Merge pull request #100 from andrewdelman/cloud_compatibility

Some fixes and edits to AWS cloud environment setup

Author: andrewdelman

Cloud_Setup/JPL_setup_instructions.md

@@ -37,26 +37,24 @@ JPL does not enable `ssh` access to AWS instances by default, instead preferring
 - *Initial set up and download GitHub repository*: Copy the following commands and paste in your SSM window (using shift-insert or right-click then **Paste**):
 
 ```
-$ cd ~ && sudo dnf update -y && sudo dnf install git -y
-$ sudo su jpluser
-$ cd ~/
-$ mkdir git_repos
-$ cd git_repos
-$ git clone https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial.git
+cd ~ && sudo dnf update -y && sudo dnf install git -y
+sudo su jpluser
+cd ~/
+git clone https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial.git
 ```
 
 - *Enable ssh access*: There is a script in the GitHub repository to enable ssh access `sshd_enable.sh`. You want to run it as the *root* user, otherwise you will not have the necessary permissions. Again, copy and paste the following in your SSM window:
 
 ```
-$ sudo ~/git_repos/ECCO-v4-Python-Tutorial/Cloud_Setup/sshd_enable.sh
+sudo ~/ECCO-v4-Python-Tutorial/Cloud_Setup/sshd_enable.sh
 ```
 
-The script will ask if you want to move the git repo and change its ownership. Answer **Y** and enter **jpluser** for user name.
+The script will ask if you want to generate new SSH keys, answer **Y**. Then it will ask if you want to move the git repo and change its ownership. Answer **Y** and enter **jpluser** for user name.
 
 Once the script is completed, you should be able to ssh into your new instance. You can **Terminate** the SSM window. Then from your machine's terminal window, connect to the instance's *private* IPv4 address (given on the AWS instance summary page) with user name **jpluser**. For example, if the key file is `~/.ssh/aws_ec2_jupyter.pem` and the private IPv4 address is 100.104.70.37, then:
 
 ```
-$ ssh -i "~/.ssh/aws_ec2_jupyter.pem" [email protected] -L 9889:localhost:9889
+ssh -i "~/.ssh/aws_ec2_jupyter.pem" [email protected] -L 9889:localhost:9889
 ```
 
 The `-L` option indicates a tunnel from the local machine's port 9889 to the instance's port 9889; this will be used later to open Jupyterlab through your local machine's web browser.
@@ -80,7 +78,7 @@ Now you need to install software (conda/miniconda/miniforge) to run Python, and
 To run `jupyter_env_setup.sh`, copy, paste, and execute the following two commands on the instance:
 
 ```
-$ sudo chmod 755 ~/git_repos/ECCO-v4-Python-Tutorial/Cloud_Setup/jupyter_env_setup.sh && ~/git_repos/ECCO-v4-Python-Tutorial/Cloud_Setup/jupyter_env_setup.sh
+sudo chmod 755 ~/ECCO-v4-Python-Tutorial/Cloud_Setup/jupyter_env_setup.sh && ~/ECCO-v4-Python-Tutorial/Cloud_Setup/jupyter_env_setup.sh
 ```
 
 The script takes several minutes to run, but it should set up our environment with the packages we need. Now you can return to Step 4 of the [AWS Cloud: getting started](https://ecco-v4-python-tutorial.readthedocs.io/AWS_Cloud_getting_started.html) tutorial.

Cloud_Setup/install_packages.sh

@@ -21,6 +21,8 @@ red_start='\033[0;31m'
 blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
+
+source ~/.bashrc
 mamba init
 
 # create jupyter environment

Cloud_Setup/install_packages_bigmem.sh

@@ -15,6 +15,7 @@ blue_start='\033[0;34m'
 nocolor_start='\033[0m'
 
 
+source ~/.bashrc
 conda init
 
 # create conda environment called 'jupyter'

Cloud_Setup/jupyter_env_setup.sh

@@ -1,11 +1,14 @@
 #!/bin/bash
 
+# get path of directory where script is located
+script_dir=$(dirname "$0")
+
 # install wget and tmux 
-sh ./install_wget_tmux.sh
+sh ${script_dir}/install_wget_tmux.sh
 
 # download and install miniforge/conda/mamba 
-sh ./install_conda_mamba.sh
+sh ${script_dir}/install_conda_mamba.sh
 
 # download and install a bunch of packages
 # including ecco_v4_py and jupyterlab
-sh ./install_packages_bigmem.sh
+sh ${script_dir}/install_packages_bigmem.sh

Intro_to_PO_Tutorials/Steric_height.ipynb

@@ -213,7 +213,7 @@
    "source": [
     "### Sea surface height file\n",
     "\n",
-    "To look at the impact of steric height variations, we will also be looking at the actual sea surface height field from ECCOv4. To compare steric height with sea surface height, we of course need to download and retrieve sea surface height output. You can do this by importing the **ecco_download** module and calling the function *ecco_podaac_download* (see the Geostrophic Balance tutorial for an example). Consulting the [variable list](https://raw.githubusercontent.com/ECCO-GROUP/ECCO-v4-Python-Tutorial/master/varlist/v4r4_nctiles_monthly_varlist.txt) for monthly mean output, we find that the datasets containing sea surface height have ShortName ```ECCO_L4_SSH_LLC0090GRID_MONTHLY_V4R4```. To start, download the granule of that dataset corresponding to January 2000 (2000-01). Once you have this file downloaded, view its structure using the code below."
+    "To look at the impact of steric height variations, we will also be looking at the actual sea surface height field from ECCOv4. Consulting the [variable list](https://raw.githubusercontent.com/ECCO-GROUP/ECCO-v4-Python-Tutorial/master/varlist/v4r4_nctiles_monthly_varlist.txt) for monthly mean output, we find that the datasets containing sea surface height have ShortName ```ECCO_L4_SSH_LLC0090GRID_MONTHLY_V4R4```. To start, we access the granule of that dataset corresponding to January 2000 (2000-01)."
    ]
   },
   {