From ebea7cbebddc070a95707d02bb1f77409a8ea89b Mon Sep 17 00:00:00 2001 From: Sebastian Spreizer Date: Fri, 22 Dec 2023 14:46:20 +0100 Subject: [PATCH 1/3] Maintenance documentation for NEST Server and related projects (line length: 120 letters) --- doc/htmldoc/connect_nest/nest_server.rst | 359 ++++++++++------------- doc/htmldoc/related_projects.rst | 36 ++- 2 files changed, 174 insertions(+), 221 deletions(-) diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst index c873d93fc6..d47b0c699f 100644 --- a/doc/htmldoc/connect_nest/nest_server.rst +++ b/doc/htmldoc/connect_nest/nest_server.rst @@ -6,30 +6,20 @@ NEST Server What is NEST Server? -------------------- -NEST Server enables users to interact with the NEST simulation engine -via a RESTful API. Using this approach, you can perform the same basic -operations as with :ref:`PyNEST `, but -instead of doing so by directly importing the ``nest`` module, all -commands, including their arguments and result data, are channeled -through HTTP requests and responses over a TCP/IP connection. - -The main advantage of using NEST in this way is that it decouples the -*simulation backend* in the form of the NEST simulation kernel from the -*frontend*, i.e., the code that controls the simulation. In such a -scenario, only the backend (the *server*) depends on NEST, while the -frontend could really be anything that can talk HTTP. Under the hood, -NEST Server forwards the commands it receives to PyNEST, and sends -back the result data in response packets. - -NEST Server was initially developed as a backend for :doc:`NEST Desktop -`, a web-based graphical -frontend for NEST. With growing interest in a more general server -backend for NEST, the functionality of the original NEST Server was -extended to accommodate for this broader range of application. -Starting with NEST 3.0, the NEST Server was integrated into the main -source code repository of NEST to make it available to everyone in a -convenient way. +NEST Server enables users to interact with the NEST simulation engine via a RESTful API. Using this approach, you can +perform the same basic operations as with :ref:`PyNEST `, but instead of doing so by directly importing the +``nest`` module, all commands, including their arguments and result data, are channeled through HTTP requests and +responses over a TCP/IP connection. +The main advantage of using NEST in this way is that it decouples the *simulation backend* in the form of the NEST +simulation kernel from the *frontend*, i.e., the code that controls the simulation. In such a scenario, only the backend +(the *server*) depends on NEST, while the frontend could really be anything that can talk HTTP. Under the hood, NEST +Server forwards the commands it receives to PyNEST, and sends back the result data in response packets. + +NEST Server was initially developed as a backend for :doc:`NEST Desktop `, a web-based graphical frontend +for NEST. With growing interest in a more general server backend for NEST, the functionality of the original NEST Server +was extended to accommodate for this broader range of application. Starting with NEST 3.0, the NEST Server was +integrated into the main source code repository of NEST to make it available to everyone in a convenient way. Use cases for NEST Server ------------------------- @@ -39,98 +29,90 @@ Use cases for NEST Server :alt: NEST Server concept :width: 240px -NEST Server can be considered a language independent interface to NEST -that can be deployed either locally or on a remote machine. To give -you a better idea of what NEST Server is good for, here are some of -its main use cases. - -One scenario in which NEST Server comes in handy, is if you want to -work on your laptop, but run your NEST simulations on a machine with -higher performance or more memory, for instance, a big workstation or -computer cluster at your lab. For this, you would deploy NEST Server -on the remote machine, and use the :ref:`NEST Client ` -locally or write your own client using one of the recipes provided in -the :ref:`section on advanced applications `. - -:doc:`NEST Desktop `, the web-based -graphical user interface for NEST, uses NEST Server as its simulation -backend. It supports server instances running either locally or -remotely. More details about how to configure and run this setup can -be found in the documentation of NEST Desktop. - -Last but not least, the latest version of the `HBP Neurorobotic -Platform `_ use the NEST Server to run the -neuronal simulation as part of closed-loop robotic experiments. As