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Software environment

The software environment on Tursa is primarily controlled through the module command. By loading and switching software modules you control which software and versions are available to you.

Information

A module is a self-contained description of a software package -- it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.

By default, all users on Tursa start with the default software environment loaded.

Software modules on Tursa are provided by both ATOS and by EPCC.

In this section, we provide:

  • A brief overview of the module command
  • A brief description of how the module command manipulates your environment

Using the module command

We only cover basic usage of the module command here. For full documentation please see the Linux manual page on modules

The module command takes a subcommand to indicate what operation you wish to perform. Common subcommands are:

  • module list [name] - List modules currently loaded in your environment, optionally filtered by [name]
  • module avail [name] - List modules available, optionally filtered by [name]
  • module savelist - List module collections available (usually used for accessing different programming environments)
  • module restore name - Restore the module collection called name (usually used for setting up a programming environment)
  • module load name - Load the module called name into your environment
  • module remove name - Remove the module called name from your environment
  • module swap old new - Swap module new for module old in your environment
  • module help name - Show help information on module name
  • module show name - List what module name actually does to your environment

These are described in more detail below.

Information on the available modules

The module list command will give the names of the modules and their versions you have presently loaded in your environment. By default, you will have no modules loaded when you first log into Tursa

Finding out which software modules are available on the system is performed using the module avail command. To list all software modules available, use:

[dc-user1@tursa-login1 ~]$ module avail
------------------------------------------ /mnt/lustre/tursafs1/apps/cuda-11.0.2-modulefiles -------------------------------------------
cuda/11.0.2  openmpi/4.1.1-cuda11.0.2  ucx/1.10.1-cuda11.0.2  

------------------------------------------- /mnt/lustre/tursafs1/apps/cuda-11.4-modulefiles --------------------------------------------
cuda/11.4.1  openmpi/4.1.1-cuda11.4  ucx/1.12.0-cuda11.4  

------------------------------------------ /mnt/lustre/tursafs1/apps/cuda-11.4.1-modulefiles -------------------------------------------
cuda/11.4.1  openmpi/4.1.1-cuda11.4.1  ucx/1.12.0-cuda11.4.1  

------------------------------------------------ /mnt/lustre/tursafs1/apps/modulefiles -------------------------------------------------
cuda/11.0.3  dot  gcc/9.3.0  module-git  module-info  modules  null  openmpi/4.1.1  ucx/1.10.1  use.own  xpmem/2.6.5   

This will list all the names and versions of the modules available on the service. Not all of them may work in your account though due to, for example, licencing restrictions. You will notice that for many modules we have more than one version, each of which is identified by a version number. One of these versions is the default. As the service develops the default version will change and old versions of software may be deleted.

You can list all the modules of a particular type by providing an argument to the module avail command. For example, to list all available versions of the OpenMPI library, use:

[dc-user1@tursa-login1 ~]$ module avail openmpi
------------------------------------------ /mnt/lustre/tursafs1/apps/cuda-11.0.2-modulefiles -------------------------------------------
openmpi/4.1.1-cuda11.0.2  

------------------------------------------- /mnt/lustre/tursafs1/apps/cuda-11.4-modulefiles --------------------------------------------
openmpi/4.1.1-cuda11.4  

------------------------------------------ /mnt/lustre/tursafs1/apps/cuda-11.4.1-modulefiles -------------------------------------------
openmpi/4.1.1-cuda11.4.1  

----------------

The module show command reveals what operations the module actually performs to change your environment when it is loaded. We provide a brief overview of what the significance of these different settings mean below. For example, for the default openmpi module:

[dc-user1@tursa-login1 ~]$ module show openmpi
-------------------------------------------------------------------
/mnt/lustre/tursafs1/apps/cuda-11.0.2-modulefiles/openmpi/4.1.1-cuda11.0.2:

module-whatis   Sets up OpenMPI on your environment
setenv          MPI_ROOT        /mnt/lustre/tursafs1/apps/basestack/cuda-11.0.2/openmpi/4.1.1/
prepend-path    PATH /mnt/lustre/tursafs1/apps/basestack/cuda-11.0.2/openmpi/4.1.1/bin/
prepend-path    LD_LIBRARY_PATH /mnt/lustre/tursafs1/apps/basestack/cuda-11.0.2/openmpi/4.1.1/lib
prepend-path    MANPATH /opt/mpi/openmpi/4.0.4.1/share/man
module load     ucx/1.10.1
setenv          OMPI_CC cc
setenv          OMPI_CXX        g++
setenv          OMPI_CFLAGS     -g -m64
setenv          OMPI_CXXFLAGS   -g -m64
-------------------------------------------------------------------

Loading, removing and swapping modules

To load a module to use the module load command. For example, to load the default version of OpenMPI into your environment, use:

[dc-user1@tursa-login1 ~]$ module load openmpi

        UCX 1.10 loaded


        OpenMPI 4.1.1 loaded

Once you have done this, your environment will be setup to use the OpenMPI library. The above command will load the default version of OpenMPI. If you need a specific version of the software, you can add more information:

[dc-user1@tursa-login1 ~]$ module load openmpi/4.1.1-cuda11.4.1

        UCX 1.12.0 compiled with cuda 11.4.1 loaded


        OpenMPI 4.1.1 with cuda-11.4.1 and UCX 1.12.0  loaded

will load OpenMPI version 4.1.1 with CUDA 11.4.1 into your environment, regardless of the default.

