This is a custom Confluence template that is intended to be re-used in the creation of workshops presented by ARCC on the Wiki. All of the content in these sections is intended to be replaced by the author of the workshop. The first step in this style guide is to ensure that the the page is in wide mode to maximize the real estate for content when possible. The Title of the Page should be the same as the Title of the workshop and this section should include a quick intro to the topic, why it’s important for ARCC users, and what users should expect to get out of this workshop. Next should be a Table of Contents macro in vertical format. The Table is intended to be used as an agenda section for presenter mode as well as navigation for non-presenting viewing so that users can find the documentation and navigate to what they need to brush up on. Finally, at the end of each section, there should be a divider to indicate the separation of “slides”
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Headers and Sections
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Code Examples
Two Column Tables are nice ways to separate content/ Background info along with a code example on the same “Slide”. Please notice the table width. This should stop scroll bars from appearing
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Bullets are nice to include for distinct points
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yep
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they
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sure
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Please use the "code snippet" in the + button when creating code examples. Also please do not go
past the width of the table. This is to prevent scroll bars appearing
This is the Max number of code lines to show on an example |
Straight Code - No context
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Limit to 16 lines in the example.
This is the end |
Same Thing With Images
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Two Column Tables are nice ways to separate content/ Background info along with an image example on the same “Slide”. Please notice the table width. This should stop scroll bars from appearing
Bullets are nice to include for distinct points
yep
they
sure
are
This is 14 lines
Alternatively No Table
Finally The End
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Link to Previous sub-module or Home Module
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Goal: Introduce the LMOD Module System and the concept of dependencies.
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What Have We Seen
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Although on the login nodes we do have a We can see that R is not available, nor most of the applications that researchers will require. There are:
We can not provide a system that provides everything all at once. |
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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. |
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LMOD: An Environment Module System
ARCC: Lmod – Software
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What do we have available?
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Check the MedicineBow Software Page. |
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What is Available?
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What’s available: Using the Module System
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Use |
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# Modules currently loaded.
[]$ module list
Currently Loaded Modules:
1) slurm/latest (S) 2) arcc/1.0 (S) |
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Use |
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# What's available within my 'current' environment.
# With respect to what modules I 'currently' have loaded.
[]$ module avail
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Notice: There are various categories of available software: containers, compilers, conda environments, Linux binaries… |
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Modules have a name and a version: |
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The two modules These make available various commands and scripts that ALL users require (such as Slurm commands). If you |
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What’s available? Compiler tree
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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. |
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Some commands have shortcuts. Using |
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[]$ 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 |
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The There are libraries that need to be loaded for gcc to work. They are loaded automatically so you don’t have to. |
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[] module avail |
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Question What changed? We can now see all the modules available that have been compiled with |
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These are only available after the |
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Change Compiler
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Let’s see what happens to our environment if we load a different compiler. |
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[]# module load nvhpc-sdk/24.3
Lmod is automatically replacing "gcc/13.2.0" with "nvhpc-sdk/24.3". |
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Again, what happened? |
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[]$ ml
Currently Loaded Modules:
1) slurm/latest (S) 2) arcc/1.0 (S) 3) nvhpc-sdk/24.3
[]$ module avail |
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Only modules relating to |
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You can only have one module compiler loaded at a time. Compilers of the same name, but different versions ( |
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Purge Your Modules
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Use the |
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[]$ module purge
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) slurm/latest 2) arcc/1.0 |
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Again, what has changed? |
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[]$ ml
[]$ module avail |
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We are back to having the two modules |
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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… |
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As mentioned earlier, do not use the |
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Looking for Modules: module spider
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[]$ 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
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Module load/spider: Dependencies
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If you |
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[]$ 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. ... |
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Try loading before loading |
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[]$ 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). |
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Load the required dependencies, then re-try: |
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[]$ module load gcc/13.2.0
[]$ module load openmpi/4.1.6
[]$ |
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Let’s check everything has been loaded successfully: |
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[]$ 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?
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After loading |
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[]$ ml
[]$ module avail |
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Notice we have opened up an additional set of modules: |
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---- /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
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Due to dependencies, there can be a hierarchy of core modules that need to be loaded to make other libraries and software available. For example, some libraries, such as Typically their version number will be prefixed with Try: |
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What’s different between these command-lines?
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What do we notice about the required dependencies for the following versions of Python? |
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[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
[]$ module spider python2 |
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What’s different between these command-lines? Dependencies
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The two |
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[]$ module spider python/3.10.6
[]$ module spider python/3.12.0
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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
arcc/1.0 gcc/14.2.0
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The |
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[]$ 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
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The |
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[]$ 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:
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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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