No use of portals, fix #21, thanks @paran1

UPPMAX · May 7, 2024 · 9dfdaea · 9dfdaea
1 parent f37a287
commit 9dfdaea
Show file tree

Hide file tree

Showing 19 changed files with 337 additions and 394 deletions.
diff --git a/docs/cluster_guides/bianca.md b/docs/cluster_guides/bianca.md
@@ -1,94 +1,24 @@
 # Bianca
 
-Bianca is one of the [UPPMAX clusters](uppmax_cluster.md).
-
-Here we describe [Bianca's name](#bianca's-name)
-and [Bianca's design](#bianca's-design).
-
-!!! info "[Go to the Bianca portal](bianca_portal.md)"
-
-    [The Bianca portal](bianca_portal.md) 
-    is the starting page on using Bianca.
-
-## Bianca's name
-
-Bianca, like all [UPPMAX clusters](uppmax_cluster.md), 
-is named after a Tintin character,
-in this case after Bianca Castafiore.
-
 ![Bianca Castafiore, from https://en.wikipedia.org/wiki/File:Bianca_Castafiore-Tintin_comics_series.png](./img/bianca_castafiore_192_x_226.png)
 
-???- question "What are the UPPMAX clusters?"
-
-    All UPPMAX clusters can be found [here](uppmax_cluster.md).
-
-## Bianca's design
-
-Bianca is an high-performance computing (HPC) cluster for sensitive data.
-
-???- question "What is an HPC cluster for sensitive data?"
-
-    What an HPC cluster for sensitive data is, is described [here](uppmax_cluster.md).
-
-Or: Bianca is a group of computers that can effectively run many calculations, 
-as requested by multiple people, at the same time.
-As the data is sensitive, it is protected to remain only on Bianca.
-
-Bianca is designed to:
-
-- make accidental data leaks difficult
-- make correct data management as easy as possible
-- emulate the HPC cluster environment that SNIC users were familiar with
-- provide a maximum amount of resources
-- satisfy regulations
-
-???- info "The Bianca architecture"
-
-    ![The Bianca architecure](./img/bianca_architecture.png)
-
-    > Bianca's architecture.
-    > Red shows the university networks.
-    > Blue shows the whole cluster, with hundreds of nodes.
-    > Green shows virtual project clusters.
-    > Yellow shows where file transfer occurs.
-
-Bianca's architecture reflects that 
-she is an HPC cluster for sensitive data:
-the whole Bianca cluster has hundreds 
-of virtual project clusters, 
-each of which is isolated from each other and the Internet.
-File transfer is only possible through the the so-called 'wharf', 
-which is a special file area that is visible from the Internet.
-
-!!! info "Bianca has no internet"
-
-    - You *can* log in, but with extra steps
-    - You *can* transfer files, but with extra steps
-    - We recommend using the remote desktop login, 
-      see [here](../getting_started/login_bianca.md)
-
-As Bianca is an HPC cluster that should be as easy to 
-use as possible, there are two ways to interact with Bianca:
-one more visual, the other a command-line environment.
-Both environments are shown below.
-
-As Bianca has sensitive data, there are constraints on how to
-access Bianca.
-
-One such constraint in accessing Bianca, 
-is that one has to be within the university
-networks, as described at [get within the university networks](#get-within-the-university-networks).
-
-Another such constraint, is that data can be
-transferred to or from a virtual project cluster through the so-called 'wharf', 
-which is a special file area that is visible from the Internet.
-File transfer is described in more detail [here](../cluster_guides/transfer_bianca.md).
-
-Bianca runs the Linux operating system and all users need some
-basic Linux knowledge to use Bianca.
-
-???- tip "Using Linux"
-
-    Using Linux (and especially the so-called command-line/terminal) is essential
-    to use Bianca. Learning the essential Linux commands 
-    is described [here](../getting_started/linux.md).
+[Bianca](bianca.md) is one of the [UPPMAX clusters](uppmax_cluster.md),
+suitable for working with sensitive data.
+
+- [Bianca's name](biancas_name.md)
+- [Bianca's design](biancas_design.md)
+- [Log in](../getting_started/login_bianca.md)
+- [Submitting jobs, using Slurm](slurm.md)
+- [Starting an interactive node](start_interactive_node_on_bianca.md)
+- [File transfer](transfer_bianca.md)
+    - [File transfer using a graphical program](bianca_file_transfer_using_gui.md)
+- [The module system](bianca_modules.md)
+- [IDEs](ides_on_bianca.md)
+    - [Jupyter](../software/jupyter.md)
+    - [RStudio](rstudio_on_bianca.md)
+    - :no_entry: [VSCode](vscode_on_bianca.md)
+    - [VSCodium](vscodium_on_bianca.md)
