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tools:rtools [2024/07/04 14:54]
vagudets [2024] 		tools:rtools [2025/06/13 12:33] (current)
vagudets [Environment Modules]
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 The Workstations, the BSC-ES Hub and the HPC machines use [[https://earth.bsc.es/wiki/doku.php?id=library:environment_modules | environment modules]], which are maintained by our IT team. Each module contains a set of software packages that can only be used if the module has been loaded in the environment.  The Workstations, the BSC-ES Hub and the HPC machines use [[https://earth.bsc.es/wiki/doku.php?id=library:environment_modules | environment modules]], which are maintained by our IT team. Each module contains a set of software packages that can only be used if the module has been loaded in the environment. 
  
-For example, to load CDO and R in the workstation, you should load the corresponding modules with the 'module load' command: +For example, to load CDO and R in the hub, you should load the corresponding modules with the 'module load' command: 
-    module load CDO/1.9.8-foss-2015a +    module load CDO/2.4.4-gompi-2023b 
-    module load R/4.1.2-foss-2015a-bare+    module load R/4.4.1-gfbf-2023b 
 +    module load R-bundle-CRAN/2024.06-foss-2023b
  
 The currently maintained R module versions are: The currently maintained R module versions are:
  
-  * Workstations: R/4.1.2-foss-2015a-bare (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:workstations| Computing - Workstations]]) +  * BSC-ES Hub: R/4.4.1-gfbf-2023b (+ R-bundle-CRAN/2024.06-foss-2023b for most CRAN Packages; and R-bundle-Bioconductor/3.19-foss-2023b-R-4.4.1 for Bioconductor packages. See: [[https://earth.bsc.es/wiki/doku.php?id=computing:bsceshub | Computing - Bsceshub]])
-  * BSC-ES Hub: R/4.2.1-foss-2021b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:bsceshub|Computing - Bsceshub (Testing phase)]])+
   * Nord3v2: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:nord3-v2|Computing - Nord3v2]])   * Nord3v2: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:nord3-v2|Computing - Nord3v2]])
   * CTE-AMD: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:amd|Computing - AMD]])   * CTE-AMD: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:amd|Computing - AMD]])
 +  * Nord4: R/4.1.2-foss-2019b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:nord4|Computing - Nord4]])
 +  * BSC-ES Hub (deprecated): R/4.2.1-foss-2021b (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:bsceshub|Computing - Bsceshub (Testing phase)]])
 +  * Workstations (deprecated): R/4.1.2-foss-2015a-bare (See: [[https://earth.bsc.es/wiki/doku.php?id=computing:workstations| Computing - Workstations]])
  
 Check the wiki page for each machine to see if you need to follow any additional steps to be able to load the correct modules. Check the wiki page for each machine to see if you need to follow any additional steps to be able to load the correct modules.
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   * RStudio Server is available on the Workstations and Nord3v2. See the section ‘RStudio Server’ below. RStudio Server is not yet available on the Hub, but you can use VSCode. See the ‘R tips’ section below.    * RStudio Server is available on the Workstations and Nord3v2. See the section ‘RStudio Server’ below. RStudio Server is not yet available on the Hub, but you can use VSCode. See the ‘R tips’ section below. 
   * To use Jupyter Notebooks in the BSC-ES Hub, see the [[https://earth.bsc.es/wiki/doku.php?id=computing:howto:jupyter_notebooks#r_experimental | Jupyter Notebook wiki page]]. For the workstations, the up-to-date R version is not working with Jupyter Notebooks.   * To use Jupyter Notebooks in the BSC-ES Hub, see the [[https://earth.bsc.es/wiki/doku.php?id=computing:howto:jupyter_notebooks#r_experimental | Jupyter Notebook wiki page]]. For the workstations, the up-to-date R version is not working with Jupyter Notebooks.
 +  
 +===== In-house Packages =====
 +
 +Brief Summary and links to in-house packages: {{ :tools:package_summary.pdf | Package Summary}}
 +
 +See specific information for each tool:
 +
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:startR&s[]=startR|startR]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:CSTools&s[]=CSTools|CSTools]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:ClimProjDiags&s[]=ClimProjDiags|ClimProjDiags]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:s2dv&s[]=s2dv|s2dv]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:multiApply&s[]=multiApply|multiApply]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:easyNCDF&s[]=easyNCDF|easyNCDF]]
 +  * [[https://earth.bsc.es/wiki/doku.php?id=tools:s2dverification&s[]=s2dverification|s2dverification]] //[deprecated 04/09/2020]//
 +
 +===== Presentations =====
 +  * {{ :tools:r_tool_roadmap_2024.pdf |R Tools Roadmap 2024}}
 +  * {{ :tools:day2_04_handson_r_tools.pdf | BSC Training (PATC) 2023 - Climate Forecast Analysis hands-on tutorial: R tools}}
 +  * {{ :tools:create_r_package_in_bsc-es.pdf | Create R Package in BSC-ES}} (2023-05-26)
 +  * {{ :tools:r_tool_roadmap_2023.pdf | R Tools Roadmap 2023}}
 +  * {{ :tools:patc2022_r_handson.pdf | PATC2022 - Climate Forecast Analysis hands-on tutorial: R tools}}
 +  * {{ :tools:training_introductiontothedeptrtools.pdf | Training: Introduction to the department tools }} (2021-01-26)
 +  * [[https://docs.google.com/presentation/d/1AfVKHxSDbMw0HD5yDCZ6evx2PpbsFG9_gsRDxMNFhU8/edit#slide=id.g60506b0e68_0_432|General scheme of the department R tools]]
 +  * {{ :tools:18nov2020-ivmw-o.pdf |Overview Development and Maintenance}}
 +
 +===== How to report an issue =====
 +We use issues to identify and address bugs and propose new developments in the codebase. If you find a problem in our tools, please read this document to see if you should and how to report an issue. [[https://docs.google.com/document/d/1zRlmsRwFDJctDB94x6HGf6ezu3HFHhEjaBu0hVcrwTI/edit?usp=sharing|Guidelines for R-related questions in Earth Sciences]]
  