it -has rather specific requirements on the client side, it uses a custom -client for the NEST Server instead of the generic one shipped with NEST. - -If you yourself have an interesting situation in which you use NEST -Server and would like to have it listed here, feel free to `drop us a -line `_. +NEST Server can be considered a language independent interface to NEST that can be deployed either locally or on a +remote machine. To give you a better idea of what NEST Server is good for, here are some of its main use cases. + +One scenario in which NEST Server comes in handy, is if you want to work on your laptop, but run your NEST simulations +on a machine with higher performance or more memory, for instance, a big workstation or computer cluster at your lab. +For this, you would deploy NEST Server on the remote machine, and use the :ref:`NEST Client ` locally or +write your own client using one of the recipes provided in the :ref:`section on advanced applications +`. + +:doc:`NEST Desktop `, the web-based graphical user interface for NEST, uses NEST Server as its simulation +backend. It supports server instances running either locally or remotely. More details about how to configure and run +this setup can be found in the documentation of NEST Desktop. + +Last but not least, the latest version of the `HBP Neurorobotic Platform `_ use the NEST +Server to run the neuronal simulation as part of closed-loop robotic experiments. As it has rather specific requirements +on the client side, it uses a custom client for the NEST Server instead of the generic one shipped with NEST. + +If you yourself have an interesting situation in which you use NEST Server and would like to have it listed here, feel +free to `drop us a line `_. Install and run NEST Server --------------------------- -NEST Server is included in all source code distributions of NEST and -consequently, also available in derived packages, our virtual -machine, and Docker images. +NEST Server is included in all source code distributions of NEST and consequently, also available in derived packages, +our virtual machine, and Docker images. -For native installations, the requirements can be simply installed via -``pip``:: +For native installations, the requirements can be simply installed via ``pip``:: pip3 install Flask Flask-Cors gunicorn RestrictedPython -or by installing the full NEST development environment in case you -prefer using ``conda``:: +or by installing the full NEST development environment in case you prefer using ``conda``:: cd conda env create -p conda/ conda activate conda/ -As an alternative to a native installation, NEST Server is available -from the NEST Docker image. Please check out the corresponding -:ref:`installation instructions ` for more details. +As an alternative to a native installation, NEST Server is available from the NEST Docker image. Please check out the +corresponding :ref:`installation instructions ` for more details. .. _sec_server_vars: Set environment variables for security options ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -NEST Server comes with a number of access restrictions that are meant to protect your -computer. After careful consideration, each of the restrictions can be disabled by setting -a corresponding environment variable. +NEST Server comes with a number of access restrictions that are meant to protect your computer. After careful +consideration, each of the restrictions can be disabled by setting a corresponding environment variable. + +* ``NEST_SERVER_DISABLE_AUTH``: By default, the NEST Server requires a NESTServerAuth tokens. Setting this variable to + ``1`` disables this restriction. A token is automatically created and printed to the console by NEST Server upon + start-up. If needed, a custom token can be set using the environment variable ``NEST_SERVER_ACCESS_TOKEN`` +* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see `CORS + `_). Other hosts can be explicitly allowed by supplying them + in the form `http://host_or_ip:*`` to this variable (By default: http://localhost:*). +* ``NEST_SERVER_ENABLE_EXEC_CALL``: By default, NEST Server only allows calls to its PyNEST-like API. If the use-case + requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT + THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION. +* ``NEST_SERVER_DISABLE_RESTRICTION``: By default, NEST Server runs all code passed to the ``/exec`` route through + RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. For increased security, + code passed in this way only allows