+- [Workshops and courses](../workshops_courses/workshops_courses.md)
+- NAISS-sens
+- Best practices
+- Bianca installation guides
diff --git a/docs/cluster_guides/bianca_portal.md b/docs/cluster_guides/bianca_portal.md
diff --git a/docs/cluster_guides/biancas_design.md b/docs/cluster_guides/biancas_design.md
@@ -0,0 +1,70 @@
+# Bianca's design
+
+Bianca is an high-performance computing (HPC) cluster for sensitive data.
+
+???- question "What is an HPC cluster for sensitive data?"
+
+    What an HPC cluster for sensitive data is, is described [here](uppmax_cluster.md).
+
+Or: Bianca is a group of computers that can effectively run many calculations, 
+as requested by multiple people, at the same time.
+As the data is sensitive, it is protected to remain only on Bianca.
+
+Bianca is designed to:
+
+- make accidental data leaks difficult
+- make correct data management as easy as possible
+- emulate the HPC cluster environment that SNIC users were familiar with
+- provide a maximum amount of resources
+- satisfy regulations
+
+???- info "The Bianca architecture"
+
+    ![The Bianca architecure](./img/bianca_architecture.png)
+
+    > Bianca's architecture.
+    > Red shows the university networks.
+    > Blue shows the whole cluster, with hundreds of nodes.
+    > Green shows virtual project clusters.
+    > Yellow shows where file transfer occurs.
+
+Bianca's architecture reflects that 
+she is an HPC cluster for sensitive data:
+the whole Bianca cluster has hundreds 
+of virtual project clusters, 
+each of which is isolated from each other and the Internet.
+File transfer is only possible through the the so-called 'wharf', 
+which is a special file area that is visible from the Internet.
+
+!!! info "Bianca has no internet"
+
+    - You *can* log in, but with extra steps
+    - You *can* transfer files, but with extra steps
+    - We recommend using the remote desktop login, 
+      see [here](../getting_started/login_bianca.md)
+
+As Bianca is an HPC cluster that should be as easy to 
+use as possible, there are two ways to interact with Bianca:
+one more visual, the other a command-line environment.
+Both environments are shown below.
+
+As Bianca has sensitive data, there are constraints on how to
+access Bianca.
+
+One such constraint in accessing Bianca, 
+is that one has to be within the university
+networks, as described at [get within the university networks](#get-within-the-university-networks).
+
+Another such constraint, is that data can be
+transferred to or from a virtual project cluster through the so-called 'wharf', 
+which is a special file area that is visible from the Internet.
+File transfer is described in more detail [here](../cluster_guides/transfer_bianca.md).
+
+Bianca runs the Linux operating system and all users need some
+basic Linux knowledge to use Bianca.
+
+???- tip "Using Linux"
+
+    Using Linux (and especially the so-called command-line/terminal) is essential
+    to use Bianca. Learning the essential Linux commands 
+    is described [here](../getting_started/linux.md).
diff --git a/docs/cluster_guides/biancas_name.md b/docs/cluster_guides/biancas_name.md
@@ -0,0 +1,11 @@
+# Bianca's name
+
+Bianca, like all [UPPMAX clusters](uppmax_cluster.md), 
+is named after a Tintin character,
+in this case after Bianca Castafiore.
+
+![Bianca Castafiore, from https://en.wikipedia.org/wiki/File:Bianca_Castafiore-Tintin_comics_series.png](./img/bianca_castafiore_192_x_226.png)
+
+???- question "What are the UPPMAX clusters?"
+
+    All UPPMAX clusters can be found [here](uppmax_cluster.md).
diff --git a/docs/cluster_guides/dardel.md b/docs/cluster_guides/dardel.md
@@ -4,4 +4,13 @@
 
 Dardel is an HPC cluster at Stockholm maintained by PDC.
 
-See [the Dardel portal](dardel_portal.md) on how to use it.
+If you are working on [Rackham](rackham.md), 
+consider moving to Dardel.
+
+- [Login to Dardel](../getting_started/login_dardel.md)
+- [Create and upload SSH key for Dardel](../software/ssh_key_use_dardel.md)
+- [Migration to Dardel](dardel_migration.md)
+
+## Links
+
+- [PDC page about Dardel](https://www.pdc.kth.se/hpc-services/computing-systems/dardel)
diff --git a/docs/cluster_guides/dardel_portal.md b/docs/cluster_guides/dardel_portal.md
diff --git a/docs/cluster_guides/rackham.md b/docs/cluster_guides/rackham.md
@@ -1,5 +1,7 @@
 # Rackham
 
+![Red Rackham, from https://tintin.fandom.com/wiki/Red_Rackham](./img/red_rackham_103_x_238.jpg)
+
 Rackham is one of the [UPPMAX clusters](uppmax_cluster.md).
 
