From 3846baf8a573ffe0bf26d9801a4620bc73673c3e Mon Sep 17 00:00:00 2001 From: Dylan Daniels Date: Wed, 28 Aug 2024 06:45:24 -0400 Subject: [PATCH 1/4] add virtual sign in option --- workshop-instructions/instructions.html | 7 +++++++ workshop-instructions/instructions.md | 9 +++++++++ 2 files changed, 16 insertions(+) diff --git a/workshop-instructions/instructions.html b/workshop-instructions/instructions.html index d90e4d4..9aaad34 100644 --- a/workshop-instructions/instructions.html +++ b/workshop-instructions/instructions.html @@ -88,6 +88,7 @@

Table of Contents

+

Workshop Sign-In (Optional but Encouraged)

+

Please consider ‘signing in’ to the workshop by providing your institution/location, position, and field of study. This information is used in reporting on milestones for the grants that continue to fund our dissemination and development. We don’t ask for name or email, and the form should take no more than 30 seconds to complete.

+

Click here to navigate to our Virtual Sign-In Form.

+

+Thanks for your support. 😁 +

Cloning the HNN-Data Repository

To follow along with the workshop, you’ll need the hnn-data repository on your local machine / virtual environment.

You can download the file here or you can run the following command to clone the repository.

diff --git a/workshop-instructions/instructions.md b/workshop-instructions/instructions.md index 31494f1..bda7d63 100644 --- a/workshop-instructions/instructions.md +++ b/workshop-instructions/instructions.md @@ -1,5 +1,6 @@ **Table of Contents** +- [Workshop Sign-In (Optional but Encouraged)](#workshop-sign-in-optional-but-encouraged) - [Cloning the HNN-Data Repository](#cloning-the-hnn-data-repository) - [Preferred Installation Method: Google CoLab](#preferred-installation-method-google-colab) - [Alternative Installation Methods](#alternative-installation-methods) @@ -14,6 +15,14 @@ - [Installing MPI for Parallel Simulations](#installing-mpi-for-parallel-simulations) - [Launch the GUI](#launch-the-gui) +# Workshop Sign-In (Optional but Encouraged) + +Please consider 'signing in' to the workshop by providing your institution/location, position, and field of study. This information is used in reporting on milestones for the grants that continue to fund our dissemination and development. We don't ask for name or email, and the form should take no more than 30 seconds to complete. + +Click [here](https://forms.gle/YnZX9ZRm8WvWpAGU7) to navigate to our Virtual Sign-In Form. + +

Thanks for your support. 😁

+ # Cloning the HNN-Data Repository To follow along with the workshop, you'll need the [hnn-data repository](https://github.com/jonescompneurolab/hnn-data) on your local machine / virtual environment. From 9a34ecd899cf700195ed5d9f634541f86b1b3b02 Mon Sep 17 00:00:00 2001 From: Dylan Daniels Date: Wed, 28 Aug 2024 07:47:19 -0400 Subject: [PATCH 2/4] swap colab link --- workshop-instructions/instructions.html | 2 +- workshop-instructions/instructions.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workshop-instructions/instructions.html b/workshop-instructions/instructions.html index 9aaad34..78a0e55 100644 --- a/workshop-instructions/instructions.html +++ b/workshop-instructions/instructions.html @@ -124,7 +124,7 @@

Cloning the HNN-Data Repository

git pull

Preferred Installation Method: Google CoLab

This installation method is the quickest way to get up and running with the HNN-Core GUI, though it does require a Google Account. If you do not have a Google account, you can either create one for free to run the notebook, or try one of the other installation methods listed below.

-

We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up.

+

We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up.

Alternative Installation Methods

Warning: You may experience considerable lag in navigating the virtual desktop environment if you do not have a strong WiFi connection. If you experience this issue, we encourage you to try one of the other installation methods here to get started.

Oscar On Demand (OOD) Virtual Desktop

diff --git a/workshop-instructions/instructions.md b/workshop-instructions/instructions.md index bda7d63..9fe0169 100644 --- a/workshop-instructions/instructions.md +++ b/workshop-instructions/instructions.md @@ -44,7 +44,7 @@ git pull This installation method is the quickest way to get up and running with the HNN-Core GUI, though it does require a Google Account. If you do not have a Google account, you can either create one for free to run the notebook, or try one of the other installation methods listed below. -We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up. +We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up. # Alternative Installation Methods From 0fe0ef2efaa66b47d39be4ddb65f38dac5afc2ef Mon Sep 17 00:00:00 2001 From: Dylan Daniels Date: Wed, 28 Aug 2024 07:57:27 -0400 Subject: [PATCH 3/4] update instructions for downloading workshop materials. --- workshop-instructions/instructions.html | 70 +++++++++++++------------ workshop-instructions/instructions.md | 21 ++++---- 2 files changed, 48 insertions(+), 43 deletions(-) diff --git a/workshop-instructions/instructions.html b/workshop-instructions/instructions.html index 78a0e55..ba960ec 100644 --- a/workshop-instructions/instructions.html +++ b/workshop-instructions/instructions.html @@ -89,7 +89,7 @@