explictly whitelisted modules to be imported. To import modules, the variable + ``NEST_SERVER_MODULES`` can be set to a standard Python import line like this: ``NEST_SERVER_MODULES='import nest; + import scipy as sp; from numpy import random'`` -* ``NEST_SERVER_DISABLE_AUTH``: By default, the NEST Server requires a NESTServerAuth tokens. Setting this variable to ``1`` disables this restriction. A token is automatically created and printed to the console by NEST Server upon start-up. If needed, a custom token can be set using the environment variable ``NEST_SERVER_ACCESS_TOKEN`` -* ``NEST_SERVER_CORS_ORIGINS``: By default, the NEST Server only allows requests from localhost (see `CORS `_). Other hosts can be explicitly allowed by supplying them in the form `http://host_or_ip`` to this variable. -* ``NEST_SERVER_ENABLE_EXEC_CALL``: By default, NEST Server only allows calls to its PyNEST-like API. If the use-case requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION. -* ``NEST_SERVER_DISABLE_RESTRICTION``: By default, NEST Server runs all code passed to the ``/exec`` route through RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. For increased security, code passed in this way only allows explictly whitelisted modules to be imported. To import modules, the variable ``NEST_SERVER_MODULES`` can be set to a standard Python import line like this: - ``NEST_SERVER_MODULES='import nest; import scipy as sp; from numpy import random'`` Run NEST Server ~~~~~~~~~~~~~~~ -All NEST Server operations are managed using the ``nest-server`` -command that can either be run directly: +All NEST Server operations are managed using the ``nest-server`` command that can either be run directly: .. code-block:: text nest-server start -or supplied to the execution command line for running the Docker -container: +or supplied to the execution command line for running the Docker container: .. code-block:: text docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -p 52425:52425 nest/nest-simulator:dev nest-server start -The generic invocation command line for the ``nest-server`` command -looks as follows: +The generic invocation command line for the ``nest-server`` command looks as follows: .. code-block:: text nest-server [-d] [-h ] [-o] [-p ] -Possible commands are ``start``, ``stop``, ``status``, or ``log``. The meaning -of the other arguments is as follows: +Possible commands are ``start``, ``stop``, ``status``, or ``log``. The meaning of the other arguments is as follows: -d Run NEST Server in the background (i.e., daemonize it) @@ -144,56 +126,43 @@ of the other arguments is as follows: Run with MPI ~~~~~~~~~~~~ -If NEST was compiled with support for :ref:`distributed computing via -MPI `, it will usually execute the exact same -simulation script on each of the :hxt_ref:`MPI` processes. With NEST Server, this -would normally mean that one NEST Server instance would be spawned for -each rank in a multi-process NEST simulation. To prevent this from -happening, we provide a special version of the NEST Server command for -use with MPI. It can be run as follows: +If NEST was compiled with support for :ref:`distributed computing via MPI `, it will usually +execute the exact same simulation script on each of the :hxt_ref:`MPI` processes. With NEST Server, this would normally +mean that one NEST Server instance would be spawned for each rank in a multi-process NEST simulation. To prevent this +from happening, we provide a special version of the NEST Server command for use with MPI. It can be run as follows: .. code-block:: text mpirun -np N nest-server-mpi [--host HOST] [--port PORT] -If run like this, the RESTful API of the NEST Server will only be -served by the :hxt_ref:`MPI` process with rank 0 (called the `master`), while all -other N-1 ranks will start the NEST Server in `worker` mode. Upon -receiving a request, the master relays all commands to the workers, -which execute them, collect all result data, and send it back to the -master. The master then receives and combines all worker responses, -and replies to the caller of the NEST Server API. +If run like this, the RESTful API of the NEST Server will only be served by the :hxt_ref:`MPI` process with rank 0 +(called the `master`), while all other N-1 ranks will start the NEST Server in `worker` mode. Upon receiving a request, +the master relays all commands to the workers, which execute them, collect all result data, and send it back to the +master. The master then receives and combines all worker responses, and replies to the caller of the NEST Server