 !!! info "Consider migrating to Dardel already"
@@ -10,41 +12,22 @@ Rackham is one of the [UPPMAX clusters](uppmax_cluster.md).
 
     See the page on file transfer to Dardel [here](transfer_dardel.md).
 
-Here we describe [Rackham's name](#rackham's-name)
-and [Rackham's design](#rackham's-design).
-
-!!! info "[Go to the Rackham portal](rackham_portal.md)"
-
-    [The Rackham portal](rackham_portal.md) 
-    is the starting page on using Rackham.
-
-## Rackham's name
-
-Rackham, like all [UPPMAX clusters](uppmax_cluster.md), 
-is named after a Tintin character,
-in this case after Red Rackham.
-
-![Red Rackham, from https://tintin.fandom.com/wiki/Red_Rackham](./img/red_rackham_103_x_238.jpg)
-
-???- question "What are the UPPMAX clusters?"
-
-    All UPPMAX clusters can be found [here](uppmax_cluster.md).
-
-## Rackham's design
-
-Rackham is an (general-purpose) high-performance computing (HPC) cluster.
-
-???- question "What is an HPC cluster?"
-
-    What an HPC cluster is, is described [here](uppmax_cluster.md).
-
-Or: Rackham is a group of computers that can effectively run many calculations, 
-as requested by multiple people, at the same time.
-Rackham runs the Linux operating system and all users need some
-basic Linux knowledge to use Rackham.
-
-???- tip "Using Linux"
-
-    Using Linux (and especially the so-called command-line/terminal) is essential
-    to use Rackham. Learning the essential Linux commands 
-    is described [here](../getting_started/linux.md).
+- [Rackham's name](rackhams_name.md)
+- [Rackham's name](rackhams_design.md)
+- [Log in](../getting_started/login_rackham.md)
+- [Starting an interactive node](start_interactive_node_on_rackham.md)
+- [File transfer](transfer_rackham.md)
+    - [using a graphical program](rackham_file_transfer_using_gui.md)
+    - [using SCP](rackham_file_transfer_using_scp.md)
+    - [using SFTP](rackham_file_transfer_using_sftp.md)
+- [The module system](rackham_modules.md)
+- [IDEs](ides_on_rackham.md)
+    - [Jupyter](../software/jupyter.md)
+    - [RStudio](rstudio_on_rackham.md)
+    - [VSCode](vscode_on_rackham.md)
+    - :no_entry: [VSCodium](vscodium_on_rackham.md)
+- Isolated environments
+    - [venv](venv_on_rackham.md)
+- Best practices
+- Rackham installation guides
+- Rackham workshops
diff --git a/docs/cluster_guides/rackham_portal.md b/docs/cluster_guides/rackham_portal.md
diff --git a/docs/cluster_guides/rackhams_design.md b/docs/cluster_guides/rackhams_design.md
@@ -0,0 +1,18 @@
+# Rackham's design
+
+[Rackham](rackham.md) is an (general-purpose) high-performance computing (HPC) cluster.
+
+???- question "What is an HPC cluster?"
+
+    What an HPC cluster is, is described [here](uppmax_cluster.md).
+
+Or: Rackham is a group of computers that can effectively run many calculations, 
+as requested by multiple people, at the same time.
+Rackham runs the Linux operating system and all users need some
+basic Linux knowledge to use Rackham.
+
+???- tip "Using Linux"
+
+    Using Linux (and especially the so-called command-line/terminal) is essential
+    to use Rackham. Learning the essential Linux commands 
+    is described [here](../getting_started/linux.md).
diff --git a/docs/cluster_guides/rackhams_name.md b/docs/cluster_guides/rackhams_name.md
@@ -0,0 +1,11 @@
+# Rackham's name
+
+[Rackham](rackham.md), like all [UPPMAX clusters](uppmax_cluster.md), 
+is named after a Tintin character,
+in this case after Red Rackham.
+
+![Red Rackham, from https://tintin.fandom.com/wiki/Red_Rackham](./img/red_rackham_103_x_238.jpg)
+
+???- question "What are the UPPMAX clusters?"
+
+    All UPPMAX clusters can be found [here](uppmax_cluster.md).