Table of Contents

  • Workshop Sign-In (Optional but Encouraged)
    • -
  • Cloning the HNN-Data Repository
    • +
  • Download Workshop Materials
  • Preferred Installation Method: Google CoLab
  • Alternative Installation Methods
      @@ -115,13 +115,17 @@

      Workshop Sign-In (Optional but

      Thanks for your support. 😁

      -

      Cloning the HNN-Data Repository

      -

      To follow along with the workshop, you’ll need the hnn-data repository on your local machine / virtual environment.

      -

      You can download the file here or you can run the following command to clone the repository.

      -
      git clone https://github.com/jonescompneurolab/hnn-data.git
      -

      If you already cloned the hnn-data repository on your machine, be sure to update it to include the latest changes.

      -
      cd hnn-data
-git pull
      +

      Download Workshop Materials

      +

      To follow along with the workshop, you’ll need to download the following materials:

      + +

      Click here to download the hnn-data folder, and here to download the hnn-workshop-materials folder.

      +

      Altenatively, you can clone the repositores with the follwing commands.

      +
      git clone https://github.com/jonescompneurolab/hnn-data.git
+git clone https://github.com/jasmainak/hnn-workshop-materials.git
      +

      If you’ve already cloned the repositories in the past, be sure to run git pull to download the latest updates.

      Preferred Installation Method: Google CoLab

      This installation method is the quickest way to get up and running with the HNN-Core GUI, though it does require a Google Account. If you do not have a Google account, you can either create one for free to run the notebook, or try one of the other installation methods listed below.

      We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up.

      @@ -176,49 +180,49 @@

      Launching the Desktop App on OscarLaunching HNN-Core GUI via Oscar

      With the Oscar desktop instance open, launch a Terminal via the “Terminal Emulator” at the bottom of the Desktop or via the Applications drop-down at the top-left of the Desktop.

      Type the following into the terminal to activate the environment.

      -
      module purge
-module load python/3.11
-module load  hpcx-mpi/4.1.5rc2
-source /oscar/data/ccv_workshop/hnn_env/bin/activate
      +
      module purge
+module load python/3.11
+module load  hpcx-mpi/4.1.5rc2
+source /oscar/data/ccv_workshop/hnn_env/bin/activate

      Within the same terminal with the hnn_env activated, type the following to launch the GUI.

      -
      hnn-gui
      +
      hnn-gui

      Launching HNN-Core (Python) via Oscar

      From the Oscar virtual desktop, open a new terminal and run the following commands.

      -
      module purge
-module load python/3.11
-module load  hpcx-mpi/4.1.5rc2
-source /oscar/data/ccv_workshop/hnn_env/bin/activate
-
-git clone https://github.com/jasmainak/hnn-workshop-materials.git
-cd hnn-workshop-materials/
-jupyter lab # or `jupyter notebook` alternatively
      +
      module purge
+module load python/3.11
+module load  hpcx-mpi/4.1.5rc2
+source /oscar/data/ccv_workshop/hnn_env/bin/activate
+
+git clone https://github.com/jasmainak/hnn-workshop-materials.git
+cd hnn-workshop-materials/
+jupyter lab # or `jupyter notebook` alternatively

      Installing HNN-Core GUI on Your Local Machine without Conda

      You can easily install HNN-Core GUI on your local machine with pip.

      To do so, open a Terminal and and enter the following command:

      For bash/Powershell

      -
      pip install --pre hnn-core[gui]
      +
      pip install --pre hnn-core[gui]

      For zsh

      -
      pip install --pre hnn-core'[gui]'
      +
      pip install --pre hnn-core'[gui]'

      Once installed, you can launch the GUI with the following command.

      -
      hnn-gui
      +
      hnn-gui

      Note that you will not be able to utilize the MPI backend to run simulation in parallel without also installing MPI on your machine. We recommend using the Conda install method below if you would like to utilize MPI, as it significantly streamlines the MPI setup process.

      For our workshops, we will be running simulations with only a few trials at most, and so MPI is not strictly necessary to keep up with the materials.

      Installing HNN-Core GUI on Your Local Machine via Conda

      Creating a Conda Env and Installing Dependencies

      Note: We recommend using use Windows Subsystem for Linux (WSL) to run HNN on Windows machines. Installation instructions can be found here

      Start by creating a new conda environment. We recommend creating an environment with the fewest number of dependencies to speed up the installation process.