If you want to remove software from your environment, module rm will remove a loaded module:

[dc-user1@tursa-login1 ~]$ module rm openmpi

will unload what ever version of openmpi (even if it is not the default) you might have loaded.

There are many situations in which you might want to change the presently loaded version to a different one, such as trying the latest version which is not yet the default or using a legacy version to keep compatibility with old data. This can be achieved most easily by using module swap oldmodule newmodule.

Suppose you have loaded version 4.1.1 of openmpi, the following command will change to version 4.1.1-cuda11.4.1:

[dc-user1@tursa-login1 ~]$ module swap openmpi openmpi/4.1.1-cuda11.4.1

        UCX 1.12.0 compiled with cuda 11.4.1 loaded


        OpenMPI 4.1.1 with cuda-11.4.1 and UCX 1.12.0  loaded

You did not need to specify the version of the loaded module in your current environment as this can be inferred as it will be the only one you have loaded.

Capturing your environment for reuse

Sometimes it is useful to save the module environment that you are using to compile a piece of code or execute a piece of software. This is saved as a module collection. You can save a collection from your current environment by executing:

[dc-user1@tursa-login1 ~]$ module save [collection_name]

Note

If you do not specify the environment name, it is called default.

You can find the list of saved module environments by executing:

[dc-user1@tursa-login1 ~]$ module savelist
Named collection list:
 1) default

To list the modules in a collection, you can execute, e.g.,:

[dc-user1@tursa-login1 ~]$ module saveshow default
-------------------------------------------------------------------
/home/z01/z01/dc-turn1/.module/default:

module use --append /mnt/lustre/tursafs1/apps/cuda-11.0.2-modulefiles
module use --append /mnt/lustre/tursafs1/apps/cuda-11.4-modulefiles
module use --append /mnt/lustre/tursafs1/apps/cuda-11.4.1-modulefiles
module use --append /mnt/lustre/tursafs1/apps/modulefilesintel
module use --append /mnt/lustre/tursafs1/apps/modulefiles
module load ucx/1.12.0-cuda11.4.1
module load openmpi/4.1.1-cuda11.4.1

-------------------------------------------------------------------

Note again that the details of the collection have been saved to the home directory (the first line of output above). It is possible to save a module collection with a fully qualified path, e.g.,

[dc-user1@tursa-login1 ~]$ module save /home/t01/z01/auser/my-module-collection

if you want to save to a specific file name.

To delete a module environment, you can execute:

[dc-user1@tursa-login1 ~]$ module saverm <environment_name>

Shell environment overview

When you log in to Tursa, you are using the bash shell by default. As any other software, the bash shell has loaded a set of environment variables that can be listed by executing printenv or export.

The environment variables listed before are useful to define the behaviour of the software you run. For instance, OMP_NUM_THREADS define the number of threads.

To define an environment variable, you need to execute:

export OMP_NUM_THREADS=4

Please note there are no blanks between the variable name, the assignation symbol, and the value. If the value is a string, enclose the string in double quotation marks.

You can show the value of a specific environment variable if you print it:

echo $OMP_NUM_THREADS

Do not forget the dollar symbol. To remove an environment variable, just execute:

unset OMP_NUM_THREADS

Compiler environment

The system supports the following compilers and MPI library:

  • GCC 9.3.0
  • CUDA 11.4
  • OpenMPI 4.1.1

To compile on the system, you would typically load the required modules:

[dc-user1@tursa-login1 ~]$ module load gcc/9.3.0
[dc-user1@tursa-login1 ~]$ module load cuda/11.4.1 
[dc-user1@tursa-login1 ~]$ module load openmpi/4.1.1-cuda11.4
[dc-user1@tursa-login1 ~]$ module list
Currently Loaded Modulefiles:
 1) gcc/9.3.0   2) cuda/11.4.1   3) ucx/1.12.0-cuda11.4   4) openmpi/4.1.1-cuda11.4 

Once you have loaded the modules, the standard OpenMPI compiler wrapper scripts are available:

  • mpicc
  • mpicxx
  • mpif90

You can find more information on these scripts in the OpenMPI documentation.