rstudio

Author: MattBixley

docs/Using_eRI/OpenOnDemand/Connect_to_Open_OnDemand.md

@@ -0,0 +1,26 @@
+# How to connect to Open OnDemand
+
+Open OnDemand can be described as providing access to your organisation’s computational resources via a web browser. No client software installation is required.
+
+Start computing immediately. A simple interface makes Open OnDemand easy to learn and use. Launch on any device with a browser. 
+
+The Open OnDemand (OOD) web interface allows AgResearch staff to access the eRI via a web browser. This article explains how to connect to it. 
+
+blue book Instructions
+
+Ensure you are connected the the AgResearch network (direct or via VPN):
+
+Open your web browser and navigate to https://ondemand.eri.agresearch.co.nz/
+
+Authenticate using your username@agresearch.co.nz (or email address) and password when prompted.
+
+Find helpful links in the ‘Help’ menu on the top of the screen.
+
+![alt text](../../assets/images/ood_apps.png)
+
+Select from the options of the top menu bar.
+Apps are presented as cards so users can launch an instance in a very simple way. 
+
+Open OnDemand is simplifying HPC access to scheduled compute resources for both interactive and non-interactive workloads.
+
+Find the Job Composer (submission templates), browse the project directories and access files, visualise results using available apps.

docs/Using_eRI/OpenOnDemand/RStudio.md

@@ -1,60 +1,16 @@
-# RStudio via OnDemand
-
-!!! warning
-
-    NeSI OnDemand is in development and accessible to early access users only.
-    If you are interested in helping us test it please [contact us](mailto:support@nesi.org.nz).
+# RStudio
 
 ## Logging in
 ![UPDATE WITH PROJECT](../../../assets/images/RStudio_via_OOD_on_NeSI_0.png){width=35%} ![](../../../assets/images/RStudio_via_OOD_on_NeSI_1.png){fig.align="right" width=62%}
 
 ## Settings
 Recommendation to set *Save Workspace to Never* to avoid saving large files to the workspace. This can be done by going to `Tools` -> `Global Options` -> `General` and setting the `Save workspace to .RData on exit` to `Never`. This will prevent the workspace from being unable to load due to not enough memory in the selected session.
 
-## Bugs
-
 ### Plots not showing
-The current R modules on NeSI OnDemand do not support the default graphics device due to a missing depedency, `cairo`. There is a one off fix for this by changing the backend graphics device from `Default` to `AGG` (Anti-Grain Geometry) in the RStudio settings. 
+The current R modules on OnDemand do not support the default graphics device due to a missing depedency, `cairo`. There is a one off fix for this by changing the backend graphics device from `Default` to `AGG` (Anti-Grain Geometry) in the RStudio settings. 
 
 This can be done by going to `Tools` -> `Global Options` -> `Graphics` and switch `Default` to `AGG`. This will allow the plots to be displayed in the RStudio interface. You do not need to restart the RStudio session for this to take effect.
 
 ![](../../../assets/images/RStudio_via_OOD_on_NeSI_2.png)
 
 Modules from 4.4 onwards will have this issue fixed.
-
-### Libraries not showing
-There is a bug with the R-Geo and R-bundle-Biocondutor libraries not showing up in the RStudio interface. This is a known issue and is being worked on. There are two workarounds for this issue:
-
-1. Manually add the library to `.libPaths()` in the R console as shown below:
-
-```R
-myPaths <- .libPaths()
-myPaths <- c(myPaths, "/opt/nesi/CS400_centos7_bdw/R-Geo/4.3.2-foss-2023a")
-
-# reorder paths
-myPaths <- c(myPaths[1], myPaths[3], myPaths[2]) 
-
-# reasign the library paths
-.libPaths(myPaths)
-
-# confirm the library paths
-.libPaths()
-[1] "/nesi/home/$USER/R/foss-2023a/4.3"
-[2] "/opt/nesi/CS400_centos7_bdw/R-Geo/4.3.2-foss-2023a"
-[3] "/opt/nesi/CS400_centos7_bdw/R/4.3.2-foss-2023a/lib64/R/library"
-```
-2. Permanent fix by adding the library path(s) to the `.Rprofile` file in your home directory. This will automatically add the library path to the R console when it starts up. Copy and Paste the following lines to the file:
-
-```
-# CHECK LIBRARY PATHS
-myPaths <- .libPaths()
-newPaths <- c("/opt/nesi/CS400_centos7_bdw/R-Geo/4.3.1-gimkl-2022a",
-        "/opt/nesi/CS400_centos7_bdw/R-bundle-Bioconductor/3.17-gimkl-2022a-R-4.3.1>
-
-# join the two lists
-myPaths <- c(myPaths, newPaths)
-
-# reassign the library paths
-.libPaths(myPaths)
-```
-NOTE: Replace the paths with the correct paths for the libraries you want to add.