diff --git a/_data/sidebars/merlin6_sidebar.yml b/_data/sidebars/merlin6_sidebar.yml index ac975d0..fcd359c 100644 --- a/_data/sidebars/merlin6_sidebar.yml +++ b/_data/sidebars/merlin6_sidebar.yml @@ -23,6 +23,12 @@ entries: url: /merlin6/request-project.html - title: Accessing Interactive Nodes url: /merlin6/interactive.html + - title: Accessing from a Linux client + url: /merlin6/connect-from-linux.html + - title: Accessing from a Windows client + url: /merlin6/connect-from-windows.html + - title: Accessing from a MacOS client + url: /merlin6/connect-from-macos.html - title: Merlin6 Storage url: /merlin6/storage.html - title: Accessing Slurm Cluster @@ -31,7 +37,7 @@ entries: url: /merlin6/transfer-data.html - title: NoMachine url: /merlin6/nomachine.html - - title: Merlin6 Slurm + - title: Job Submission folderitems: - title: Using PModules url: /merlin6/using-modules.html @@ -39,6 +45,8 @@ entries: url: /merlin6/slurm-basics.html - title: Running Jobs url: /merlin6/running-jobs.html + - title: Interactive Jobs + url: /merlin6/interactive-jobs.html - title: Slurm Examples url: /merlin6/slurm-examples.html - title: Slurm Configuration diff --git a/css/customstyles.css b/css/customstyles.css index 908a224..87473d3 100644 --- a/css/customstyles.css +++ b/css/customstyles.css @@ -2,6 +2,38 @@ body { font-size:15px; } +/* HPCE Custom CSS styles - BEGIN */ +pre.terminal { + background-color: black; + color: white; + font-size: 75%; + font-family: Consolas,Monaco,Lucida Console,Liberation Mono,DejaVu Sans Mono,Bitstream Vera Sans Mono,Courier New, monospace; + width: 100%; + display: inline-block; +} +details { + border: 1px solid #347DBE; + border-radius: 4px; + padding: .5em .5em 0; + color: #347DBE +} + +summary { + font-weight: bold; + margin: -.5em -.5em 0; + padding: .5em; +} + +details[open] { + padding: .5em; +} + +details[open] summary { + border-bottom: 1px solid #347DBE; + margin-bottom: .5em; +} +/* HPCE Custom CSS styles - END */ + .bs-callout { padding: 20px; margin: 20px 0; diff --git a/images/PuTTY/Putty_Disable_Kerberos_GSSAPI.png b/images/PuTTY/Putty_Disable_Kerberos_GSSAPI.png new file mode 100644 index 0000000..267400a Binary files /dev/null and b/images/PuTTY/Putty_Disable_Kerberos_GSSAPI.png differ diff --git a/images/PuTTY/Putty_Mouse_XTerm.png b/images/PuTTY/Putty_Mouse_XTerm.png new file mode 100644 index 0000000..d6bcf8d Binary files /dev/null and b/images/PuTTY/Putty_Mouse_XTerm.png differ diff --git a/images/PuTTY/Putty_Session.png b/images/PuTTY/Putty_Session.png new file mode 100644 index 0000000..8f609af Binary files /dev/null and b/images/PuTTY/Putty_Session.png differ diff --git a/images/PuTTY/Putty_X11_Forwarding.png b/images/PuTTY/Putty_X11_Forwarding.png new file mode 100644 index 0000000..89addf9 Binary files /dev/null and b/images/PuTTY/Putty_X11_Forwarding.png differ diff --git a/pages/merlin6/02 accessing-merlin6/accessing-interactive-nodes.md b/pages/merlin6/02 accessing-merlin6/accessing-interactive-nodes.md index 014c671..88f5eea 100644 --- a/pages/merlin6/02 accessing-merlin6/accessing-interactive-nodes.md +++ b/pages/merlin6/02 accessing-merlin6/accessing-interactive-nodes.md @@ -21,9 +21,6 @@ The Merlin6 login nodes are the following: | merlin-l-001.psi.ch | yes | yes | 2 x 22 | 2 | Intel Xeon Gold 6152 | 384GB | 1.8TB NVMe | ``/scratch`` | | merlin-l-002.psi.ch | yes | yes | 2 x 22 | 2 | Intel Xeon Gold 6142 | 384GB | 1.8TB NVMe | ``/scratch`` | | merlin-l-01.psi.ch | yes | - | 2 x 16 | 2 | Intel Xeon E5-2697Av4 | 512GB | 100GB SAS | ``/scratch`` | -| ~~merlin-l-02.psi.ch~~ | - | - | 2 x 16 | 2 | Intel Xeon E5-2697Av4 | 512GB | 100GB SAS | ``/scratch`` | - -* **merlin-l-02.psi.ch** has an severe incident and is not available to users: HP is trying to locate and fix the problem. --- @@ -31,22 +28,29 @@ The Merlin6 login nodes are the following: ### SSH Access -For interactive command shell access, use an SSH client. We recommend to activate SSH's X11 forwarding to allow you to use graphical applications (e.g. a text editor. For more performant graphical access, refer to the sections below). +For interactive command shell access, use an SSH client. We recommend to activate SSH's X11 forwarding to allow you to use graphical +applications (e.g. a text editor, but for more performant graphical access, refer to the sections below). X applications are supported +in the login nodes and X11 forwarding can be used for those users who have properly configured