 ===== R User Meeting ===== ===== R User Meeting =====
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   * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing&s|Minutes until June 2022]]   * [[https://docs.google.com/document/d/1VqnwgeimqNLODfqAyPjIY9XprGD5JQ-NPqzQF6nNDS0/edit?usp=sharing&s|Minutes until June 2022]]
   * [[https://docs.google.com/document/d/1mdLCS7SC5-8NwAB_gAzUsEnJN4yYEYmAlVys0qT8Edk/edit?usp=sharing|Minutes since July 2022]]   * [[https://docs.google.com/document/d/1mdLCS7SC5-8NwAB_gAzUsEnJN4yYEYmAlVys0qT8Edk/edit?usp=sharing|Minutes since July 2022]]
 +
 +====2025====
 +  * R tools user meeting (Hybrid Mode, 05/06/2025){{ :tools:r_user_meeting_20250605.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 03/04/2025){{ :tools:r_user_meeting_20250403.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 06/02/2025){{ :tools:r_user_meeting_20250206.pdf | Slides}}
 +
  
 ====2024==== ====2024====
-  * R tools user meeting (Hybrid Mode, 01/02/2024){{ :tools:r_user_meeting_20240201.pdf | Slides}} +  * R tools user meeting (Hybrid Mode, 12/12/2024){{ :tools:r_user_meeting_20241212.pdf | Slides}} 
-  * R tools user meeting (Hybrid Mode, 04/04/2024){{ :tools:r_user_meeting_20240404.pdf | Slides}} +  * R tools user meeting (Slides-only, 07/11/2024){{ :tools:r_user_meeting_20241107.pdf | Slides}} 
-  * R tools user meeting (Hybrid Mode, 02/05/2024){{ :tools:r_user_meeting_20240502.pdf | Slides}} +  * R tools user meeting (Hybrid Mode, 12/09/2024){{ :tools:r_user_meeting_20240912.pdf | Slides}}
-  * R tools user meeting (Hybrid Mode, 01/06/2024){{ :tools:r_user_meeting_20240606.pdf | Slides}}+
   * R tools user meeting (Hybrid Mode, 04/07/2024){{ :tools:r_user_meeting_20240704.pdf | Slides}}   * R tools user meeting (Hybrid Mode, 04/07/2024){{ :tools:r_user_meeting_20240704.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 01/06/2024){{ :tools:r_user_meeting_20240606.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 02/05/2024){{ :tools:r_user_meeting_20240502.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 04/04/2024){{ :tools:r_user_meeting_20240404.pdf | Slides}}
 +  * R tools user meeting (Hybrid Mode, 01/02/2024){{ :tools:r_user_meeting_20240201.pdf | Slides}}
 +
 ====2023==== ====2023====
   * R tools user meeting (Mix Mode, 14/12/2023){{ :tools:r_user_meeting_20231214.pdf | Slides}}   * R tools user meeting (Mix Mode, 14/12/2023){{ :tools:r_user_meeting_20231214.pdf | Slides}}
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 ====2019==== ====2019====
   * R tools user meeting (BSC, 07/11/2019) {{ :tools:rtools_user_meeting_20191107.pdf |Slides}}{{ :tools:rtools_user_meeting_minutes_20191107.pdf |minutes}}   * R tools user meeting (BSC, 07/11/2019) {{ :tools:rtools_user_meeting_20191107.pdf |Slides}}{{ :tools:rtools_user_meeting_minutes_20191107.pdf |minutes}}
-   
-===== In-house Packages ===== 
- 
-Brief Summary and links to in-house packages: {{ :tools:package_summary.pdf | Package Summary}} 
- 
-See specific information for each tool: 
- 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:startR&s[]=startR|startR]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:CSTools&s[]=CSTools|CSTools]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:ClimProjDiags&s[]=ClimProjDiags|ClimProjDiags]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:s2dv&s[]=s2dv|s2dv]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:multiApply&s[]=multiApply|multiApply]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:easyNCDF&s[]=easyNCDF|easyNCDF]] 
-  * [[https://earth.bsc.es/wiki/doku.php?id=tools:s2dverification&s[]=s2dverification|s2dverification]] //[deprecated 04/09/2020]// 
- 
- 
-===== Presentations ===== 
-  * {{ :tools:r_tool_roadmap_2024.pdf |R Tools Roadmap 2024}} 
-  * {{ :tools:day2_04_handson_r_tools.pdf | BSC Training (PATC) 2023 - Climate Forecast Analysis hands-on tutorial: R tools}} 
-  * {{ :tools:create_r_package_in_bsc-es.pdf | Create R Package in BSC-ES}} (2023-05-26) 
-  * {{ :tools:r_tool_roadmap_2023.pdf | R Tools Roadmap 2023}} 
-  * {{ :tools:patc2022_r_handson.pdf | PATC2022 - Climate Forecast Analysis hands-on tutorial: R tools}} 
-  * {{ :tools:training_introductiontothedeptrtools.pdf | Training: Introduction to the department tools }} (2021-01-26) 
-  * [[https://docs.google.com/presentation/d/1AfVKHxSDbMw0HD5yDCZ6evx2PpbsFG9_gsRDxMNFhU8/edit#slide=id.g60506b0e68_0_432|General scheme of the department R tools]] 
-  * {{ :tools:18nov2020-ivmw-o.pdf |Overview Development and Maintenance}} 
- 
-===== How to report an issue ===== 
-We use issues to identify and address bugs and propose new developments in the codebase. If you find a problem in our tools, please read this document to see if you should and how to report an issue. [[https://docs.google.com/document/d/1zRlmsRwFDJctDB94x6HGf6ezu3HFHhEjaBu0hVcrwTI/edit?usp=sharing|Guidelines for R-related questions in Earth Sciences]] 
- 
  
 ===== How to source a function from GitLab repository ===== ===== How to source a function from GitLab repository =====
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 This package could be used by loading the following modules (note that order may affect): This package could be used by loading the following modules (note that order may affect):
  
-(on workstation)   +(on nord4)
-    module load R/4.1.2-foss-2015a-bare +
-    module load GDAL/2.2.1-foss-2015a  +
-    module load PROJ/4.8.0-foss-2015a  +
-    module load GEOS/3.7.2-foss-2015a-Python-2.7.9 +
- +
-(on nord3v2)+
     module load R/4.1.2-foss-2019b     module load R/4.1.2-foss-2019b
     module load GDAL/3.3.2-foss-2019b-Python-3.7.4      module load GDAL/3.3.2-foss-2019b-Python-3.7.4 
     module load PROJ/7.2.1-foss-2019b      module load PROJ/7.2.1-foss-2019b 
     module load GEOS/3.7.2-foss-2019b-Python-3.7.4     module load GEOS/3.7.2-foss-2019b-Python-3.7.4
-  +
 (on hub) (on hub)
 +  module load R/4.4.1-gfbf-2023b
 +  module load R-bundle-CRAN/2024.06-foss-2023b
 +  module load GEOS/3.12.1-GCC-13.2.0
 +  module load GDAL/3.9.0-foss-2023b
 +  module load PROJ/9.3.1-GCCcore-13.2.0
 +
 +(on bsceshub02 (deprecated))
     module load R/4.2.1-foss-2021b       module load R/4.2.1-foss-2021b  
     module load GDAL/3.5.2-foss-2021b-Python-3.9.6      module load GDAL/3.5.2-foss-2021b-Python-3.9.6 
     module load PROJ/9.1.0-foss-2021b      module load PROJ/9.1.0-foss-2021b 
     module load GEOS/3.11.0-GCC-11.2.0     module load GEOS/3.11.0-GCC-11.2.0
 +    
 +(on workstation)  
 +    module load R/4.1.2-foss-2015a-bare
 +    module load GDAL/2.2.1-foss-2015a 
 +    module load PROJ/4.8.0-foss-2015a 
 +    module load GEOS/3.7.2-foss-2015a-Python-2.7.9
  
 Note: Avoid to include them in your bashrc, just load them when it is a requirement.   Note: Avoid to include them in your bashrc, just load them when it is a requirement.  
tools/rtools.1720104864.txt.gz · Last modified: 2024/07/04 14:54 by vagudets

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