API. -The response data in such a distributed scenario looks almost -completely the same as one coming from the serial version of the NEST -Server. The only difference may be that information pertaining to -process-local data structures is being replaced by generic values. +The response data in such a distributed scenario looks almost completely the same as one coming from the serial version +of the NEST Server. The only difference may be that information pertaining to process-local data structures is being +replaced by generic values. .. _nest_client: The NEST Client --------------- -The easiest way to interact with the NEST Server is the `NEST Client` -provided in ``_. It can be used -either by directly starting a Python session in a clone of that -repository, or by installing it by running ``python3 setup.py -install`` therein. NEST itself does not have to be installed in order -to use the NEST Client. +The easiest way to interact with the NEST Server is the `NEST Client` provided in +``_. It can be used either by directly starting a Python session in a clone of +that repository, or by installing it by running ``python3 setup.py install`` therein. NEST itself does not have to be +installed in order to use the NEST Client. -Using a dynamic function mapping mechanism, the NEST Client supports -the same functions as PyNEST does. However, instead of directly -executing calls in NEST, it forwards them together with their -arguments to the NEST Server, which in turn executes them. To you as a -user, everything looks much like a typical simulation code for NEST -Simulator. +Using a dynamic function mapping mechanism, the NEST Client supports the same functions as PyNEST does. However, instead +of directly executing calls in NEST, it forwards them together with their arguments to the NEST Server, which in turn +executes them. To you as a user, everything looks much like a typical simulation code for NEST Simulator. Basic usage ~~~~~~~~~~~ -To give you an idea of the usage, the following table shows a -comparison of a typical simulation once for PyNEST and once using the -NEST Client. +To give you an idea of the usage, the following table shows a comparison of a typical simulation once for PyNEST and +once using the NEST Client. .. list-table:: @@ -251,11 +220,9 @@ NEST Client. Run scripts ~~~~~~~~~~~ -The NEST Client is able to send complete simulation scripts to -the NEST Server using the functions ``exec_script`` and ``from_file``. -The following listing shows a Python snippet using the NEST Server -Client to execute a simple script on the Server using the -``exec_script`` function: +The NEST Client is able to send complete simulation scripts to the NEST Server using the functions ``exec_script`` and +``from_file``. The following listing shows a Python snippet using the NEST Server Client to execute a simple script on +the Server using the ``exec_script`` function: .. code-block:: Python @@ -271,10 +238,8 @@ Client to execute a simple script on the Server using the models = response['data'] print(models) # the list of models -In a more realistic scenario, you probably already have your -simulation script stored in a file. Such scripts can be sent to the -NEST Server for execution using the ``from_file`` function provided by -the NEST Client. +In a more realistic scenario, you probably already have your simulation script stored in a file. Such scripts can be +sent to the NEST Server for execution using the ``from_file`` function provided by the NEST Client. .. code-block:: Python @@ -288,10 +253,9 @@ the NEST Client. .. note:: - By default, the NEST Server only imports the PyNEST module during - startup for security reasons. In case you require additional - Python modules for your simulation script, please see the section - on :ref:`security and modules ` below. + By default, the NEST Server only imports the PyNEST module during startup for security reasons. In case you require + additional Python modules for your simulation script, please see the section on :ref:`security and modules + ` below. NEST Client API @@ -303,18 +267,17 @@ NEST Client API .. py:method:: NESTClient.