From d9491cc0ce50936e764e685cc7e45d7777513cd2 Mon Sep 17 00:00:00 2001 From: Heli Juottonen Date: Wed, 8 Jan 2025 14:44:07 +0200 Subject: [PATCH 01/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 62 +++++++++++++++++++++++--- 1 file changed, 55 insertions(+), 7 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 1b573d67a3..755bd2e8fc 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -1,9 +1,57 @@ -The RStudio application will launch a RStudio session on Puhti -with the specified resources using the selected -[r-env](../../apps/r-env.md) version. +--- +editor_options: + markdown: + wrap: 100 +--- -Selecting Multithreaded will set `OMP_NUM_THREADS` -to the number of requested CPU cores. +# RStudio -The user is automatically logged in to the rstudio session -when pressing the **Connect to RStudio Server** button. +The RStudio application will launch an RStudio session on Puhti with the specified resources using +the selected [r-env](../../apps/r-env.md#available) version. Currently, the latest available r-env +(and R) version is 4.4.0. + +The user is automatically logged in to the RStudio session when pressing the **Connect to RStudio +Server** button. + +Selecting Multithreaded will set the environment variable `OMP_NUM_THREADS`, controlling the number +of OpenMP threads, to the number of requested CPU cores. See [r-env documentation on +threading](../../apps/r-env.md#improving-performance-using-threading) for more details. + +!!! info + RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses. Long, memory-intensive, or otherwise resource-heavy tasks +are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). + +## Frequently asked questions about RStudio + +### RStudio is not starting and I see a grey screen. What should I do? + +If an RStudio session fails to start or RStudio is extremely slow, first try resetting your +RStudio user state as described below. These steps will clean up leftover data from previous interrupted RStudio +sessions in two hidden folders in the user's home directory. + +Use the file viewer in the Puhti web interface (click **show dotfiles**) or a terminal to rename or +delete these folders : + +`~/.config/rstudio`\ +`~/.local/share/rstudio` + +If after this RStudio still fails to start or remains very slow, please contact [CSC Service +Desk](../support/contact.md). + +### How do I install an R package? + +The R environment on Puhti has over 1400 pre-installed R packages packages ready to use. The easiest +way to check if a package is available is to try to load it with `library(packagename)`. If a +package is missing, you can install it yourself for your project following the [instructions for R package +installation](../../apps/r-env.md#r-package-installations), or you can contact [CSC Service +Desk](../support/contact.md) for an installation available to all users. + +### How do I change the directory shown in the RStudio files panel? + +By default, your Puhti home directory is shown in the files panel. To change the directory, click the three dots on the top right of the panel. In the box that appears, type the target directory, for example `/scratch/`. + +## More information + +For more information on the R environment on Puhti, see the [r-env +documentation](../../apps/r-env.md). If you have a question, contact [CSC Service +Desk](../support/contact.md). From db8c7c3723e55d4f49fc64db703f2e222282b347 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Wed, 8 Jan 2025 16:44:59 +0200 Subject: [PATCH 02/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 755bd2e8fc..a46c7dff13 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -19,7 +19,7 @@ threading](../../apps/r-env.md#improving-performance-using-threading) for more d !!! info RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses. Long, memory-intensive, or otherwise resource-heavy tasks -are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). + are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). ## Frequently asked questions about RStudio @@ -32,11 +32,11 @@ sessions in two hidden folders in the user's home directory. Use the file viewer in the Puhti web interface (click **show dotfiles**) or a terminal to rename or delete these folders : -`~/.config/rstudio`\ +`~/.config/rstudio` `~/.local/share/rstudio` If after this RStudio still fails to start or remains very slow, please contact [CSC Service -Desk](../support/contact.md). +Desk](../../support/contact.md). ### How do I install an R package? @@ -44,7 +44,7 @@ The R environment on Puhti has over 1400 pre-installed R packages packages ready way to check if a package is available is to try to load it with `library(packagename)`. If a package is missing, you can install it yourself for your project following the [instructions for R package installation](../../apps/r-env.md#r-package-installations), or you can contact [CSC Service -Desk](../support/contact.md) for an installation available to all users. +Desk](../../support/contact.md) for an installation available to all users. ### How do I change the directory shown in the RStudio files panel? @@ -54,4 +54,4 @@ By default, your Puhti home directory is shown in the files panel. To change the For more information on the R environment on Puhti, see the [r-env documentation](../../apps/r-env.md). If you have a question, contact [CSC Service -Desk](../support/contact.md). +Desk](../../support/contact.md). From 6d252944657c18e8954473e5a7e22d20c724185b Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Wed, 8 Jan 2025 17:10:11 +0200 Subject: [PATCH 03/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index a46c7dff13..92924548c5 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -7,19 +7,19 @@ editor_options: # RStudio The RStudio application will launch an RStudio session on Puhti with the specified resources using -the selected [r-env](../../apps/r-env.md#available) version. Currently, the latest available r-env -(and R) version is 4.4.0. +the selected R environment ([r-env](../../apps/r-env.md#available)) version. Currently, the latest available r-env +(and R) version is **4.4.0**. The user is automatically logged in to the RStudio session when pressing the **Connect to RStudio Server** button. -Selecting Multithreaded will set the environment variable `OMP_NUM_THREADS`, controlling the number +Selecting **Multithreaded** will set the environment variable `OMP_NUM_THREADS`, controlling the number of OpenMP threads, to the number of requested CPU cores. See [r-env documentation on threading](../../apps/r-env.md#improving-performance-using-threading) for more details. -!!! info - RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses. Long, memory-intensive, or otherwise resource-heavy tasks - are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). +!!! note "Please note" + RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses up to a few hours. Long, memory-intensive, or otherwise resource- + heavy tasks are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). ## Frequently asked questions about RStudio From ec703dbb86df335b049b9e300bfb0e5eb4846fbf Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Wed, 8 Jan 2025 17:17:42 +0200 Subject: [PATCH 04/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 92924548c5..dcba6ac9ce 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -17,9 +17,9 @@ Selecting **Multithreaded** will set the environment variable `OMP_NUM_THREADS`, of OpenMP threads, to the number of requested CPU cores. See [r-env documentation on threading](../../apps/r-env.md#improving-performance-using-threading) for more details. -!!! note "Please note" - RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses up to a few hours. Long, memory-intensive, or otherwise resource- - heavy tasks are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). +!!! note "When to use RStudio?" + RStudio sessions on Puhti are meant for interactive work, for example R script development and running light and medium-heavy analyses up to a few hours. Long, + memory-intensive, or otherwise resource-heavy tasks are best carried out as [non-interactive batch jobs](../../apps/r-env.md#non-interactive-use). ## Frequently asked questions about RStudio @@ -48,7 +48,7 @@ Desk](../../support/contact.md) for an installation available to all users. ### How do I change the directory shown in the RStudio files panel? -By default, your Puhti home directory is shown in the files panel. To change the directory, click the three dots on the top right of the panel. In the box that appears, type the target directory, for example `/scratch/`. +By default, the files panel shows your home directory on Puhti. To change the directory, click the three dots on the top right of the panel. In the box that appears, type the target directory, for example `/scratch/`. ## More information From 6faa69c6632ee2a141bbe2a6bfef898a94a44a07 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Wed, 8 Jan 2025 17:24:00 +0200 Subject: [PATCH 05/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index dcba6ac9ce..3a3c6582eb 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -42,9 +42,9 @@ Desk](../../support/contact.md). The R environment on Puhti has over 1400 pre-installed R packages packages ready to use. The easiest way to check if a package is available is to try to load it with `library(packagename)`. If a -package is missing, you can install it yourself for your project following the [instructions for R package +package is missing, you can install it yourself for your project by following the [instructions for R package installation](../../apps/r-env.md#r-package-installations), or you can contact [CSC Service -Desk](../../support/contact.md) for an installation available to all users. +Desk](../../support/contact.md) for a general installation available to all users. ### How do I change the directory shown in the RStudio files panel? From 7e4c25112a29a477f6e7ed543c5170807c18b743 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Wed, 8 Jan 2025 17:31:18 +0200 Subject: [PATCH 06/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 3a3c6582eb..0e3f876af8 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -7,7 +7,7 @@ editor_options: # RStudio The RStudio application will launch an RStudio session on Puhti with the specified resources using -the selected R environment ([r-env](../../apps/r-env.md#available)) version. Currently, the latest available r-env +the selected [R environment (r-env) version](../../apps/r-env.md#available)). Currently, the latest available r-env (and R) version is **4.4.0**. The user is automatically logged in to the RStudio session when pressing the **Connect to RStudio @@ -35,7 +35,7 @@ delete these folders : `~/.config/rstudio` `~/.local/share/rstudio` -If after this RStudio still fails to start or remains very slow, please contact [CSC Service +If after this RStudio still fails to start or remains very slow, please [contact CSC Service Desk](../../support/contact.md). ### How do I install an R package? @@ -43,7 +43,7 @@ Desk](../../support/contact.md). The R environment on Puhti has over 1400 pre-installed R packages packages ready to use. The easiest way to check if a package is available is to try to load it with `library(packagename)`. If a package is missing, you can install it yourself for your project by following the [instructions for R package -installation](../../apps/r-env.md#r-package-installations), or you can contact [CSC Service +installation](../../apps/r-env.md#r-package-installations), or you can [contact CSC Service Desk](../../support/contact.md) for a general installation available to all users. ### How do I change the directory shown in the RStudio files panel? @@ -53,5 +53,5 @@ By default, the files panel shows your home directory on Puhti. To change the di ## More information For more information on the R environment on Puhti, see the [r-env -documentation](../../apps/r-env.md). If you have a question, contact [CSC Service +documentation](../../apps/r-env.md). If you have a question, please [contact CSC Service Desk](../../support/contact.md). From 39b507a59aa139574520a3d59a7d2ae1d81ca3e9 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:13:03 +0200 Subject: [PATCH 07/11] Extend RStudio documentation Expand folder renaming/deleting instructions. --- docs/computing/webinterface/rstudio.md | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 0e3f876af8..f28f5f19f7 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -27,14 +27,22 @@ threading](../../apps/r-env.md#improving-performance-using-threading) for more d If an RStudio session fails to start or RStudio is extremely slow, first try resetting your RStudio user state as described below. These steps will clean up leftover data from previous interrupted RStudio -sessions in two hidden folders in the user's home directory. - -Use the file viewer in the Puhti web interface (click **show dotfiles**) or a terminal to rename or -delete these folders : +sessions in two hidden folders in the user's home directory: `~/.config/rstudio` `~/.local/share/rstudio` +**Option 1:** Use the file viewer in the Puhti web interface: + +1. In the top left corner of the Puhti web interface dashboard, choose **Files** and **Home Directory**. +2. Click **Show dotfiles**. +3. Delete or rename the `rstudio` folders under `.config` and `.local` -> `share`. + +**Option 2:** Use a terminal (for example a login node shell in the Puhti web interface) to rename or delete these folders. Here is an example how renaming would work: + +`mv ~/.config/rstudio ~/.config/rstudio-old` +`mv ~/.local/share/rstudio ~/.local/share/rstudio-old` + If after this RStudio still fails to start or remains very slow, please [contact CSC Service Desk](../../support/contact.md). From b16e264fbc2b771be945dd4b63eecf2814bce7c5 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:15:20 +0200 Subject: [PATCH 08/11] Extend RStudio documentation Fix linebreak type --- docs/computing/webinterface/rstudio.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index f28f5f19f7..b829163a2e 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -40,7 +40,7 @@ sessions in two hidden folders in the user's home directory: **Option 2:** Use a terminal (for example a login node shell in the Puhti web interface) to rename or delete these folders. Here is an example how renaming would work: -`mv ~/.config/rstudio ~/.config/rstudio-old` +`mv ~/.config/rstudio ~/.config/rstudio-old` `mv ~/.local/share/rstudio ~/.local/share/rstudio-old` If after this RStudio still fails to start or remains very slow, please [contact CSC Service From 13c344d9df1e154cf0c33b6c6f08cb2da5697546 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:21:40 +0200 Subject: [PATCH 09/11] Extend RStudio documentation Fix folder name location. --- docs/computing/webinterface/rstudio.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index b829163a2e..6ee05f02b5 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -27,10 +27,7 @@ threading](../../apps/r-env.md#improving-performance-using-threading) for more d If an RStudio session fails to start or RStudio is extremely slow, first try resetting your RStudio user state as described below. These steps will clean up leftover data from previous interrupted RStudio -sessions in two hidden folders in the user's home directory: - -`~/.config/rstudio` -`~/.local/share/rstudio` +sessions in two hidden folders in the user's home directory: `.config/rstudio` and `.local/share/rstudio`. **Option 1:** Use the file viewer in the Puhti web interface: From ad0301f2d439fecb5bfab56e013e1fc5b610ce8c Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:41:01 +0200 Subject: [PATCH 10/11] Extend RStudio documentation Renaming/deleting specifications. --- docs/computing/webinterface/rstudio.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index 6ee05f02b5..e7b4d26d03 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -27,7 +27,7 @@ threading](../../apps/r-env.md#improving-performance-using-threading) for more d If an RStudio session fails to start or RStudio is extremely slow, first try resetting your RStudio user state as described below. These steps will clean up leftover data from previous interrupted RStudio -sessions in two hidden folders in the user's home directory: `.config/rstudio` and `.local/share/rstudio`. +sessions in two hidden folders in the user's home directory: `.config/rstudio` and `.local/share/rstudio`. These folders can be either renamed (to keep the contents) or deleted (if you are sure the contents are not needed). **Option 1:** Use the file viewer in the Puhti web interface: @@ -35,7 +35,7 @@ sessions in two hidden folders in the user's home directory: `.config/rstudio` a 2. Click **Show dotfiles**. 3. Delete or rename the `rstudio` folders under `.config` and `.local` -> `share`. -**Option 2:** Use a terminal (for example a login node shell in the Puhti web interface) to rename or delete these folders. Here is an example how renaming would work: +**Option 2:** Use a terminal (for example a login node shell in the Puhti web interface) to delete or rename these folders. Here is an example how renaming would work: `mv ~/.config/rstudio ~/.config/rstudio-old` `mv ~/.local/share/rstudio ~/.local/share/rstudio-old` From db29b7c3c5178c03abf69ff598999a3c90c0d115 Mon Sep 17 00:00:00 2001 From: Heli Juottonen <90921070+helijuottonen@users.noreply.github.com> Date: Thu, 9 Jan 2025 13:46:04 +0200 Subject: [PATCH 11/11] Extend RStudio documentation --- docs/computing/webinterface/rstudio.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/docs/computing/webinterface/rstudio.md b/docs/computing/webinterface/rstudio.md index e7b4d26d03..d36949d511 100644 --- a/docs/computing/webinterface/rstudio.md +++ b/docs/computing/webinterface/rstudio.md @@ -1,9 +1,3 @@ ---- -editor_options: - markdown: - wrap: 100 ---- - # RStudio The RStudio application will launch an RStudio session on Puhti with the specified resources using