diff --git a/bih-cluster/docs/connecting/advanced-ssh/overview.md b/bih-cluster/docs/connecting/advanced-ssh/overview.md index ebcbf35dc..c2da9330b 100644 --- a/bih-cluster/docs/connecting/advanced-ssh/overview.md +++ b/bih-cluster/docs/connecting/advanced-ssh/overview.md @@ -2,5 +2,5 @@ Here we describe custom scenarios for using SSH to connect to BIH HPC. To keep it consise, this section is divided into separate documents for -- [Linux](./linux.md) and +- [Linux](./unix.md) and - [Windows](./windows.md) users. diff --git a/bih-cluster/docs/connecting/advanced-ssh/linux.md b/bih-cluster/docs/connecting/advanced-ssh/unix.md similarity index 98% rename from bih-cluster/docs/connecting/advanced-ssh/linux.md rename to bih-cluster/docs/connecting/advanced-ssh/unix.md index 68e0abaea..16caab995 100644 --- a/bih-cluster/docs/connecting/advanced-ssh/linux.md +++ b/bih-cluster/docs/connecting/advanced-ssh/unix.md @@ -1,4 +1,4 @@ -# Connecting via SSH on Unix +# Connecting via SSH with Unix-like Operating Systems ## Activating your Key in the SSH Key Agent !!! note The big Linux distributions automatically manage ssh-agent for you and unlock your keys at login time. diff --git a/bih-cluster/docs/connecting/connecting.md b/bih-cluster/docs/connecting/connecting.md index a6d9dc70a..2b77cf5eb 100644 --- a/bih-cluster/docs/connecting/connecting.md +++ b/bih-cluster/docs/connecting/connecting.md @@ -15,7 +15,7 @@ In case you're not familiar with SSH, you should probably start via the web port Follow these steps to connect to BIH HPC via the command line: 1. [Register an account](../admin/getting-access.md) via your PI. :memo: -2. [Generate a SSH key pair :key: in Linux](generate-key/linux.md) or [Windows](generate-key/windows.md) +2. [Generate a SSH key pair :key: in Linux](generate-key/unix.md) or [Windows](generate-key/windows.md) 3. [Submit your public key :arrow_up: to Charite](submit-key/charite.md) or [to MDC](submit-key/mdc.md). 4. Connect to one of the two login nodes. @@ -45,7 +45,7 @@ Follow these steps to connect to BIH HPC via the command line: $ srun --pty bash -i ``` -6. Bonus: [Configure your SSH client :wrench: on Linux and Mac](advanced-ssh/linux.md) or [Windows](advanced-ssh/windows.md). +6. Bonus: [Configure your SSH client :wrench: on Linux and Mac](advanced-ssh/unix.md) or [Windows](advanced-ssh/windows.md). 7. Bonus: [Connect from external networks :flying_saucer:](./from-external.md). !!! tip "tl;dr" diff --git a/bih-cluster/docs/connecting/generate-key/linux.md b/bih-cluster/docs/connecting/generate-key/unix.md similarity index 94% rename from bih-cluster/docs/connecting/generate-key/linux.md rename to bih-cluster/docs/connecting/generate-key/unix.md index 08ed11dd7..1c8f4510a 100644 --- a/bih-cluster/docs/connecting/generate-key/linux.md +++ b/bih-cluster/docs/connecting/generate-key/unix.md @@ -1,4 +1,4 @@ -# Generating an SSH Key in Linux +# Generating an SSH Key with Unix-like Operating Systems - You might already have one, check whether a file `~/.ssh/id_xxx.pub` is present. - Otherwise, create key using the following command (marking your key with your email address will make it easier to reidentify your key later on): diff --git a/bih-cluster/docs/help/faq.md b/bih-cluster/docs/help/faq.md index de7ece4bd..e63df8072 100644 --- a/bih-cluster/docs/help/faq.md +++ b/bih-cluster/docs/help/faq.md @@ -387,7 +387,7 @@ In the example above, user1 has one job with one GPU running on hpc-gpu-3, user2 Also see: - [Running graphical(X11) applications on Windows](../connecting/advanced-ssh/windows.md#x11) -- [Running graphical(X11) applications on Linux](../connecting/advanced-ssh/linux.md#x11) +- [Running graphical(X11) applications on Linux](../connecting/advanced-ssh/unix.md#x11) ## How can I log into a node outside of the scheduler? diff --git