diff --git a/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx b/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx index a92a6fc1e7..444bf17ba1 100644 --- a/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx +++ b/docs/genai/04_how_to_guides/03_retrieval_augmented_generation.mdx @@ -47,7 +47,7 @@ The LLM now has the associated context it needs to generate an relevant response You can run it to ask a question about a recent event that occurred after the knowledge cutoff for the dataset used to train the LLM: ```sh -ss19980@ITS-JQKQGQQMTX ~/D/p/r/g/rag (main)> uv run rag_basic.py \ +uv run rag_basic.py \ https://en.wikipedia.org/wiki/2025_London_Marathon \ "Which athletes won the 2025 London Marathon?" ... @@ -76,5 +76,4 @@ The athletes who won the 2025 London Marathon are: * **Wheelchair men:** Marcel Hug * **Wheelchair women:** Catherine Debrunner E20250611 14:32:54.595919 362220 server.cpp:47] [SERVER][BlockLock][] Process exit -ss19980@ITS-JQKQGQQMTX ~/D/p/r/g/rag (main)> ``` diff --git a/docs/hpc/11_system_status.mdx b/docs/hpc/11_system_status.mdx index c601dc5942..8c69ba3dc9 100644 --- a/docs/hpc/11_system_status.mdx +++ b/docs/hpc/11_system_status.mdx @@ -21,8 +21,7 @@ To be able to see the panels below you need to be within NYU network (use VPN if Below you may find data for the following file system mounts -- GPFS file system: `/home`, `/scratch`, `/archive` -- VAST file system: `/vast` +- VAST file system: `/home`, `/scratch`, `/archive` diff --git a/docs/hpc/12_tutorial_intro_shell_hpc/02_connecting_to_hpc.mdx b/docs/hpc/12_tutorial_intro_shell_hpc/02_connecting_to_hpc.mdx index d1d8d21d49..0bd66abb67 100644 --- a/docs/hpc/12_tutorial_intro_shell_hpc/02_connecting_to_hpc.mdx +++ b/docs/hpc/12_tutorial_intro_shell_hpc/02_connecting_to_hpc.mdx @@ -202,25 +202,16 @@ Once you are on the NYU WiFi or VPN you can connect with: ssh @login.torch.hpc.nyu.edu ``` -When you are logged in you will see information about your last login, the host you've connected to, and your storage quota. It should look something like this: +When you are logged in you will see information about your last login. It should look something like this: ```bash -Last login: Fri May 9 09:45:18 2025 from 0.0.0.0 - -Hostname: log-1 at Mon May 12 10:48:19 EDT 2025 - -Filesystem Environment Backed up? Allocation Current Usage -Space Variable /Flushed? Space / Files Space(%) / Files(%) - -/home $HOME Yes/No 50.0GB/30.0K 23.74GB(47.48%)/4913(16.38%) -/scratch $SCRATCH No/Yes 5.0TB/1.0M 35.91GB(0.70%)/19585(1.96%) -/archive $ARCHIVE Yes/No 2.0TB/20.0K 0.00GB(0.00%)/1(0.00%) -/vast $VAST NO/YES 2TB/5.0M 0.0TB(0.0%)/2(0%) - -[NetID@log-1 ~]$ +> ssh login.torch.hpc.nyu.edu +(NetID@login.torch.hpc.nyu.edu) Authenticate with PIN ... at https://login.microsoft.com/device and press ENTER. +Last login: Tue Mar 17 17:16:15 2026 from 10.27.3.62 +[NetID@torch-login-4 ~]$ ``` -By looking at the information after *Hostname:* and in the prompt you'll notice that the machine you're currently logged into is not Torch. This is expected. You've just logged into a _login node_ that is connected to Torch. It is from the login nodes that you will submit jobs to Torch. +By looking at the information after *Hostname:* and in the prompt you'll notice that the machine you're currently logged into is not Torch. This is expected. You've just logged into a _login node_ that is connected to Torch. It is from the login nodes that you will submit jobs to Torch. If you logged in using PuTTY this will not apply because it does not offer a local terminal. diff --git a/docs/hpc/13_tutorial_intro_hpc/03_exploring_remote_resources.mdx b/docs/hpc/13_tutorial_intro_hpc/03_exploring_remote_resources.mdx index 5c5f3e7545..4f03acb4be 100644 --- a/docs/hpc/13_tutorial_intro_hpc/03_exploring_remote_resources.mdx +++ b/docs/hpc/13_tutorial_intro_hpc/03_exploring_remote_resources.mdx @@ -43,18 +43,19 @@ The remote computer’s home directory shares almost nothing in common with the Most high-performance computing systems run the Linux operating system, which is built around the [UNIX Filesystem Hierarchy Standard](https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard). Instead of having a separate root for each hard drive or storage medium, all files and devices are anchored to the “root” directory, which is `/`: ```bash -[NetID@log-1 ~]$ ls / -afs bin@ dev gpfs lib@ media mnt opt root sbin@ share state tmp var -archive boot etc home lib64@ misc net proc run scratch srv sys usr vast +[NetID@torch-login-4 ~]$ ls / +afs boot home media net projects sbin srv tmp +archive dev lib misc opt root scratch state usr +bin etc lib64 mnt proc run share sys var +[NetID@torch-login-4 ~]$ ``` -The `/home/NetID`, `/scratch/NetID`, `/archive/NetID`, and `/vast/NetID` directories are created for you by default and they are where you'll probably store most of your files, but there are other options as well. Please see the tip below and our [storage documentation](../03_storage/01_intro_and_data_management.mdx) for details about how these directories differ, as well as other storage options available. Other folders on a UNIX OS contain system files and change as you install new software or upgrade your OS. +The `/home/NetID`, `/scratch/NetID` and `/archive/NetID` directories are created for you by default and they are where you'll probably store most of your files, but there are other options as well. Please see the tip below and our [storage documentation](../03_storage/01_intro_and_data_management.mdx) for details about how these directories differ, as well as other storage options available. Other folders on a UNIX OS contain system files and change as you install new software or upgrade your OS. :::tip[Using the HPC filesystems] On Geene, you have a number of places where you can store your files. These differ in both the amount of space allocated and whether or not they are backed up. - **Home** – data stored here is available throughout the HPC system, and often backed up periodically. Please note the limit on the number of files (inodes) which can get used up easily. Use the `myquota` command to ensure that you are not running out of inodes! - **Scratch** – used for temporary file storage while running jobs. It is not backed up and files that are unused for over 60 days are purged. It should not be used for long term storage. -- **Vast** – flash-drive based system that is optimal for workloads with high I/O rates. Like the `scratch` storage, it is also not backed up and files that are unused for over 60 days are purged. - **Research Project Space (RPS)** – provides data storage space for research projects that is easily shared amongst collaborators, backed up, and not subject to the old file purging policy. Note that it is a paid service. - **Archive** – provides a space for long-term storage of research output. It is only accessible from the login nodes, so it is inaccessible by running jobs. ::: diff --git a/docs/hpc/13_tutorial_intro_hpc/05_environment_variables.mdx b/docs/hpc/13_tutorial_intro_hpc/05_environment_variables.mdx index 82373d82c2..d63cb46858 100644 --- a/docs/hpc/13_tutorial_intro_hpc/05_environment_variables.mdx +++ b/docs/hpc/13_tutorial_intro_hpc/05_environment_variables.mdx @@ -20,26 +20,45 @@ The shell is just a program, and like other programs, it has variables. Those va Variables are a great way of saving information under a name you can access later. In programming languages like Python and R, variables can store pretty much anything you can think of. In the shell, they usually just store text. The best way to understand how they work is to see them in action. -Let’s start by running the command `set` and looking at some of the variables in a typical shell session: +Let’s start by running the command `printenv` and looking at some of the variables in a typical shell session: ```bash -$ set +$ printenv +[NetID@torch-login-4 ~]$ printenv SHELL=/bin/bash -WINDOWID=87 -SINGULARITY_CACHEDIR=/state/partition1/NYUNetID-singularity-cache -COLORTERM=truecolor +SINGULARITY_CACHEDIR=/scratch/NetID/singularity-cache HISTCONTROL=ignoredups HISTSIZE=1000 -HOSTNAME=log-3 -FPATH=/usr/share/zsh/5.5.1/functions:/usr/share/zsh/5.5.1/functions:/share/apps/lmod/8.4.9/lmod/lmod/init/ksh_funcs -SSH_AUTH_SOCK=/tmp/ssh-XXXXb32gan/agent.3025643 -__LMOD_REF_COUNT_MODULEPATH=/share/apps/modulefiles:1 -VAST=/vast/NYUNetID -LMOD_DIR=/share/apps/lmod/8.4.9/lmod/lmod/libexec +HOSTNAME=torch-login-4.hpc-infra.svc.cluster.local +SSH_AUTH_SOCK=/tmp/ssh-XXXXSgS6Tp/agent.120512 +LMOD_DIR=/share/apps/lua-modules/lmod/lmod/libexec +PWD=/home/NetID +LOGNAME=NetID +XDG_SESSION_TYPE=tty +MODULESHOME=/share/apps/lua-modules/lmod/lmod +SBATCH_IGNORE_PBS=1 +MOTD_SHOWN=pam +SCRATCH=/scratch/NetID +LMOD_SETTARG_FULL_SUPPORT=no +APPTAINER_BINDPATH=/scratch,/projects,/share/apps,/mnt,/state/partition1 +LMOD_DISABLE_SAME_NAME_AUTOSWAP=yes +LMOD_VERSION=8.7.64 +HF_HOME=/scratch/NetID/.huggingface +ARCHIVE=/archive/NetID +XDG_SESSION_CLASS=user +LMOD_PKG=/share/apps/lua-modules/lmod/lmod +SELINUX_ROLE_REQUESTED= +TERM=xterm-256color +LESSOPEN=||/usr/bin/lesspipe.sh %s +USER=NetID +SELINUX_USE_CURRENT_RANGE= +LMOD_ROOT=/share/apps/lua-modules/lmod +SHLVL=1 +BASH_ENV=/etc/profile.d/cluster.sh +APPTAINER_CACHEDIR=/scratch/NetID/apptainer-cache ... ``` -As you can see, there are quite a few — in fact, four or five times more than what’s shown here. And yes, using `set` to *show* things might seem a little strange, even for Unix, but if you don’t give it any arguments, it might as well show you things you *could* set. -Every variable has a name. All shell variables’ values are strings, even those (like `UID`) that look like numbers. It’s up to programs to convert these strings to other types when necessary. For example, if a program wanted to find out how many processors the computer had, it would convert the value of the `NUMBER_OF_PROCESSORS` variable from a string to an integer. +As you can see, there are quite a few — in fact, four or five times more than what’s shown here. Every variable has a name. All shell variables’ values are strings, even those (like `UID`) that look like numbers. It’s up to programs to convert these strings to other types when necessary. For example, if a program wanted to find out how many processors the computer had, it would convert the value of the `NUMBER_OF_PROCESSORS` variable from a string to an integer. ## Showing the Value of a Variable Let’s show the value of the variable HOME: