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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.

Tip

You may wish to consider using Spack on Tursa to manage your software installations and to help you compile software.

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

Software modules on Tursa are provided by both Eviden 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
---------------------------------------- /home/y07/shared/tursa-modules ----------------------------------------
cmake/3.27.4        openmpi/4.1.5                       ucx/1.15.0                       
cudnn/9.3.0-cuda12  openmpi/4.1.5-gcc9-cpu              ucx/1.15.0-gcc9-cpu              
gcc/9.3.0(default)  openmpi/4.1.5-gcc9-cuda12(default)  ucx/1.15.0-gcc9-cuda12(default)  
gcc/12.2.0          openmpi/4.1.5-gcc12-cpu             ucx/1.15.0-gcc12-cpu             
gdrcopy/2.5.1       openmpi/4.1.5-gcc12-cuda12          ucx/1.15.0-gcc12-cuda12          
nvhpc/23.5-nompi    setup-env                           

------------------------------- /mnt/lustre/tursafs1/apps/cuda-12.3-modulefiles --------------------------------
cuda/12.3  openmpi/4.1.5-cuda12.3  ucx/1.15.0-cuda12.3  

------------------------------ /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  gcc/9.3.0(default)  module-info  null           openmpi/4.1.1  use.own      
dot          module-git          modules      openmpi/4.0.4  ucx/1.10.1     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
---------------------------------------- /home/y07/shared/tursa-modules ----------------------------------------
openmpi/4.1.5           openmpi/4.1.5-gcc9-cuda12(default)  openmpi/4.1.5-gcc12-cuda12  
openmpi/4.1.5-gcc9-cpu  openmpi/4.1.5-gcc12-cpu             

------------------------------- /mnt/lustre/tursafs1/apps/cuda-12.3-modulefiles --------------------------------
openmpi/4.1.5-cuda12.3  

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

------------------------------------ /mnt/lustre/tursafs1/apps/modulefiles -------------------------------------
openmpi/4.0.4  openmpi/4.1.1

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
-------------------------------------------------------------------
/home/y07/shared/tursa-modules/openmpi/4.1.5-gcc9-cuda12:

module-whatis   Sets up OpenMPI on your environment
setenv          MPI_ROOT        /mnt/lustre/tursafs1/apps/basestack/cuda-12.3/openmpi/4.1.5-cuda12.3-slurm
prepend-path    PATH /mnt/lustre/tursafs1/apps/basestack/cuda-12.3/openmpi/4.1.5-cuda12.3-slurm/bin
prepend-path    LD_LIBRARY_PATH /mnt/lustre/tursafs1/apps/basestack/cuda-12.3/openmpi/4.1.5-cuda12.3-slurm/lib
prepend-path    MANPATH /mnt/lustre/tursafs1/apps/basestack/cuda-12.3/openmpi/4.1.5-cuda12.3-slurm/share/man
module load     ucx/1.15.0-cuda12.3
setenv          OMPI_CC cc
setenv          OMPI_CXX        g++
setenv          OMPI_CFLAGS     -g -m64
setenv          OMPI_CXXFLAGS   -g -m64
setenv          OMPI_MCA_pml    ucx
setenv          OMPI_MCA_osc    ucx
setenv          OMPI_MCA_btl    ^openib
-------------------------------------------------------------------

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 1.15.0 compiled with cuda 12.3 loaded

        OpenMPI 4.1.5 with cuda-12.3 and UCX 1.15.0 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/4.1.5-gcc12-cuda12

will load OpenMPI version 4.1.5 compiled with GCC 12.2 and CUDA 12.3 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 4.1.5-gcc9-cuda12 of openmpi, the following command will change to version 4.1.5-gcc12-cuda12:

[dc-user1@tursa-login1 ~]$ module swap openmpi openmpi/4.1.5-gcc12-cuda12

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/t01/t01/dc-user1/.module/default:

module use --append /mnt/lustre/tursafs1/apps/cuda-11.0.2-modulefiles
module use --append /mnt/lustre/tursafs1/apps/cuda-11.4.1-modulefiles
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/t01/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>

Restoring original environment: module purge plus reload

Unlike some other HPC systems, you cannot restore the original module environment with just the module purge command. You also need to reload the base environment setup module, i.e.

module purge
module load /home/y07/shared/tursa-modules/setup-env

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 three different primary compiler environments for GPU nodes:

  • GCC GPU toolchain: GCC 12.2.0, CUDA 12.3, OpenMPI 4.1.5
  • GCC GPU toolchain: GCC 9.3.0, CUDA 12.3, OpenMPI 4.1.5
  • NVHPC GPU toolchain: NVHPC 23.5 (CUDA 12.1), OpenMPI 4.1.5

and two compiler environments for CPU nodes:

  • GCC CPU toolchain: GCC 12.2.0, OpenMPI 4.1.5
  • GCC CPU toolchain: GCC 9.3.0, OpenMPI 4.1.5

GCC GPU toolchain

To compile on the system for GPU nodes using the GCC toolchain, you would typically load the required modules:

module load gcc/9.3.0
module load cuda/12.3 
module load openmpi/4.1.5-gcc9-cuda12


module list

Currently Loaded Modulefiles:
 1) /mnt/lustre/tursafs1/home/y07/shared/tursa-modules/setup-env   5) openmpi/4.1.5-gcc12-cuda12  
 2) ucx/1.15.0-cuda12.3                                            6) gcc/9.3.0(default)          
 3) openmpi/4.1.5-gcc9-cuda12(default)                             7) cuda/12.3                   
 4) ucx/1.15.0-gcc12-cuda12

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.

NVHPC GPU toolchain

Important

Compiling with OpenMPI and Fortran using the NVHPC toolchain is not yet supported on Tursa. We hope to add this functionality soon.

To compile on the system for GPU nodes using the NVHPC toolchain, you would typically load the required modules:

module load gcc/9.3.0
module load nvhpc/23.5-nompi
module load openmpi/4.1.5-gcc9-cuda12

module list

Currently Loaded Modulefiles:
 1) /home/y07/shared/tursa-modules/setup-env   3) nvhpc/23.5-nompi      5) openmpi/4.1.5-gcc9-cuda12(default)  
 2) gcc/9.3.0(default)                         4) ucx/1.15.0-cuda12.3

Once you have loaded the modules, the standard OpenMPI compiler wrapper scripts are available (for C and C++):

  • mpicc
  • mpicxx

and the NVIDIA C and C++ compilers are available as:

  • nvcc
  • nvc++

Tip

Both the NVIDIA compilers and the MPI compiler wrapper scripts will use the GCC compilers directly in the default configuration - this is often what you want. If you want the compiler wrappers to call the NVIDIA compilers themselves rather than GCC directly, you would use:

export OMPI_CC=nvcc
export OMPI_CXX=nvc++

GCC CPU toolchain

To compile on the system for CPU nodes using the GCC toolchain, you would typically load the required modules:

module load gcc/9.3.0
module load openmpi/4.1.5-gcc9-cpu

module list

Currently Loaded Modulefiles:
 1) /home/y07/shared/tursa-modules/setup-env   3) ucx/1.15.0              
 2) gcc/9.3.0(default)                         4) openmpi/4.1.5-gcc9-cpu

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.

Other build tools

cmake

CMake is available by using the commands:

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

Spack

See the Spack on Tursa section for information on using the Spack software package manager to install and manage software.