13 Jan
2023
13 Jan
'23
2:38 p.m.
I would like to install a custom neuron model in NEST so I followed the instructions for
the nest-extension-module. It is able to build the .so files but it errors during the
final install of the project as seen in the below message.
Install the project...
-- Install configuration: ""
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py",
line 444
err = AttributeError(f"Cannot set attribute '{attr}' on module
'nest'")
I am trying to install one of the example neurons provided first (pif_psc_alpha) so I do
not expect that it is an issue within the source files. Thanks for any advice in
correcting this issue!
13 Jan
13 Jan
2:40 p.m.
Hi,
This is not addressing your actual question, but I just wanted to check whether you know
about NESTML for writing custom neuron models (https://nestml.readthedocs.org/) and
whether there were any reasons you might prefer to write the model "by hand" in
C++ (there certainly might be! Just curious.)
With kind regards,
Charl
On Fri, Jan 13, 2023, at 14:38, bstrohmer(a)gmail.com wrote:
I would like to install a custom neuron model in NEST
so I followed the
instructions for the nest-extension-module. It is able to build the .so
files but it errors during the final install of the project as seen in
the below message.
Install the project...
-- Install configuration: ""
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py",
line 444
err = AttributeError(f"Cannot set attribute '{attr}' on module
'nest'")
I am trying to install one of the example neurons provided first
(pif_psc_alpha) so I do not expect that it is an issue within the
source files. Thanks for any advice in correcting this issue!
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
2:45 p.m.
Hi Charl, Yes, I actually started out in NESTML and was able to integrate a
new neuron model in NEST so it worked really well. Unfortunately, I need to
add gap junction support to my neuron model which is why I was forced to
code "by hand".
On Fri, Jan 13, 2023 at 2:41 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
This is not addressing your actual question, but I just wanted to check
whether you know about NESTML for writing custom neuron models (
https://nestml.readthedocs.org/) and whether there were any reasons you
might prefer to write the model "by hand" in C++ (there certainly might be!
Just curious.)
With kind regards,
Charl
On Fri, Jan 13, 2023, at 14:38, bstrohmer(a)gmail.com wrote:
I would like to install a custom neuron model in
NEST so I followed the
instructions for the nest-extension-module. It is able to build the .so
files but it errors during the final install of the project as seen in
the below message.
Install the project...
-- Install configuration: ""
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py",
line 444
err = AttributeError(f"Cannot set attribute '{attr}' on module
'nest'")
I am trying to install one of the example neurons provided first
(pif_psc_alpha) so I do not expect that it is an issue within the
source files. Thanks for any advice in correcting this issue!
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
2:50 p.m.
Ah, OK, understood! In case you find you need to add a small bit of custom C++ code to an
otherwise "standard" NESTML neuron model, you could also add this into the Jinja
templates, optionally with an extra clause like {% if neuronName ==
"my_custom_neuron_model" %} ... {% endif %}. Optionally you can make a copy of
the default templates and specify the paths to the customized copy via the mechanism
described at
https://nestml.readthedocs.io/en/latest/extending.html#running-nestml-with-…
Please let me know in case you run into any trouble should you decide to give this
approach a chance.
On Fri, Jan 13, 2023, at 14:45, Beck Strohmer wrote:
Hi Charl, Yes, I actually started out in NESTML and
was able to integrate a new neuron model in NEST so it worked really well. Unfortunately,
I need to add gap junction support to my neuron model which is why I was forced to code
"by hand".
On Fri, Jan 13, 2023 at 2:41 PM Charl Linssen <nest-users(a)turingbirds.com> wrote:
Hi,
This is not addressing your actual question, but I just wanted to check whether you know
about NESTML for writing custom neuron models (https://nestml.readthedocs.org/) and
whether there were any reasons you might prefer to write the model "by hand" in
C++ (there certainly might be! Just curious.)
With kind regards,
Charl
On Fri, Jan 13, 2023, at 14:38, bstrohmer(a)gmail.com wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
I would like to install a custom neuron model in
NEST so I followed the
instructions for the nest-extension-module. It is able to build the .so
files but it errors during the final install of the project as seen in
the below message.
Install the project...
-- Install configuration: ""
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py",
line 444
err = AttributeError(f"Cannot set attribute '{attr}' on module
'nest'")
I am trying to install one of the example neurons provided first
(pif_psc_alpha) so I do not expect that it is an issue within the
source files. Thanks for any advice in correcting this issue!
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org 
3:03 p.m.
Dear bstrohmer(a)gmail.com,
which version of NEST are you using and from where (release? git?),
which are the "instructions" you followed (links!) and what is the
sequence of commands leading to this error (bash/Python)?
Please be more specific. Right now, your inquiry reads like "I did
something and it did not work. Help!" and I am afraid, we can't help you
much with just the information you provided.
Cheers,
Jochen!
On 13.01.23 14:38, bstrohmer(a)gmail.com wrote:
I would like to install a custom neuron model in NEST
so I followed the instructions for the nest-extension-module. It is able to build the .so
files but it errors during the final install of the project as seen in the below message.
Install the project...
-- Install configuration: ""
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/include/piftestmodule/pif_psc_alpha.h
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/piftestmodule.so
-- Installing:
/home/bs/git_repos/extension/nest-simulator/result/lib/nest/libpiftestmodule.so
Traceback (most recent call last):
File "<string>", line 1, in <module>
File
"/home/bs/git_repos/extension/nest-simulator/result/lib/python3.8/site-packages/nest/__init__.py",
line 444
err = AttributeError(f"Cannot set attribute '{attr}' on module
'nest'")
I am trying to install one of the example neurons provided first (pif_psc_alpha) so I do
not expect that it is an issue within the source files. Thanks for any advice in
correcting this issue!
_______________________________________________
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 (he/him)
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
4:16 p.m.
Hi Jochen, thanks for the response. I am using NEST 3.3 on Ubuntu 20.04.5 LTS which I
installed from the command line (sudo apt-get install nest). However, when I build the
nest-extension-module code it installs a fresh version of NEST from git (git clone
https://github.com/nest/nest-simulator.git). I have followed the README from the extension
module git (https://github.com/nest/nest-extension-module/). I cloned the repository to my
local machine and then updated the CMakeLists.txt files in the outermost directory to have
a unique short name for the module as well as read from the pif_psc_alpha.h file for the
MODULE_HEADER. Finally, I updated the CMakeLists.txt in the src directory so that it only
has one source (pif_psc_alpha.cpp pif_psc_alpha.h). These are the only changes that I make
to the provided files. After this I run ./build.sh from the terminal, this installs the
fresh NEST installation as mentioned above and it builds the .so files but errors on the
installation. Let me know if I can provide any other details. Thanks!
4:17 p.m.
SOLVED! I was running a different NEST simulation and accidentally called the simulation
with python sim.py instead of python3 and it threw me the same error. I then saw that
'python' is used in the build.sh file so I replaced it with 'python3' and
it worked. Thanks for taking the time to write to me and I hope if anyone else has this
issue with python versioning, this thread might help. :)
708
days inactive
708
days old
6 comments
4 participants
participants (4)
-
Beck Strohmer -
bstrohmer＠gmail.com
-
Charl Linssen -
Jochen Martin Eppler