Merge pull request #345 from NYU-RTS/robjy-troubleshoot

added storage troubleshooting section

Author: s-sajid-ali

docs/hpc/03_storage/01_intro_and_data_management.mdx

@@ -65,5 +65,3 @@ There are also limits to the data transfer rate in moving to/from Google Drive.
 | /scratch                    | $SCRATCH             | Best for large files                                  | NO / Files not accessed for 60 days | 5 TB / 5 M                         |
 | /archive                    | $ARCHIVE             | Long-term storage                                     | YES / NO                            | 2 TB / 20 K                        |
 | HPC Research Project Space  | NA                   | Shared disk space for research projects               | YES / NO                            | Payment based  TB-year/inodes-year |
-
-Please see the next page for best practices for data management on NYU HPC systems.

docs/hpc/03_storage/05_best_practices.mdx

@@ -8,40 +8,6 @@ _One of the common issues users report is running out of inodes in their home di
 
 Users can check their current utilization of quota using the myquota command. The myquota command provides a report of the current quota limits on mounted file systems, the user's quota utilization, as well as the percentage of quota utilization.  For details, please see [myquota](../06_tools_and_software/08_utils.mdx#myquota)
 
-You can use the following command to print the list of files within each sub-folder for a given directory:
-```sh
-$cd $HOME
-$du --inodes -h --max-depth=1
-6	./.ssh
-88	./.config
-2	./.vnc
-2	./.aws
-3	./.lmod.d
-5.3K	./.local
-3	./.dbus
-408	./ondemand
-2	./.virtual_documents
-6	./.nv
-6.7K	./.pixi
-33	./workshop_scripts
-5	./.cupy
-6	./.gnupg
-1	./.emacs.d
-194	./.nextflow
-6	./.terminfo
-2	./.conda
-2	./.singularity
-3	./.vast-dev
-1	./custom
-185	./genai-workshop
-6	./.atuin
-1	./.apptainer
-9	./.subversion
-4	./packages
-1.4K	./.cache
-15K	.
-```
-
 ## Large number of small files
 In case your dataset or workflow requires to use large number of small files, this can create a bottleneck due to read/write rates. Please refer to [our page on working with a large number of files](./06_large_number_of_small_files.md) to learn about some of the options we recommend to consider.
 
@@ -51,3 +17,49 @@ Your home directory is limited to a relatively small number of inodes (30,000).
 :::
 
 Please review the [Package Management section](../06_tools_and_software/01_intro.md#package-management-for-r-python--julia-and-conda-in-general) of the [Torch Software Page](../06_tools_and_software/01_intro.md).
+
+## Troubleshooting quota issues
+
+:::warning
+Being over your quota can cause problems logging into OOD and other issues.  If you find that you're suddenly unable to log in, one of the first things you should check is your quota with the [`myquota`](../06_tools_and_software/08_utils.mdx#myquota) command.
+:::
+
+If you find that you're over your quota, `myquota` will show you if you are over your quota for space or i-nodes or both.  You can then see which folders most contribute to you being over quota with the following commands:
+
+Here's how you can see which folders contain the most files:
+```bash
+du --inodes -h -s -- * .[!.]* ..?* 2>/dev/null | sort -hr | head -n 5
+```
+and here's how you can see which ones most contribute to your disk usage:
+```bash
+du -h -s -- * .[!.]* ..?* 2>/dev/null | sort -hr | head -n 5
+```
+
+### Moving common dot directories from `/home` to `/scratch`
+
+As mentioned elsewhere in our documentation, a problem we often see for our users is that of filling their `/home` directories by using common tools like VSCode, Cursor, etc.  These applications put a dot directory in your `/home` directory and it can quickly overwhelm your quota.
+
+Our recommended fix for this is to make a directory for these files in your `/scratch` directory and then make a symbolic link in your `/home` that points to the one you just created in `/scratch`.  This allows these applications to write to what appears to be your `/home` directory, but is actually stored in your `/scratch` directory.  This can be accomplished with the following commands:
+
+:::warning
+The first part of the following commands will remove the contents of the dot directory in your `${HOME}` directory.  Be sure to copy anything you'd like to save from that directory before executing.
+:::
+
+For VSCode:
+```bash
+rm -rf ${HOME}/.vscode-server && mkdir -p ${SCRATCH}/vscode-server && ln -s ${SCRATCH}/vscode-server ${HOME}/.vscode-server
+```
+
+For Cursor:
+```bash
+rm -rf ${HOME}/.cursor-server && mkdir -p ${SCRATCH}/cursor-server && ln -s ${SCRATCH}/cursor-server ${HOME}/.cursor-server
+```
+
+For RStudio:
+```bash
+rm -rf ${HOME}/.local/share/rstudio && mkdir -p ${SCRATCH}/.local/share/rstudio && ln -s ${SCRATCH}/.local/share/rstudio ${HOME}/.local/share/rstudio
+```
+
+For details about changing your default RStudio directory please see [User state storage](https://docs.posit.co/ide/server-pro/admin/rstudio_pro_sessions/workspace_management.html#user-state-storage).
+
+Please contact [hpc@nyu.edu](mailto:hpc@nyu.edu) if you have any questions.

docs/hpc/06_tools_and_software/08_utils.mdx

@@ -20,17 +20,6 @@ Space        Variable          /Flushed?    Space / Files        Space(%) / File
 /archive     $ARCHIVE          YES/NO       2.0TB/0.02M          0.0TB(0.0%)/1(0%)
 ```
 
-:::tip
-Here's how you can see which folders contain the most files:
-```bash
-du --inodes -h -s -- * .[!.]* ..?* 2>/dev/null | sort -hr | head -n 5
-```
-and here's how you can see which ones most contribute to your disk usage:
-```bash
-du -h -s -- * .[!.]* ..?* 2>/dev/null | sort -hr | head -n 5
-```
-:::
-
 ## `my_slurm_accounts`
 
 `my_slurm_accounts` returns a list of `SLURM` accounts associated with your HPC account: