# Software on Yen Servers ## Overview The Yen servers host a variety of software packages for research and computing needs. This guide provides information on available software, how to load specific versions, and how to manage software modules on the Yen servers. ## Available Software Here's a list of software packages currently available on the Yen servers: - AMPL - Anaconda - AWS CLI - Bats - Bbcp - Claude Code - Codex - Dotnet - Emacs - Gemini CLI - GitHub CLI - Google Cloud - Google Drive - Go - GSL - Gurobi - HDF5 - Intel-python - Julia - Knitro - Ludwig - Mathematica - Matlab - Microsoft-R - Mosek - OpenMPI - PostgreSQL - Python - PyTorch - R - Rclone - SAS - Singularity - Stata - TensorFlow - Tomlab To check the current list of available software and versions, use the following command: Terminal Command ``` module avail ``` You should see the following: Terminal Output ``` ----------------------------------------------------------------- Global Aliases ----------------------------------------------------- statamp/17 -> stata/17 ------------------------------------------------------------- /software/modules/Core ------------------------------------------------- R/3.6.3 gurobi/9.0.2 julia/1.10.2 (D) python/3.10.11 statamp/16 R/4.0.2 gurobi/9.5.2 knitro/12.0.0 python/3.11.3 statamp/17 (D) R/4.1.3 gurobi/10.0.0 (D) knitro/12.1.1 pytorch/2.0.1 (g) statamp/18 R/4.2.1 gurobipy/9.5.2 knitro/12.3.0 pytorch/2.1.2 (g,D) tensorflow/2 (g) R/4.3.0 (D) gurobipy/10.0.0 (D) knitro/14.0.0 (D) rclone/1.47.0 tomlab/8.8 ampl/20231031 gurobipy3/9.5.2 ludwig/0.8.6 (g) rclone/1.54.0 xstata-mp/now anaconda/5.2.0 gurobipy3/10.0.0 (D) mathematica/11.2 rclone/1.60.0 xstata-mp/16 anaconda3/5.2.0 hdf5/1.12.0 mathematica/14.1.0 (D) rclone/1.62.2 xstata-mp/17 (D) anaconda3/2022.05 intel-python/2019.4 matlab/R2018a rclone/1.63.1 (D) xstata-mp/18 anaconda3/2023.09 (D) intel-python3/2019.4 matlab/R2018b sas/9.4 xstata/now awscli/2.13.22 intel/2019.4 matlab/R2019b singularity/3.4.0 xstata/16 bats/1.5.0 julia/0.7.0 matlab/R2021b singularity/3.11.5 (D) xstata/17 (D) bbcp/17.12.00.00.0 julia/1.0.0 matlab/R2022a stata-mp/now xstata/18 dotnet/2.1.500 julia/1.0.2 matlab/R2022b (D) stata-mp/16 xstatamp/now dotnet/3.0.0-p2 (D) julia/1.2.0 matlab/R2024a stata-mp/17 (D) xstatamp/16 emacs/27.2 julia/1.3.1 microsoft-r-open/3.5.3 stata-mp/18 xstatamp/17 (D) gcloud/448.0.0 julia/1.5.1 mosek/10.2 stata/now xstatamp/18 gdrive/2.1.0 julia/1.6.2 openmpi/4.1.0 stata/16 go/1.13 julia/1.7.3 postgresql/15.1 (g) stata/17 (D) gsl/2.7.1 julia/1.8.0 python/2.7.18 stata/18 gurobi/8.0.1 julia/1.9.2 python/3.10.5 (D) statamp/now Where: g: built for GPU D: Default Module ``` The `(D)` stands for the default module. These will be loaded when the version is not specified. The `(g)` means these modules were built with GPU support, meaning they will support use with our GPU nodes. You can filter `module avail` for a specific software with the command: Terminal Command ``` module avail R/ ``` Terminal Output ``` -------------------------------------------------------------------------- Global Aliases --------------------------------------------------------------------------- ---------------------------------------------------------------------- /software/modules/Core ----------------------------------------------------------------------- R/3.6.3 R/4.0.2 R/4.1.3 R/4.2.1 R/4.3.0 (D) Where: D: Default Module ``` ## Loading Software Modules To load a software module, use the following command: Terminal Command ``` module load ``` Tip You may also use the `ml` command as a shorthand for `module load`. AI Agents Carry Data Responsibilities AI coding agents such as `claude-code`, `codex`, and `gemini` are available as modules. These tools send the files they can access to external providers. It is **your** responsibility to know what data may be shared with AI tools and to keep data covered by a signed DUA or NDA out of them. See [AI Coding Agents](/_user_guide/ai_agents/) before loading these modules, and contact [gsb-library_research-data-coordination@stanford.edu](mailto:gsb-library_research-data-coordination@stanford.edu) with any questions. For example, to load R, run: Terminal Command ``` module load R ``` To see the currently loaded modules, use the following command: Terminal Command ``` module list ``` or with the shorthand: Terminal Command ``` ml ``` If you have loaded the R module, you should see the following output: Terminal Output ``` Currently Loaded Modules: 1) R/4.3.0 ``` ## Switching Versions If multiple versions of a software are available, the default version is indicated by a `(D)`. To load a specific version, you'll need to specify the version number. For example, to load R version 4.1.3, use the following command: Terminal Command ``` module load R/4.1.3 ``` Now if you run the command `module list`, you should see the following output: Terminal Output ``` Currently Loaded Modules: 1) R/4.1.3 ``` You can also swap versions of R with the following command: Terminal Command ``` module swap R/3.6.3 ``` Terminal Output ``` Currently Loaded Modules: 1) R/3.6.3 ``` ## Unloading Modules You can unload an individual module with: Terminal Command ``` module unload R/3.6.3 ``` or with the shorthand: Terminal Command ``` ml -R/3.6.3 ``` Alternatively, you can unload all currently loaded modules with: Terminal Command ``` ml purge ``` Now, if you run: Terminal Command ``` ml ``` you will see: Terminal Output ``` No modules loaded ``` ## Managing Software Modules Sometimes you want to know the path where software binary is installed. For example, this information can be useful when installing certain R packages from source. To get details about a currently loaded module, you can use the following commands: Terminal Command ``` ml R/4.2.1 ml show R ``` These commands will display information about the module, including details that might be useful for your task. Terminal Output ``` -------------------------------------------------------------------------------------------------- /software/modules/Core/R/4.2.1.lua: --------------------------------------------------------------------------------------------------- whatis("Name: R") whatis("Version: 4.2.1") whatis("Category: tools") whatis("URL: http://cran.cnr.berkeley.edu/") whatis("Description: R") family("R") load("rstudio") prepend_path("PATH","/software/free/R/R-4.2.1/bin") ``` Linux modules modify only your current working environment. This means that if you lose connection to the Yen servers or close your terminal window, you will need to reload the modules. However, all the libraries or packages you have installed as a user will persist and only need to be installed once. Once the software you want to use is loaded, the binary becomes available for use from the command line. For example, to install R packages or run the interactive R console, type: Terminal Command ``` R ``` The interactive R console will open with the R version matching the module you have loaded: Terminal Output ``` R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. ``` Type `q()` to exit the interactive R console: Terminal Command ``` q() ``` Type `n` when prompted to save the workspace. This is generally recommended to prevent clutter from unwanted saved objects and to provide a clean start for your next session: Terminal Output ``` Save workspace image? [y/n/c]: n ```