a/bih-cluster/docs/how-to/software/jupyter.md b/bih-cluster/docs/how-to/software/jupyter.md index b3f7345d1..9420f4dec 100644 --- a/bih-cluster/docs/how-to/software/jupyter.md +++ b/bih-cluster/docs/how-to/software/jupyter.md @@ -40,7 +40,7 @@ If you are running multiple server on one or more nodes, one can separate them b ## Connecting to the Running Session -This is slightly trickier as we have to create a SSH connection/tunnel with potentially multiple hops in between. The easiest way is probably to configure your `.ssh/config` to automatically route your connection via the login node (and possibly MDC jail). This is described in our [Advanced SSH config documentation](../../connecting/advanced-ssh/linux.md#configure-ssh-client) +This is slightly trickier as we have to create a SSH connection/tunnel with potentially multiple hops in between. The easiest way is probably to configure your `.ssh/config` to automatically route your connection via the login node (and possibly MDC jail). This is described in our [Advanced SSH config documentation](../../connecting/advanced-ssh/unix.md#configure-ssh-client) In short,add these lines to `~/.ssh/config` (replace curly parts): diff --git a/bih-cluster/docs/hpc-tutorial/episode-0.md b/bih-cluster/docs/hpc-tutorial/episode-0.md index 4045a77ce..609d782f0 100644 --- a/bih-cluster/docs/hpc-tutorial/episode-0.md +++ b/bih-cluster/docs/hpc-tutorial/episode-0.md @@ -44,7 +44,7 @@ That was easy! In preparation for our first steps tutorial series, we would like you to install the software for this tutorial. In general the users on the cluster will manage their own software with the help of conda. If you haven't done so so far, please [follow the instructions in installing conda](../best-practice/software-installation-with-conda.md) first. -The only premise is that you are able to [log into the cluster](../connecting/advanced-ssh/linux.md). +The only premise is that you are able to [log into the cluster](../connecting/advanced-ssh/unix.md). Make also sure that you are logged in to a computation node using `srun -p medium --time 1-00 --mem=4G --cpus-per-task=1 --pty bash -i`. Now we will create a new environment, so as to not interfere diff --git a/bih-cluster/docs/overview/storage.md b/bih-cluster/docs/overview/storage.md index d164808ed..74021bcd7 100644 --- a/bih-cluster/docs/overview/storage.md +++ b/bih-cluster/docs/overview/storage.md @@ -3,7 +3,7 @@ !!! info "No mounting **on** the cluster itself." For various technical and security-related reasons it is not possible to mount anything on the cluster nodes by users. - For mounting the cluster storage on your computer, please read [Connecting: SSHFS Mounts](../connecting/advanced-ssh/linux.md#file-system-mount-via-sshfs). + For mounting the cluster storage on your computer, please read [Connecting: SSHFS Mounts](../connecting/advanced-ssh/unix.md#file-system-mount-via-sshfs). This document gives an overview of the nodes and volumes on the cluster. diff --git a/bih-cluster/mkdocs.yml b/bih-cluster/mkdocs.yml index f8b8c2e7b..273fb4f9d 100644 --- a/bih-cluster/mkdocs.yml +++ b/bih-cluster/mkdocs.yml @@ -88,14 +88,14 @@ nav: - "SSH Basics": connecting/ssh-basics.md - "Windows": "connecting/connecting-windows.md" - "Generate Keys": - - "Linux": connecting/generate-key/linux.md + - "Linux/macOS": connecting/generate-key/unix.md - "Windows": connecting/generate-key/windows.md - "Submit Keys": - "Charite": connecting/submit-key/charite.md - "MDC": connecting/submit-key/mdc.md - "Advanced SSH": - "Overview": connecting/advanced-ssh/overview.md - - "Linux": connecting/advanced-ssh/linux.md + - "Linux/macOS": connecting/advanced-ssh/unix.md - "Windows": connecting/advanced-ssh/windows.md - "From External": connecting/from-external.md - "Connection Problems": connecting/connection-problems.md