(*args, **kwargs) - Execute a PyNEST function ```` on the NEST Server; the - arguments ``args`` and ``kwargs`` will be forwarded to the function + Execute a PyNEST function ```` on the NEST Server; the arguments ``args`` and ``kwargs`` will be forwarded to + the function .. py:method:: NESTClient.exec_script(source, return_vars=None) - Execute a Python script on the NEST Server; the script has to be - given as a string in the ``source`` argument + Execute a Python script on the NEST Server; the script has to be given as a string in the ``source`` argument .. py:method:: NESTClient.from_file(filename, return_vars=None) - Execute a Python script on the NEST Server; the argument - ``filename`` is the name of the file in which the script is stored + Execute a Python script on the NEST Server; the argument ``filename`` is the name of the file in which the script is + stored REST API overview ----------------- @@ -344,9 +307,8 @@ REST API overview Low-level API usage ~~~~~~~~~~~~~~~~~~~ -The preferred command line tool for interacting with NEST Server using -a terminal is ``curl``. For more information, please visit the `curl -website `_. +The preferred command line tool for interacting with NEST Server using a terminal is ``curl``. For more information, +please visit the `curl website `_. To obtain basic information about the running server, run: @@ -380,27 +342,22 @@ Send API request with function arguments in JSON format: .. note:: - You can beautify the output of NEST Server by piping the output of - ``curl`` through the JSON processor ``jq``. A sample command line - to display the available functions in this way looks like this:: + You can beautify the output of NEST Server by piping the output of ``curl`` through the JSON processor ``jq``. A + sample command line to display the available functions in this way looks like this:: curl -s localhost:52425/api | jq -r . - For more information, check the `documentation on jq - `_. + For more information, check the `documentation on jq `_. API access from Python ~~~~~~~~~~~~~~~~~~~~~~ -If you prefer Python over ``curl``, you can use the ``requests`` module, -which provides a convenient API for communicating with RESTful APIs. -On most systems this is already installed or can be easily installed -using ``pip``. Extensive documentation is available on the pages about -`HTTP for Humans `_. +If you prefer Python over ``curl``, you can use the ``requests`` module, which provides a convenient API for +communicating with RESTful APIs. On most systems this is already installed or can be easily installed using ``pip``. +Extensive documentation is available on the pages about `HTTP for Humans `_. -Sending a simple request to the NEST Server using Python works as -follows: +Sending a simple request to the NEST Server using Python works as follows: .. code-block:: @@ -429,28 +386,22 @@ Create neurons in NEST and return a list of IDs for the new nodes:: Security considerations ----------------------- -As explained above, the ``/exec`` route of the NEST Server API allows -you to run custom Python scripts within the NEST Server context. This -can greatly simplify your workflow in situations where you already -have the simulation description in the form of a Python script. On the -technical side, however, this route exposes a potential risk -for the remote execution of malicious code. - -In order to protect the execution environment from such security -breaches, we execute all user supplied code in a `RestrictedPython -`_ trusted -environment. Consequently, this environment blocks -your scripts from importing additional Python modules, unless -they are explicitly safelisted during the start-up of NEST Server. - -To mark modules as safe for execution within NEST Server and make them -available to code from user supplied scripts that run through the ``/exec`` -route, a comma separated list of Python module names can be assigned -to the environment variable ``NEST_SERVER_MODULES`` prior to starting -the NEST Server. - -For instance, if your script requires NumPy in addition to PyNEST, the -command line for starting up the server would look like this: +As explained above, the ``/exec`` route of the NEST Server API allows you to run custom Python scripts within the NEST +Server context. This can greatly simplify your workflow in situations where you already have the simulation description +in the form of a Python script. On the technical side, however, this route exposes a potential risk for the remote +execution of malicious code. + +In order to protect the execution environment from such security breaches, we execute all user supplied code in a +`RestrictedPython `_ trusted environment. Consequently, this +environment blocks your scripts from importing additional Python modules, unless they are explicitly safelisted during +the start-up of NEST Server. + +To mark modules as safe for execution within NEST Server and make them available to code from user supplied scripts