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What do we have available?

Info

  • 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.

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What is Available?

Info

  • 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

  • compile

  • rs (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.

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What’s available: Using the Module System

Info

Use module list to view the modules you are currently loaded in your session:

Code Block
# GoModules back to your home foldercurrently loaded.
[...]$ cdmodule list
~
[~]$ cd intro_to_modules/

# Modules currently loaded.
[]$ module list
Currently Loaded Modules:
Currently Loaded Modules:
  1) slurm/latest (S)   2) arcc/1.0 (S)
Info

Use module avail to see what modules are currently available that you can be loaded your current session:

Code Block
# What's available within my 'current' environment.
# With respect to what modules I 'currently' have loaded.
[]$ module avail
...

...

Info

Some commands have shortcuts. Using ml is the a shortcut to module list.

Code Block
[]$ module purge
[]$ 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

...

Code Block
[] module avail
# What has
Info

Question What changed?

Info

We can now wee see all the modules available that have been compiled with gcc/13.2.0

Note

These are only available if/when after the gcc/13.2.0 module is has been loaded.

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Change Compiler

Info

Let’s see what happens to our environment if we load a different compiler.

Code Block
[]# module load nvhpc-sdk/24.3
Lmod is automatically replacing "gcc/13.2.0" with "nvhpc-sdk/24.3".

# What happened?
Info

Again, what happened?

Code Block
[]$ ml
Currently Loaded Modules:
  1) slurm/latest (S)   2) arcc/1.0 (S)   3) nvhpc-sdk/24.3

[]$ module avail
# Modules relating to
Info

Only modules relating to nvhpc-sdk/24.3

are

now

available.

Note

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

Info

Use the module purge command to reset your environment to the initial defaults.

Code Block
[]$ module purge
The following modules were not unloaded:
  (Use "module --force purge" to unload all):
  1) slurm/latest   2) arcc/1.0

# What has changed?
Info

Again, what has changed?

Code Block
[]$ ml
[]$ module avail
Info

Use the purge command to reset your environment to the initial defaults.We are back to having the two modules slurm/latest and arcc/1.0 loaded (by default) and the initial set of available modules.

Note

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…

Note

As mentioned earlier, do not use the --force option to unload the slurm and arcc modules.

What’s available? Modules loaded by default

Code Block
[]$ 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

Info

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.

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Looking for Modules: module spider

Info

  • 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.

Code Block
[]$ module spider openmpi
----------------------------------------------------------------------------
  openmpi: openmpi/4.1.6
-----------------------------------------------------------------------------------------------------------------
  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

Code Block
[]$ 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
     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
...

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Module load/spider: Dependencies

Info

If you module spider a specific version it will list the dependencies that are required to first be loaded before it can be used:

Code Block
[]$ module spider openmpi/4.1.6
----------------------------------------------------------------------------
  openmpi: openmpi/4.1.6
----------------------------------------------------------------------------
    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
    Help:
      An open source Message Passing Interface implementation. ...
Note

Try loading before loading gcc/13.2.0:

Code Block
[]$ 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).
Info

Load the required dependencies, then re-try:

Code Block
[]$ module load gcc/13.2.0
[]$ module load openmpi/4.1.6
[]$
Info

Let’s check everything has been loaded successfully:

Code Block
[]$ which mpicc
/apps/u/opt/gcc/13.2.0/openmpi/4.1.6/bin/mpicc

[]$ mpicc --version
gcc (Spack GCC) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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What Do You Notice?

Info

After loading openmpi/4.1.6 what do we notice about what is now loaded and available?

Code Block
[]$ ml
[]$ module avail
Info

Notice we have opened up an additional set of modules:

Code Block
---- /apps/s/lmod/mf/spack/linux-rhel9-x86_64/openmpi/4.1.6-ipshyxb/gcc/13.2.0 ----
   adios2/2.9.2-ompi        netcdf-cxx4/4.3.1-ompi
   cgns/4.4.0-ompi          netlib-scalapack/2.2.0-ompi
   elpa/2023.05.001-ompi    parallel-netcdf/1.12.3-ompi
...
Info

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-linesdifferent between these command-lines?

Info

What do we notice about the required dependencies for the following versions of Python?

Code Block
[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
[]$ module spider python2

...

What’s different between these command-lines? Dependencies

Info

The two python

/3.12.0 []$ module spider python2

...

/3.x versions have both been installed using the gcc/13.2.0 compiler, and thus this needs to be loaded before we can use them.

Code Block
[]$ 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. available to load.
      arcc/1.0  gcc/13.2.0
      arcc/1.0  gcc/1314.2.0
...
Info

The python/2 module has no dependencies, can can be loaded straight away:

Code Block
[]$ 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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More module commands

Info

The module command has lots more sub-commands:

Code Block
[]$ module
Modules based on Lua: Version 8.7  2022-04-16 13:49 -05:00
    by Robert McLay mclay@tacc.utexas.edu

module [options] sub-command [args ...]

Help sub-commands:
------------------
  help                              prints this message
  help                module [...]  print help message from module(s)

Loading/Unloading sub-commands:
-------------------------------
  load | add          module [...]  load module(s)
 ...

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