      -
      conda create --name hnn_core_gui python=3.11 --no-default-packages
-conda activate hnn_core_gui
-pip install --pre hnn-core[gui]
      +
      conda create --name hnn_core_gui python=3.11 --no-default-packages
+conda activate hnn_core_gui
+pip install --pre hnn-core[gui]

      Installing MPI for Parallel Simulations

      To run simulations in parallel across multiple cores, which dramatically speeds up siuations, you’ll need to set up the MPI backend.

      -
      conda activate hnn_core_gui # activate the environment if needed
-conda install -y openmpi mpi4py
-pip install psutil
      +
      conda activate hnn_core_gui # activate the environment if needed
+conda install -y openmpi mpi4py
+pip install psutil

      Additionally, for MacOS, run the following command.

      -
      export DYLD_FALLBACK_LIBRARY_PATH=${CONDA_PREFIX}/lib
      +
      export DYLD_FALLBACK_LIBRARY_PATH=${CONDA_PREFIX}/lib

      More detailedd instructions are available on our parallel backends page.

      Launch the GUI

      You can now launch the GUI from within your conda environemnt.

      -
      conda activate hnn_core_gui # activate the environment if needed
-hnn-gui
      +
      conda activate hnn_core_gui # activate the environment if needed
+hnn-gui
      diff --git a/workshop-instructions/instructions.md b/workshop-instructions/instructions.md index 9fe0169..34ab068 100644 --- a/workshop-instructions/instructions.md +++ b/workshop-instructions/instructions.md @@ -1,7 +1,7 @@ **Table of Contents** - [Workshop Sign-In (Optional but Encouraged)](#workshop-sign-in-optional-but-encouraged) -- [Cloning the HNN-Data Repository](#cloning-the-hnn-data-repository) +- [Download Workshop Materials](#download-workshop-materials) - [Preferred Installation Method: Google CoLab](#preferred-installation-method-google-colab) - [Alternative Installation Methods](#alternative-installation-methods) - [Oscar On Demand (OOD) Virtual Desktop](#oscar-on-demand-ood-virtual-desktop) @@ -24,22 +24,23 @@ Click [here](https://forms.gle/YnZX9ZRm8WvWpAGU7) to navigate to our Virtual Sig

      Thanks for your support. 😁

      -# Cloning the HNN-Data Repository -To follow along with the workshop, you'll need the [hnn-data repository](https://github.com/jonescompneurolab/hnn-data) on your local machine / virtual environment. +# Download Workshop Materials +To follow along with the workshop, you'll need to download the following materials: -You can download the file [here](https://github.com/jonescompneurolab/hnn-data/archive/refs/heads/main.zip) or you can run the following command to clone the repository. +- The [hnn-data repository](https://github.com/jonescompneurolab/hnn-data) (needed for the HNN-Core GUI tutorial) +- The [hnn-workshop-materials repository](https://github.com/jasmainak/hnn-workshop-materials/tree/biomag_2024) (needed for the HNN-Core Python tutorial) -```bash -git clone https://github.com/jonescompneurolab/hnn-data.git -``` +Click [here](https://github.com/jonescompneurolab/hnn-data/archive/refs/heads/main.zip) to download the hnn-data folder, and [here](https://github.com/jasmainak/hnn-workshop-materials/archive/refs/heads/biomag_2024.zip) to download the hnn-workshop-materials folder. -If you already cloned the hnn-data repository on your machine, be sure to update it to include the latest changes. +Altenatively, you can clone the repositores with the follwing commands. ```bash -cd hnn-data -git pull +git clone https://github.com/jonescompneurolab/hnn-data.git +git clone https://github.com/jasmainak/hnn-workshop-materials.git ``` +If you've already cloned the repositories in the past, be sure to run `git pull` to download the latest updates. + # Preferred Installation Method: Google CoLab This installation method is the quickest way to get up and running with the HNN-Core GUI, though it does require a Google Account. If you do not have a Google account, you can either create one for free to run the notebook, or try one of the other installation methods listed below. From 41077517853a29a20b36798c43ea7a6d1e34b6c8 Mon Sep 17 00:00:00 2001 From: Dylan Daniels Date: Wed, 28 Aug 2024 08:37:27 -0400 Subject: [PATCH 4/4] some reworks to the sections --- workshop-instructions/instructions.html | 25 +++++++++++++------------ workshop-instructions/instructions.md | 21 ++++++++++++--------- 2 files changed, 25 insertions(+), 21 deletions(-) diff --git a/workshop-instructions/instructions.html b/workshop-instructions/instructions.html index ba960ec..e8fc8bd 100644 --- a/workshop-instructions/instructions.html +++ b/workshop-instructions/instructions.html @@ -89,7 +89,11 @@

      Table of Contents

      • Workshop Sign-In (Optional but Encouraged)
        • -
      • Download Workshop Materials
        • +
      • Workshop Materials +
      • Preferred Installation Method: Google CoLab
      • Alternative Installation Methods
          @@ -115,17 +119,14 @@

          Workshop Sign-In (Optional but

          Thanks for your support. 😁

          -

          Download Workshop Materials

          -

          To follow along with the workshop, you’ll need to download the following materials:

          - -

          Click here to download the hnn-data folder, and here to download the hnn-workshop-materials folder.