that +run through the ``/exec`` route, a comma separated list of Python module names can be assigned to the environment +variable ``NEST_SERVER_MODULES`` prior to starting the NEST Server. + +For instance, if your script requires NumPy in addition to PyNEST, the command line for starting up the server would +look like this: .. code-block:: sh @@ -468,23 +419,20 @@ After this, NumPy can be used from within scripts in the regular way: .. danger:: - Each modification to the default security settings of NEST Server - should be carefully evaluated on a case-by-case basis. + Each modification to the default security settings of NEST Server should be carefully evaluated on a case-by-case + basis. - We are aware that some simulation code might not work (well) in a - RestrictedPython environment. To support such codes, the security - features of NEST Server can be completely disabled by starting it - in the following way: + We are aware that some simulation code might not work (well) in a RestrictedPython environment. To support such + codes, the security features of NEST Server can be completely disabled by starting it in the following way: .. code-block:: sh export NEST_SERVER_RESTRICTION_OFF=true nest-server start - Please be aware that running NEST Server like this bears a high - risk of arbitrary remote code execution, and this mode of operation - should only be used in exceptional cases. We cannot provide - any support for problems arising from such a use of NEST Server. + Please be aware that running NEST Server like this bears a high risk of arbitrary remote code execution, and this + mode of operation should only be used in exceptional cases. We cannot provide any support for problems arising from + such a use of NEST Server. .. _nest_server_advanced: @@ -494,22 +442,35 @@ Advanced topics Run scripts in NEST Server using `curl` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -As shown above, you can send custom simulation code to -``localhost:52425/exec``. On the command line, this approach might be a -bit more challenging in the case your script does not fit on a single -line. For such situations, we recommend using a JSON file as input for -``curl``: +As shown above, you can send custom simulation code to ``localhost:52425/exec``. On the command line, this approach +might be a bit more challenging in the case your script does not fit on a single line. For such situations, we recommend +using a JSON file as input for ``curl``: .. code-block:: json { - "source": "import nest\n# Reset kernel\nnest.ResetKernel()\n# Create nodes\nparams = {'rate': 6500.}\npg = nest.Create('poisson_generator', 1, params)\nneurons = nest.Create('iaf_psc_alpha', 1000)\nsr = nest.Create('spike_recorder')\n# Connect nodes\nnest.Connect(pg, neurons, syn_spec={'weight': 10.})\nnest.Connect(neurons[::10], sr)\n# Simulate\nnest.Simulate(1000.0)\n# Get events\nn_events = nest.GetStatus(sr, 'n_events')[0]\nprint('Number of events:', n_events)\n", + "source": " + import nest\n + # Reset kernel\n + nest.ResetKernel()\n + # Create nodes\nparams = {'rate': 6500.}\n + pg = nest.Create('poisson_generator', 1, params)\n + neurons = nest.Create('iaf_psc_alpha', 1000)\n + sr = nest.Create('spike_recorder')\n + # Connect nodes\n + nest.Connect(pg, neurons, syn_spec={'weight': 10.})\n + nest.Connect(neurons[::10], sr)\n + # Simulate\n + nest.Simulate(1000.0)\n + # Get events\n + n_events = nest.GetStatus(sr, 'n_events')[0]\n + print('Number of events:', n_events)\n + ", "return": "n_events" } -If we assume that the above JSON object is stored in a file called -``simulation_script.json``, you can execute it using the following -command: +If we assume that the above JSON object is stored in a file called ``simulation_script.json``, you can execute it using +the following command: .. code-block:: sh @@ -519,12 +480,10 @@ command: Interact with NEST Server using JavaScript ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -As the NEST Server is built on modern web technologies, it may be -desirable to create a frontend to it in the form of a -website. In this context, JavaScript is the natural choice for the -client-side language as it is widely supported by all web browsers and -provides libraries for handling HTTP requests and responses out of the -box. Here is a small example showing the basic idea: +As the NEST Server is built on modern web technologies, it may be desirable to create a frontend to it in the form of a +website. In this context, JavaScript is the natural choice for the client-side language as it is widely