X11 support in their desktops, however: -E.g. for Linux: - -```bash -ssh -XY $username@merlin-l-01.psi.ch -``` - -X applications are supported in the login nodes and X11 forwarding can be used for those users who have properly configured X11 support in their desktops: * Merlin6 administrators **do not offer support** for user desktop configuration (Windows, MacOS, Linux). * Hence, Merlin6 administrators **do not offer official support** for X11 client setup. - * However, a generic guide for X11 client setup (Windows, Linux and MacOS) will be provided. + * Nevertheless, a generic guide for X11 client setup (*Linux*, *Windows* and *MacOS*) is provided below. * PSI desktop configuration issues must be addressed through **[PSI Service Now](https://psi.service-now.com/psisp)** as an *Incident Request*. * Ticket will be redirected to the corresponding Desktop support group (Windows, Linux). -### More efficient graphical access using a **NoMachine** client +#### Accessing from a Linux client + +Refer to [{Accessing Merlin -> Accessing from Linux Clients}](/merlin6/connect-from-linux.html) for **Linux** SSH client and X11 configuration. + +#### Accessing from a Windows client + +Refer to [{Accessing Merlin -> Accessing from Windows Clients}](/merlin6/connect-from-windows.html) for **Windows** SSH client and X11 configuration. + +#### Accessing from a MacOS client + +Refer to [{Accessing Merlin -> Accessing from MacOS Clients}](/merlin6/connect-from-macos.html) for **MacOS** SSH client and X11 configuration. + +### Graphical access using **NoMachine** client X applications are supported in the login nodes and can run efficiently through a **NoMachine** client. This is the officially supported way to run more demanding X applications on Merlin6. The client software can be downloaded from [the Nomachine Website](https://www.nomachine.com/product&p=NoMachine%20Enterprise%20Client). diff --git a/pages/merlin6/02 accessing-merlin6/connect-from-linux.md b/pages/merlin6/02 accessing-merlin6/connect-from-linux.md new file mode 100644 index 0000000..cacda71 --- /dev/null +++ b/pages/merlin6/02 accessing-merlin6/connect-from-linux.md @@ -0,0 +1,51 @@ +--- +title: Connecting from a Linux Client + +#tags: +keywords: Linux, connecting, client, configuration, SSH, X11 +last_updated: 23 Oct 2019 +summary: "This document describes a recommended setup for a Linux client." +sidebar: merlin6_sidebar +permalink: /merlin6/connect-from-linux.html +--- + +## SSH without X11 Forwarding + +This is the standard method. Official X11 support is provided through [NoMachine](/merlin6/nomachine.html). +For normal SSH sessions, use your SSH client as follows: + +```bash +ssh $username@merlin-l-01.psi.ch +ssh $username@merlin-l-001.psi.ch +ssh $username@merlin-l-002.psi.ch +``` + +## SSH with X11 Forwarding + +Official X11 Forwarding support is through NoMachine. Please follow the document +[Job Submission -> Interactive Jobs](/merlin6/interactive-jobs.html#Requirements) and +[Accessing Merlin -> NoMachine](/merlin6/nomachine.html) for more details. However, +we provide a small recipe for enabling X11 Forwarding in Linux. + +* For enabling client X11 forwarding, add the following to the start of ``~/.ssh/config`` +to implicitly add ``-Y`` to all ssh connections: + + ```bash + ForwardAgent yes + ForwardX11Trusted yes + ``` + +* Alternatively, you can add the option ``-Y`` to the ``ssh`` command. In example: + + ```bash + ssh -Y $username@merlin-l-01.psi.ch + ssh -Y $username@merlin-l-001.psi.ch + ssh -Y $username@merlin-l-002.psi.ch + ``` + +* For testing that X11 forwarding works, just run ``xclock``. A X11 based clock should +popup in your client session: + + ```bash + xclock + ``` diff --git a/pages/merlin6/02 accessing-merlin6/connect-from-macos.md b/pages/merlin6/02 accessing-merlin6/connect-from-macos.md new file mode 100644 index 0000000..a4b6961 --- /dev/null +++ b/pages/merlin6/02 accessing-merlin6/connect-from-macos.md @@ -0,0 +1,51 @@ +--- +title: Connecting from a MacOS Client + +#tags: +keywords: MacOS, connecting, client, configuration, SSH, X11 +last_updated: 23 Oct 2019 +summary: "This document describes a recommended setup for a MacOS client." +sidebar: merlin6_sidebar +permalink: /merlin6/connect-from-macos.html +--- + +## SSH without X11 Forwarding + +This is the standard method. Official X11 support is provided through [NoMachine](/merlin6/nomachine.html). +For normal SSH sessions, use your SSH client as follows: + +```bash +ssh $username@merlin-l-01.psi.ch +ssh $username@merlin-l-001.psi.ch +ssh $username@merlin-l-002.psi.ch +``` + +## SSH with X11 Forwarding + +Official X11 Forwarding support is through NoMachine. Please follow the document +[Job Submission -> Interactive Jobs](/merlin6/interactive-jobs.html#Requirements) and +[Accessing Merlin -> NoMachine](/merlin6/nomachine.html) for more details. However, +we provide a small recipe for enabling X11 Forwarding in MacOS. + +* For enabling client X11 forwarding, add the following to the start of ``~/.ssh/config`` +to implicitly add ``-Y`` to all ssh connections: + + ```bash + ForwardAgent yes + ForwardX11Trusted yes + ``` + +* Alternatively, you can add the option ``-Y`` to the ``ssh`` command. In example: + + ```bash + ssh -Y $username@merlin-l-01.psi.ch + ssh -Y $username@merlin-l-001.psi.ch + ssh -Y $username@merlin-l-002.psi.ch + ``` + +* For testing that X11 forwarding works, just run ``xclock``. A X11 based clock should +popup in your client session. + + ```bash + xclock + ``` diff --git a/pages/merlin6/02 accessing-merlin6/connect-from-windows.md b/pages/merlin6/02 accessing-merlin6/connect-from-windows.md new file mode 100644 index 0000000..341e3c9 --- /dev/null +++ b/pages/merlin6/02 accessing-merlin6/connect-from-windows.md @@ -0,0 +1,49 @@ +--- +title: Connecting from a Windows Client + +#tags: +keywords: Windows, connecting, client, configuration, SSH, X11 +last_updated: 23 Oct 2019 +summary: "This document describes a recommended setup for a Windows client." +sidebar: merlin6_sidebar +permalink: /merlin6/connect-from-windows.html +--- + +## SSH with PuTTY without X11 Forwarding + +PuTTY is one of the most common tools for SSH. + +Check, if the following software packages are installed on the Windows workstation by +inspecting the Start menu (hint: Use the search to save time): +* PuTTY (should already be installed) +* *[Optional]* Xming (needed for [SSH with X11 Forwarding](/merlin6/connect-from-windows.html#ssh-with-x11-forwarding)) + +If they are missing, you can install them using the Software Kiosk icon on the Desktop. + +1. Start PuTTY + +2. *[Optional]* Enable ``xterm`` to have similar mouse behavour as in Linux: + + ![Enable 'xterm']({{ "/images/PuTTY/Putty_Mouse_XTerm.png" }}) + +3. Create session to a Merlin login node and *Open*: + + ![Create Merlin Session]({{ "/images/PuTTY/Putty_Session.png" }}) + + +## SSH with PuTTY with X11 Forwarding + +Official X11 Forwarding support is through NoMachine. Please follow the document +[Job Submission -> Interactive Jobs](/merlin6/interactive-jobs.html#Requirements) and +[Accessing Merlin -> NoMachine](/merlin6/nomachine.html) for more details. However, +we provide a small recipe for enabling X11 Forwarding in Windows. + +Check, if the **Xming** is installed on the Windows workstation by inspecting the +Start menu (hint: Use the search to save time). If missing, you can install it by +using the Software Kiosk icon (should be on the Desktop). + +1. Ensrue that a X server (**Xming**) is running. Otherwise, start it. + +2. Enable X11 Forwarding in your SSH client. In example, for Putty: + + ![Enable X11 Forwarding in Putty]({{ "/images/PuTTY/Putty_X11_Forwarding.png" }}) diff --git a/pages/merlin6/03 Job Submission/interactive-jobs.md b/pages/merlin6/03 Job Submission/interactive-jobs.md new file mode 100644 index 0000000..2031d4a --- /dev/null +++ b/pages/merlin6/03 Job Submission/interactive-jobs.md @@ -0,0 +1,199 @@ +--- +title: Interactive Jobs +#tags: +keywords: interactive, X11, X, srun +last_updated: 22 October 2019 +summary: "This document describes how to run interactive jobs as well as X based software." +sidebar: merlin6_sidebar +permalink: /merlin6/interactive-jobs.html +--- + +## Running interactive jobs + +There are two different ways for running interactive jobs in Slurm. This is possible by using +the ``srun`` or the ``salloc`` commands. + +### srun + +Is run is used to run parallel jobs in the batch system. It can be used within a batch script +(which can be run with ``sbatch``), or within a job allocation (which can be run with ``salloc``). +Also, it can be used as a direct command (in example, from the login nodes). + +When used inside a batch script or during a job allocation, ``srun`` is constricted to the +amount of resources allocated by the ``sbatch``/``salloc`` commands. In ``sbatch``, usually +these resources are defined inside the batch script with the format ``#SBATCH