Goal: Introduce the LMOD Module System and the concept of dependencies.
What Have We Seen
Although on the login nodes we do have a gcc compiler and the Python language this only caters for a minority of users.
We can see that R is not available, nor most of the applications that researchers will require.
There are:
10s of compilers and languages
100s of applications and utilities.
1000s of underlying libraries and commands.
We can not provide a system that provides everything all at once.
What we need is a method to enable users to find and select that they specifically need, and a method to allow them to configure and setup their sessions/environment to allow them to perform their analysis and research.
LMOD: An Environment Module System
ARCC: Lmod – Software
What do we have available?
Compilers and eco systems: GNU family, Intel’s oneAPI, Nvidia’s hpc-sdk
Languages: C/C+, Fortran, Go, Java, Julia, Perl, Python, R, Ruby, Rust
Scientific libraries and toolkits: Built with a specific compiler: GNU by default
Standalone applications and utilities: Installed using:
Conda
Containers: running Singularity (not Docker)
We can create a Singularity image from a Docker image.
Binaries/Executables
Check the MedicineBow Software Page.
What is Available?
ARCC provides a small set of core compilers , languages, libraries and application, which will be updated on a semi regular basis. When updated, we try and use the latest versions, and typically will not be support older versions.
The GNU family of compilers (i.e. gcc) is are primary focus, but we do provide Intel’s oneAPI suite of compilers/libraries as well as NVidia’s hpc-sdk toolset.
Please refer to the MedicineBow Software List for what is available and/or use the module spider command to search.
ARCC will consider adding to this on a case-by-case basis.
What’s available: Using the Module System
# Go back to your home folder. [...]$ cd ~ [~]$ cd intro_to_modules/ # Modules currently loaded. []$ ml Currently Loaded Modules: 1) slurm/latest (S) 2) arcc/1.0 (S) # What's available within my 'current' environment. # With respect to what modules I 'currently' have loaded. []$ module avail ...
Notice: There are various categories of available software: containers, compilers, conda environments, Linux binaries…
Modules have a name and a version: <module-name>/<module-version>
What’s available? Compiler tree
Some software has to be built with respect to a compiler.
By default we build using the GNU family of compilers for C/C++ and Fortran.
[]$ module load gcc/13.2.0 []$ ml Currently Loaded Modules: 1) slurm/latest (S) 3) gmp/6.2.1 5) mpc/1.3.1 7) zstd/1.5.5 2) arcc/1.0 (S) 4) mpfr/4.2.0 6) zlib-ng/2.1.4 8) gcc/13.2.0
The gmp, mpc, mpfr, zlib-ng and zstd are know as dependencies.
There are libraries that need to be loaded for gcc to work.
They are loaded automatically so you don’t have to.
[] module avail # What has changed?
We can now wee all the modules available that have been compiled with gcc/13.2.0
These are only available if/when the gcc/13.2.0 module is loaded.
Change Compiler
Let’s see what happens to our environment if we load a different compiler.
[]# module load nvhpc-sdk/24.3 Lmod is automatically replacing "gcc/13.2.0" with "nvhpc-sdk/24.3". # What happened? []$ ml Currently Loaded Modules: 1) slurm/latest (S) 2) arcc/1.0 (S) 3) nvhpc-sdk/24.3 []$ module avail # Modules relating to nvhpc-sdk/24.3 are now available.
You can only have one module compiler loaded at a time.
Compilers of the same name, but different versions (gcc/12.2.0 vs gcc/13.2.0) are considered different.
Purge Your Modules
[]$ module purge # What has changed? []$ ml []$ module avail
Use the purge command to reset your environment to the initial defaults.
The more modules you have loaded, the more dependencies you will have loaded and the more likely you are to forget what you have loaded…
What’s available? Modules loaded by default
[]$ module purge The following modules were not unloaded: (Use "module --force purge" to unload all): 1) slurm/latest 2) arcc/1.0 []$ ml Currently Loaded Modules: 1) slurm/latest (S) 2) arcc/1.0 (S) Where: S: Module is Sticky, requires --force to unload or purge
Looking for Modules: module spider
Remember: module avail only shows what is available to be loaded with respect to your current environment and what you currently have loaded. It does not show you everything.
[]$ module spider openmpi
----------------------------------------------------------------------------
openmpi: openmpi/4.1.6
----------------------------------------------------------------------------
Other possible modules matches:
nvhpc-openmpi3
You will need to load all module(s) on any one of the lines below before the "openmpi/4.1.6" module is available to load.
arcc/1.0 gcc/13.2.0
...
Module load/spider: Dependencies
[]$ module load openmpi/4.1.6 Lmod has detected the following error: These module(s) or extension(s) exist but cannot be loaded as requested: "openmpi/4.1.6" Try: "module spider openmpi/4.1.6" to see how to load the module(s). # What dependencies does openmpi have? And what is currently loaded? []$ module load gcc/13.2.0 []$ module load openmpi/4.1.6 # What do you notice? []$ ml []$ module avail
Due to dependencies, there can be a hierarchy of core modules that need to be loaded to make other libraries and software available.
and what is loaded. For example, some libraries, such as fftw, need to be built with gcc/13.2.0 and use the openmpi/4.1.6 library.
Typically their version number will be prefixed with -ompi.
Try: []$ module spider fftw
What’s different between these command-lines?
[]$ module spider python/3.10.6 []$ module spider python/3.12.0 []$ module spider python2
What’s different between these command-lines? Dependencies
[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
...
You will need to load all module(s) on any one of the lines below before the "python/3.12.0" module is available to load.
arcc/1.0 gcc/13.2.0
[]$ module spider python2
----------------------------------------------------------------------------
python2: python2/2.7.18
----------------------------------------------------------------------------
You will need to load all module(s) on any one of the lines below before the "python2/2.7.18" module is available to load.
arcc/1.0
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