supported by all +web browsers and provides libraries for handling HTTP requests and responses out of the box. Here is a small example +showing the basic idea: .. grid:: @@ -573,9 +532,8 @@ Using the above code, we can already send API-requests to NEST Server: getAPI('GetKernelStatus'); // the current kernel status dict -Sending API calls with data requires a POST request, which can handle -the data in JSON-format. To allow for this, we can define a function -with a callback for POST requests: +Sending API calls with data requires a POST request, which can handle the data in JSON-format. To allow for this, we can +define a function with a callback for POST requests: .. code-block:: JavaScript @@ -600,10 +558,9 @@ Using this function, sending an API-request to NEST Server becomes easy: // default values of iaf_psc_alpha postAPI('GetDefaults', {"model": "iaf_psc_alpha"}); -The third type of request we might want to make is sending a custom -Python script to NEST Server. As outlined above, this is supported by -the ``exec`` route. to make use of that, we define a function with -callback for POST requests to execute a script: +The third type of request we might want to make is sending a custom Python script to NEST Server. As outlined above, +this is supported by the ``exec`` route. to make use of that, we define a function with callback for POST requests to +execute a script: .. code-block:: JavaScript @@ -631,10 +588,8 @@ Now, we can send a custom Python script to NEST Server: .. note:: - A full HTML client for NEST Server based on the ideas outlined - above is available in the `nest-jsclient repository - `_ on the GitHub - account of Steffen Graber. + A full HTML client for NEST Server based on the ideas outlined above is available in the `nest-jsclient repository + `_ on the GitHub account of Steffen Graber. Control NEST from Bash ~~~~~~~~~~~~~~~~~~~~~~ diff --git a/doc/htmldoc/related_projects.rst b/doc/htmldoc/related_projects.rst index c69e2d8a85..1bcd309ab5 100644 --- a/doc/htmldoc/related_projects.rst +++ b/doc/htmldoc/related_projects.rst @@ -8,23 +8,20 @@ biologically realistic neural networks. Here you can find further information about some of these projects. - NESTML ------ :doc:`NESTML ` allows you to modify and create models for NEST in a simplified format. -It is a domain-specific language that supports the specification of neuron and synapse -models in a precise and concise syntax, based on the syntax of Python. Model equations can either be given as a simple -string of mathematical notation or as an algorithm written in the built-in procedural language. The equations are -analyzed by the associated toolchain, written in Python, to compute an exact solution if possible or use an appropriate -numeric solver otherwise. +It is a domain-specific language that supports the specification of neuron and synapse models in a precise and concise +syntax, based on the syntax of Python. Model equations can either be given as a simple string of mathematical notation +or as an algorithm written in the built-in procedural language. The equations are analyzed by the associated toolchain, +written in Python, to compute an exact solution if possible or use an appropriate numeric solver otherwise. * :doc:`Get started with NESTML ` * :doc:`List of available models ` - NEST extension module --------------------- @@ -33,18 +30,19 @@ without messing with the source code of NEST itself. It makes sharing custom ext * :doc:`Get started with the extension module ` -NEST desktop +NEST Desktop ------------ -:doc:`NEST Desktop ` is a web-based GUI application for the NEST Simulator. -The app enables the rapid construction, parametrization, and instrumentation of neuronal network models. +:doc:`NEST Desktop ` is a web-based GUI application for the NEST Simulator. The app enables the rapid +construction, parametrization, and instrumentation of neuronal network models. * :doc:`Get started with NEST desktop ` NEST GPU -------- -NEST GPU is a GPU-MPI library for simulation of large-scale networks of spiking neurons. It can be used in Python, in C++ and in C. +NEST GPU is a GPU-MPI library for simulation of large-scale networks of spiking neurons. It can be used in Python, in +C++ and in C. * :doc:`Get started with NEST GPU ` @@ -62,8 +60,8 @@ number of neuromorphic hardware systems. Elephant -------- -:doc:`Elephant (Electrophysiology Analysis Toolkit) ` is an open-source, community-centered -library for the analysis of electrophysiological data in the Python programming language. +:doc:`Elephant (Electrophysiology Analysis Toolkit) ` is an open-source, community-centered library for +the analysis of electrophysiological data in the Python programming language. * :doc:`Get started with Elephant ` @@ -80,10 +78,10 @@ multi-compartment, morphologically-detailed cells, from single cell models to ve Neuromorphic hardware --------------------- -:doc:`SpiNNaker and BrainScaleS ` are neuromorphic computing systems, which enable -energy-efficient, large-scale neuronal network simulations with simplified spiking neuron models. -The BrainScaleS system is based on physical (analog) emulations of neuron models and offers highly accelerated -operation (:math:`10^4` x real time). The SpiNNaker system is based on a digital many-core architecture and provides +:doc:`SpiNNaker and BrainScaleS ` are neuromorphic computing systems, which enable energy-efficient, +large-scale neuronal network simulations with simplified spiking neuron models. The BrainScaleS system is based on +physical (analog) emulations of neuron models and offers highly accelerated operation (:math:`10^4` x real time). The +SpiNNaker system is based on a digital many-core architecture and provides real-time operation. * :doc:`Get started with SpiNNaker ` @@ -92,8 +90,8 @@ real-time operation. TheVirtualBrain (TVB) --------------------- -:ref:`TVB ` is a framework for the simulation of the dynamics of large-scale brain -networks with biologically realistic connectivity. +:ref:`TVB ` is a framework for the simulation of the dynamics of large-scale brain networks with +biologically realistic connectivity. * :ref:`Get started with TVB ` From d4a940e26716910d507c55e070db7a71cf96ecb8 Mon Sep 17 00:00:00 2001 From: Sebastian Spreizer Date: Mon, 11 Mar 2024 12:22:12 +0100 Subject: [PATCH 2/3] Update 5th list point for env variable --- doc/htmldoc/connect_nest/nest_server.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst index d47b0c699f..131453be37 100644 --- a/doc/htmldoc/connect_nest/nest_server.rst +++ b/doc/htmldoc/connect_nest/nest_server.rst @@ -87,9 +87,9 @@ consideration, each of the restrictions can be disabled by setting a correspondi THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION. * ``NEST_SERVER_DISABLE_RESTRICTION``: By default, NEST Server runs all code passed to the ``/exec`` route through RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. For increased security, - code passed in this way only allows explictly whitelisted modules to be imported. To import modules, the variable - ``NEST_SERVER_MODULES`` can be set to a standard Python import line like this: ``NEST_SERVER_MODULES='import nest; - import scipy as sp; from numpy import random'`` + code passed in this way only allows explictly whitelisted modules to be imported. +* ``NEST_SERVER_MODULES``: To import modules, the variable can be set to a standard Python import line like this: + ``NEST_SERVER_MODULES='import nest; import scipy as sp; from numpy import random'`` Run NEST Server ~~~~~~~~~~~~~~~ From b9ab027e7323f554d9ed83895bf4253dd4dc0bb0 Mon Sep 17 00:00:00 2001 From: Sebastian Spreizer Date: Mon, 11 Mar 2024 12:24:08 +0100 Subject: [PATCH 3/3] Update 5th list point for env variable --- doc/htmldoc/connect_nest/nest_server.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/htmldoc/connect_nest/nest_server.rst b/doc/htmldoc/connect_nest/nest_server.rst index 131453be37..45f4782222 100644 --- a/doc/htmldoc/connect_nest/nest_server.rst +++ b/doc/htmldoc/connect_nest/nest_server.rst @@ -86,9 +86,9 @@ consideration, each of the restrictions can be disabled by setting a correspondi requires the execution of scripts via the ``/exec`` route, this variable can be set to ``1``. PLEASE BE AWARE THAT THIS OPENS YOUR COMPUTER TO REMOTE CODE EXECUTION. * ``NEST_SERVER_DISABLE_RESTRICTION``: By default, NEST Server runs all code passed to the ``/exec`` route through - RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. For increased security, - code passed in this way only allows explictly whitelisted modules to be imported. -* ``NEST_SERVER_MODULES``: To import modules, the variable can be set to a standard Python import line like this: + RestrictedPython to sanitize it. To disable this mechanism, this variable can be set to ``1``. +* ``NEST_SERVER_MODULES``: For increased security, code passed in this way only allows explictly whitelisted modules to + be imported. To import modules, the variable can be set to a standard Python import line like this: ``NEST_SERVER_MODULES='import nest; import scipy as sp; from numpy import random'`` Run NEST Server