          -

          Altenatively, you can clone the repositores with the follwing commands.

          -
          git clone https://github.com/jonescompneurolab/hnn-data.git
-git clone https://github.com/jasmainak/hnn-workshop-materials.git
          -

          If you’ve already cloned the repositories in the past, be sure to run git pull to download the latest updates.

          +

          Workshop Materials

          +

          HNN-Core GUI Tutorial

          +

          This section of the workshop will require you to use HNN-Core GUI. See the sections below outlining the different installation methods available for getting started with the GUI.

          +

          To follow along with the workshop, you’ll also need to clone or download the hnn-data repository.

          +

          Click here to download the hnn-data folder directly. Altenatively, you can clone the repository with the follwing command.

          +
          git clone https://github.com/jonescompneurolab/hnn-data.git
          +

          HNN-Core Python Tutorial

          +

          The HNN-Core Python tutorial will utilize the following Google CoLab notebook, which can also be downloaded as an .ipynb file and run locally: hnn-workshop-materials

          Preferred Installation Method: Google CoLab

          This installation method is the quickest way to get up and running with the HNN-Core GUI, though it does require a Google Account. If you do not have a Google account, you can either create one for free to run the notebook, or try one of the other installation methods listed below.

          We have created a Google CoLab notebook that allows you to run the HNN-Core GUI out of your browser, with access to your local filesystem. Click here to open the notebook, which includes instructions on how to get set up.

          diff --git a/workshop-instructions/instructions.md b/workshop-instructions/instructions.md index 34ab068..951c215 100644 --- a/workshop-instructions/instructions.md +++ b/workshop-instructions/instructions.md @@ -1,7 +1,9 @@ **Table of Contents** - [Workshop Sign-In (Optional but Encouraged)](#workshop-sign-in-optional-but-encouraged) -- [Download Workshop Materials](#download-workshop-materials) +- [Workshop Materials](#workshop-materials) + - [HNN-Core GUI Tutorial](#hnn-core-gui-tutorial) + - [HNN-Core Python Tutorial](#hnn-core-python-tutorial) - [Preferred Installation Method: Google CoLab](#preferred-installation-method-google-colab) - [Alternative Installation Methods](#alternative-installation-methods) - [Oscar On Demand (OOD) Virtual Desktop](#oscar-on-demand-ood-virtual-desktop) @@ -24,22 +26,23 @@ Click [here](https://forms.gle/YnZX9ZRm8WvWpAGU7) to navigate to our Virtual Sig

          Thanks for your support. 😁

          -# Download Workshop Materials -To follow along with the workshop, you'll need to download the following materials: +# Workshop Materials -- The [hnn-data repository](https://github.com/jonescompneurolab/hnn-data) (needed for the HNN-Core GUI tutorial) -- The [hnn-workshop-materials repository](https://github.com/jasmainak/hnn-workshop-materials/tree/biomag_2024) (needed for the HNN-Core Python tutorial) +## HNN-Core GUI Tutorial -Click [here](https://github.com/jonescompneurolab/hnn-data/archive/refs/heads/main.zip) to download the hnn-data folder, and [here](https://github.com/jasmainak/hnn-workshop-materials/archive/refs/heads/biomag_2024.zip) to download the hnn-workshop-materials folder. +This section of the workshop will require you to use HNN-Core GUI. See the sections below outlining the different installation methods available for getting started with the GUI. -Altenatively, you can clone the repositores with the follwing commands. +To follow along with the workshop, you'll also need to clone or download the [hnn-data repository](https://github.com/jonescompneurolab/hnn-data). + +Click [here](https://github.com/jonescompneurolab/hnn-data/archive/refs/heads/main.zip) to download the hnn-data folder directly. Altenatively, you can clone the repository with the follwing command. ```bash git clone https://github.com/jonescompneurolab/hnn-data.git -git clone https://github.com/jasmainak/hnn-workshop-materials.git ``` -If you've already cloned the repositories in the past, be sure to run `git pull` to download the latest updates. +## HNN-Core Python Tutorial + +The HNN-Core Python tutorial will utilize the following Google CoLab notebook, which can also be downloaded as an .ipynb file and run locally: [hnn-workshop-materials](https://colab.research.google.com/drive/1CvNTB_puonJiVvHmFhKhrr_CjmrfbgVB?usp=sharing) # Preferred Installation Method: Google CoLab