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
- Dotnet
- Emacs
- 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:
module avail
You should see the following:
----------------------------------------------------------------- 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:
module avail R/
-------------------------------------------------------------------------- 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:
module load <module_name>
Tip
You may also use the ml command as a shorthand for module load.
For example, to load R, run:
module load R
To see the currently loaded modules, use the following command:
module list
or with the shorthand:
ml
If you have loaded the R module, you should see the following 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:
module load R/4.1.3
module list, you should see the following output:
Currently Loaded Modules:
1) R/4.1.3
You can also swap versions of R with the following command:
module swap R/3.6.3
Currently Loaded Modules:
1) R/3.6.3
Unloading Modules
You can unload an individual module with:
module unload R/3.6.3
or with the shorthand:
ml -R/3.6.3
Alternatively, you can unload all currently loaded modules with:
ml purge
Now, if you run:
ml
you will see:
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:
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.
--------------------------------------------------------------------------------------------------
/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:
R
The interactive R console will open with the R version matching the module you have loaded:
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:
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:
Save workspace image? [y/n/c]: n