.org To unsubscribe send an email tousers-leave@nest-simulator.org

​

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.

Already working on it :-)

Cheers, Jochen!

On Tue, Nov 30, 2021 at 9:36 AM Jochen Martin Eppler j.eppler@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@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:

...

    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*


    _______________________________________________
    NEST Users mailing list --users@nest-simulator.org
    To unsubscribe send an email tousers-leave@nest-simulator.org

    ​

    -- 
    Dr. Jochen Martin Eppler
    Phone: +49(2461)61-96653
    ----------------------------------
    Simulation Laboratory Neuroscience
    Jülich Supercomputing Centre
    Institute for Advanced Simulation



    ------------------------------------------------------------------------------------------------
    ------------------------------------------------------------------------------------------------
    Forschungszentrum Juelich GmbH
    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),
    Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid
    Lambrecht,
    Prof. Dr. Frauke Melchior
    ------------------------------------------------------------------------------------------------
    ------------------------------------------------------------------------------------------------

    _______________________________________________
    NEST Users mailing list -- users@nest-simulator.org
    To unsubscribe send an email to users-leave@nest-simulator.org



-- 
Thanks and Regards

*Maryada*


_______________________________________________
NEST Users mailing list --users@nest-simulator.org
To unsubscribe send an email tousers-leave@nest-simulator.org

​

-- 
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation

_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org

-- Thanks and Regards

*Maryada*

---

NEST Users mailing list --users@nest-simulator.org To unsubscribe send an email tousers-leave@nest-simulator.org

Hi Robin!

We consciously decided against that many many times to avoid a fat interface and ending up in a situation where we have to maintain hundreds of special functions in our interfaces (C++, Python, SLI). I mean, where would you stop? Input_SD.events["times"] could be get_spike_times(), Input_SD.events could be get_events(), and so on... Performing "function calls" via SetStatus is an easy way of achieving a minimal and maintainable interface and I have not yet seen an easier way to achieve the same. I am, however, open to suggestions!

On this specific topic, the documentation should definitely improved, though.

Cheers, Jochen!

On 30.11.21 12:04, Robin Gilbert De Schepper wrote:

As an aside, if `Input_SD.n_events = 0` is the canonical way of clearing a spike recorder, maybe a `clear` function could be added. That's a bit easier to document and find?

On Mon, 29 Nov 2021, 22:24 Jochen Martin Eppler, j.eppler@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:

...

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*


_______________________________________________
NEST Users mailing list --users@nest-simulator.org
To unsubscribe send an email tousers-leave@nest-simulator.org

​

-- 
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation



------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
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),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Astrid Lambrecht,
Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org

---

NEST Users mailing list --users@nest-simulator.org To unsubscribe send an email tousers-leave@nest-simulator.org