Skip to main content

Getting Started

caution

This documentation is under development and may be incomplete.

Using a SoftPack environment​

This tutorial describes how to use a previously created SoftPack environment for running Python, R or RStudio.

SoftPack environments are made available through the module command. It's the only command you need to learn in order to use a SoftPack environment. Documentation for the module command is available at the Environment Modules site if you're new to modules.

The first step is to tell the module command where to look for your environments. The following module use command adds the directory where your modules are installed. It's generally a good idea to add this command to you shell startup file (.bashrc or equivalent) so you don't have to do this manually each time you start a new shell.

$ module use --append /software/hgi/softpack/modules/users/$USER

The module use command can also be used to verify that module knows about all the directories where your modules are installed.

$ module use
Search path for module files (in search order):
  /etc/environment-modules/modules
  /usr/share/modules/versions
  /usr/share/modules/modulefiles
  /software/hgi/softpack/modules/users/aa27

You can now run module avail to get a list of all environments available to you.

$ module avail
--------------------- /usr/share/modules/modulefiles --------------------- 
dot  module-git  module-info  modules  null  use.own

---------------- /software/hgi/softpack/modules/users/aa27 ----------------
seurat5/1.0

There are two additional module subcommands worth noting here.

  • module whatis gives you a brief synopsis of what the module is about.
  • module help describes the module in more detail.

module whatis​

$ module whatis seurat5
---------------- /software/hgi/softpack/modules/users/aa27 ----------------
         seurat5/1.0: Softpack pilot with seurat 5, bpcells and monocle3

module help​

$ module help seurat5
-------------------------------------------------------------------
Module Specific Help for /software/hgi/softpack/modules/users/aa27/seurat5/1.0:

description: Softpack pilot with seurat 5, bpcells and monocle3
build:
  id: 6cb0fb19-19c2-4cc6-8e4a-9587cca739a0
  image: /software/hgi/softpack/images/6cb0fb19-19c2-4cc6-8e4a-9587cca739a0.sif
  created: 2023-04-28 16:34:42
  updated: 2023-04-28 22:15:44
packages:
  - r-afex
  - r-affy
  - r-affyio
  - r-annotationfilter
:

Loading a module​

To load a module, simply run module load with the name of an available module.

$ module load seurat5
Loading seurat5/1.0
  Loading requirement: /software/modules/ISG/singularity/3.10.0

You can get a list of all loaded modules using the module list command.

$ module list
Currently Loaded Modulefiles:
 1) /software/modules/ISG/singularity/3.10.0   2) seurat5/1.0

Now that the module is loaded, you can run Python, R or RStudio.

Running RStudio​

SoftPack environments that include RStudio will include a new rstudio command that starts a batch job on your high performance cluster.

$ rstudio
Usage: rstudio [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  list   List running RStudio servers.
  start  Start RStudio server.
  stop   Stop RStudio server.

To start a new RStudio session, use the rstudio start command. The rstudio start command supports the following optional arguments.

$ rstudio start --help
Usage: rstudio start [OPTIONS]

  Start RStudio server.

Options:
  --home PATH            home directory inside the container.  [default:
                         /nfs/users/nfs_a/aa27]
  -M MB                  sets the memory limit for the job (in MB).  [default:
                         15000]
  -n MIN[,MAX]           submits a parallel job and specifies the number of
                         tasks in the job.  [default: 2]
  -o, --output FILENAME  output filename.  [default: rstudio_session.log]
  --pwd PATH             initial working directory inside the container.
                         [default: /nfs/users/nfs_a/aa27]
  -q, --queue QUEUE      submits the job to the specified queue.
  --r-libs-user PATH     specifies additional directories for R packages.
  --help                 Show this message and exit.
info

You can change the home directory used inside RStudio using --home argument or by changing you current directory before starting the RStudio session.

Running rstudio start submits a batch job, starts RStudio server and provides you with instructions on how to connect to your RStudio session as shown below.

$ rstudio start
LSF job options:

io:
  errorAppendFile: rstudio_session.log
  outputAppendFile: rstudio_session.log
limit:
  memLimit: 15000
properties:
  jobName: aa27/rstudio-server
resource:
  numTasks: '2'
  resReq: select[model==Intel_Platinum && mem>15000] rusage[tmp=5000, mem=15000] span[hosts=1]

Job <22845162> is submitted to default queue <normal>.

Waiting for RStudio server to start ...

To access the server, open one of these URLs in a browser and login with the credentials below:

    http://node-10-3-4.internal.sanger.ac.uk:33025
    http://172.27.224.27:33025

    username: aa27
    password: iJX7MCV1w+6IPyXcYs9H

Once you're finished with RStudio, use the rstudio stop command to terminate the session.

$ rstudio stop
Job <22845162> is being terminated

You can also use the rstudio list command to get a list of all running sessions.

$ rstudio list
JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
22845162 aa27    RUN   normal     hgi-farm5   node-10-3-4:node-10-3-4 aa27/rstudio-server May  2 11:21
Last updated on