From 8669cccd21fd27a768cd575b3ea8a2a942e47a99 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 10:57:59 -0400 Subject: [PATCH 1/7] added storage troubleshooting section --- docs/hpc/03_storage/05_best_practices.mdx | 73 +++++++++++---------- docs/hpc/06_tools_and_software/08_utils.mdx | 11 ---- 2 files changed, 39 insertions(+), 45 deletions(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index c166153c6a..7713031e6e 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/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 +17,42 @@ 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` command. +::: + +If you find that you're over your quota, you'll want to see if you are over your quota for space or i-nodes or both. You can accomplish that 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 common problem for our users is that of filling thier `/home` directories by using common tools like VSCode, Cursor, R, etc. They all 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` directory to this directory in your `/scratch` directory. This allows these applications to write to what appears to be your `/home` directory, but to actually store the files in your `/scratch` directory. This can be accomplished with the following commands: + +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 ${HOME}/.cursor-server +``` + +:::warning +The first part of the commands above will remove the contents of the dot direcotry in your `${HOME}` directory. Be sure to copy anything you'd like to save from that directory before running the commands above. +::: + +Please contact [hpc@nyu.edu](mailto:hpc@nyu.edu) if you have any questions. diff --git a/docs/hpc/06_tools_and_software/08_utils.mdx b/docs/hpc/06_tools_and_software/08_utils.mdx index a6a837f93f..828f278ad5 100644 --- a/docs/hpc/06_tools_and_software/08_utils.mdx +++ b/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: From 726c67becd2d1f2522a23d7189094fd09d404771 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 12:12:27 -0400 Subject: [PATCH 2/7] typo fix --- docs/hpc/03_storage/05_best_practices.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index 7713031e6e..f0ae49b54c 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/docs/hpc/03_storage/05_best_practices.mdx @@ -37,7 +37,7 @@ 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 common problem for our users is that of filling thier `/home` directories by using common tools like VSCode, Cursor, R, etc. They all put a dot directory in your `/home` directory and it can quickly overwhelm your quota. +As mentioned elsewhere in our documentation, a common problem for our users is that of filling their `/home` directories by using common tools like VSCode, Cursor, R, etc. They all 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` directory to this directory in your `/scratch` directory. This allows these applications to write to what appears to be your `/home` directory, but to actually store the files in your `/scratch` directory. This can be accomplished with the following commands: From cfecaba6894f9468ce0015f6460e8509a69a8f66 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 12:14:07 -0400 Subject: [PATCH 3/7] typo fix --- docs/hpc/03_storage/05_best_practices.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index f0ae49b54c..3bd4ec7f6d 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/docs/hpc/03_storage/05_best_practices.mdx @@ -52,7 +52,7 @@ rm -rf ${HOME}/.cursor-server && mkdir -p ${SCRATCH}/cursor-server && ln -s ${SC ``` :::warning -The first part of the commands above will remove the contents of the dot direcotry in your `${HOME}` directory. Be sure to copy anything you'd like to save from that directory before running the commands above. +The first part of the commands above 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 running the commands above. ::: Please contact [hpc@nyu.edu](mailto:hpc@nyu.edu) if you have any questions. From 215015f17bfc860c2274f4ad8960e4e0923e9119 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 13:48:55 -0400 Subject: [PATCH 4/7] clean-up --- docs/hpc/03_storage/05_best_practices.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index 3bd4ec7f6d..41dba50302 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/docs/hpc/03_storage/05_best_practices.mdx @@ -37,9 +37,9 @@ 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 common problem for our users is that of filling their `/home` directories by using common tools like VSCode, Cursor, R, etc. They all put a dot directory in your `/home` directory and it can quickly overwhelm your quota. +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` directory to this directory in your `/scratch` directory. This allows these applications to write to what appears to be your `/home` directory, but to actually store the files in your `/scratch` directory. This can be accomplished with the following commands: +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: For VSCode: ```bash From 572e69f25c2dfcba9f4310644d7a23d9af408871 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 15:31:57 -0400 Subject: [PATCH 5/7] clean-up --- docs/hpc/03_storage/05_best_practices.mdx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index 41dba50302..5696fe159c 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/docs/hpc/03_storage/05_best_practices.mdx @@ -21,10 +21,10 @@ Please review the [Package Management section](../06_tools_and_software/01_intro ## 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` command. +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, you'll want to see if you are over your quota for space or i-nodes or both. You can accomplish that with the following commands: +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 following commands: Here's how you can see which folders contain the most files: ```bash From b7d8ea46f328b8cb02a5798350b82e3f92388f94 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 16:15:54 -0400 Subject: [PATCH 6/7] clean-up --- docs/hpc/03_storage/05_best_practices.mdx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/hpc/03_storage/05_best_practices.mdx b/docs/hpc/03_storage/05_best_practices.mdx index 5696fe159c..5d14b713e3 100644 --- a/docs/hpc/03_storage/05_best_practices.mdx +++ b/docs/hpc/03_storage/05_best_practices.mdx @@ -24,7 +24,7 @@ Please review the [Package Management section](../06_tools_and_software/01_intro 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 following commands: +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 From 353837b65f61abd8ec2b247bfc5ffb5efb6052c2 Mon Sep 17 00:00:00 2001 From: Robert Young Date: Thu, 16 Apr 2026 17:05:18 -0400 Subject: [PATCH 7/7] clean-up --- docs/hpc/03_storage/01_intro_and_data_management.mdx | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/hpc/03_storage/01_intro_and_data_management.mdx b/docs/hpc/03_storage/01_intro_and_data_management.mdx index 4ae3d4aa33..066d0e2ef9 100644 --- a/docs/hpc/03_storage/01_intro_and_data_management.mdx +++ b/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.