An Introduction to Writing Modulefiles

This is a different kind of introduction to Lmod. Here we will remind you what Lmod is doing to change the environment via modulefiles. Then we will start with the four functions that are typically needed for any modulefile. From there we will talk about intermediate level module functions when things get more complicated. Finally we will discuss the advanced module functions to flexibly control your site via modules. All the Lua module functions available are described at Lua Modulefile Functions. This discussion shows how they can be used.

A Reminder of what Lmod is doing

All Lmod is doing is changing the environment. Suppose you want to use the “ddt” debugger installed on your system which is made available to you via the module. If you try to execute ddt without the module loaded you get:

$ ddt
bash: command not found: ddt

$ module load ddt
$ ddt

After the ddt module is loaded, executing ddt now works. Let’s remind ourselves why this works. If you try checking the environment before loading the ddt modulefile:

$ env | grep -i ddt
$ module load ddt
$ env | grep -i ddt

DDTPATH=/opt/apps/ddt/5.0.1/bin
LD_LIBRARY_PATH=/opt/apps/ddt/5.0.1/lib:...
PATH=/opt/apps/ddt/5.0.1/bin:...

$ module unload ddt
$ env | grep -i ddt
$

The first time we check the environment we find that there is no ddt stored there. But the second time there we see that the PATH and LD_LIBRARY_PATH have been modified. Note that we have shorten the path-like variables to show the important changes. There are also several environment variables which have been set. After unloading the module all the references for ddt have been removed. We can see what the modulefile looks like by doing:

$ module show ddt

help([[
For detailed instructions, go to:
   https://...

]])
whatis("Version: 5.0.1")
whatis("Keywords: System, Utility")
whatis("URL: http://content.allinea.com/downloads/userguide.pdf")
whatis("Description: Parallel, graphical, symbolic debugger")

setenv(       "DDTPATH",        "/opt/apps/ddt/5.0.1/bin")
prepend_path( "PATH",           "/opt/apps/ddt/5.0.1/bin")
prepend_path( "LD_LIBRARY_PATH","/opt/apps/ddt/5.0.1/lib")

Modulefiles state the actions that need to happen when loading. For example the above modulefile uses setenv and prepend_path to set environment variables and prepend to the PATH. If the above modulefile is unloaded then the setenv actually unsets the environment variable. The prepend_path removes the element from the PATH variable. That is unload causes the functions to be reversed.

Basic Modulefiles

There are two main module functions required, namely setenv and prepend_path; and two functions to provide documentation help and whatis. The modulefile for ddt shown above contains all the basics required to create one. Suppose you are writing this module file for ddt version 5.0.1 and you are placing it in the standard location for your site, namely /apps/modulefiles and this directory is already in MODULEPATH. Then in the directory /apps/modulefiles/ddt you create a file called 5.0.1.lua which contains the modulefile shown above.

This is the typical way of setting a modulefile up. Namely the package name is the name of the directory, ddt, and version name, 5.0.1 is the name of the file with the .lua extension added. We add the lua extension to all modulefile written in Lua. All modulefiles without the lua extension are assumed to be written in TCL.

If another version of ddt becomes available, say 5.1.2, we create another file called 5.1.2.lua to become the new modulefile for the new version of ddt.

When a user does module help ddt, the arguments to the help function are written out to the user. The whatis function provides a way to describe the function of the application or library. This data can be used by search tools such as module keyword search_words. Here at TACC we also use that data to provide search capability via the web interface to modules we provide.

Intermediate Level Modulefiles

The four basic functions describe above is all that is necessary for the majority of modulefiles for application and libraries. The intermediate level is designed to describe some situations that come up as you need to provide more than just packages modulefile but need to set up a system.

Meta Modules

Some sites create a single module to load a default set of modules for all users to start from. This is typically called a meta module because it loads other modules. As an example of that, we here at TACC have created the TACC module to provide a default compiler, mpi stack and other modules:

help([[
The TACC modulefile defines ...
]])

-- 1 --
if (os.getenv("USER") ~= "root") then
  append_path("PATH",  ".")
end

-- 2 --
load("intel", "mvapich2")

-- 3 --
try_load("xalt")

-- 4 --
-- Environment change - assume single threaded.
if (mode() == "load" and os.getenv("OMP_NUM_THREADS") == nil) then
  setenv("OMP_NUM_THREADS","1")
end

This modulefile shows the use of four new functions. The first one is append_path. This function is similar to prepend_path except that the value is placed at the end of the path-like variable instead of the beginning. We add . to our user’s path at the end, except for root. This way our new users don’t get surprised with some programs in their current directory that do not run. We used the os.getenv function built-in to Lua to get the value of environment variable “USER”.

The second function is load, this function loads the modulefiles specified. This function takes one or more names. Here we are specifying a default compiler and mpi stack. The third function is try_load, which is similar to load except that there is no error reported if the module can’t be found.

The fourth block of code shows how we set OMP_NUM_THREADS. We wish to set OMP_NUM_THREADS to have a default value of 1, but only if the value hasn’t already been set and we only want to do this when the module is being loaded and not at any other time. So when this module is loaded for the first time mode() will return “load” and OMP_NUM_THREADS won’t have a value. The setenv will set it to 1. If the TACC module is unloaded, the mode() will be “unload” so the if test will be false and therefore the setenv will not be reversed. If the user changes OMP_NUM_THREADS and reloads the TACC modulefile, their value won’t change because os.getenv(“OMP_NUM_THREADS”) will return a non-nil value, therefore the setenv command won’t run. Now this may not be the best way to handle this. It might be better to set OMP_NUM_THREADS in a file that is sourced in /etc/profile.d/ and have all the important properties. Namely that there will be a default value that the user can change. However this example shows how to do something tricky in a modulefile.

Typically meta modules are a single file and not versioned. So the TACC modulefile can be found at /apps/modulefiles/TACC.lua. There is no requirement that this will be this way but it has worked well in practice.

Modules with dependencies

Suppose that you have a package which needs libraries or an application. For example the octave application needs gnuplot. Let’s assume that you have a separate applications for both. Inside the octave module you can do:

prereq("gnuplot")
...

So if you execute:

$ module unload gnuplot
$ module load octave
$ module load gnuplot octave
$ module unload octave

The second module command will fail, but the third one will succeed because we have met the prerequisites. The advantage of using prereq is after fourth module command is executed, the gnuplot module will be loaded.

This can be contrasted with including the load of gnuplot in the octave modulefile:

load("gnuplot")
...

This simplifies the loading of the octave module. The trouble is that when a user does the following:

$ module load   gnuplot
$ module load   octave
$ module unload octave

is that after unloading octave, the gnuplot module is also unloaded. It seems better to either use the prereq function shown above or use the always_load function in the octave module:

always_load("gnuplot")
...

Then when a user does:

$ module load   gnuplot
$ module load   octave
$ module unload octave

The gnuplot module will still be loaded after unloading octave. This will lead to the least confusion to users.

Fancy dependencies

Sometimes an application may depend on another application but it has to be a certain version or newer. Lmod can support this with the atleast modifier to both load, always_load or prereq. For example:

-- Use either the always_load or prereq but not both:

prereq(     atleast("gnuplot","5.0"))
always_load(atleast("gnuplot","5.0"))

The atleast modifier to prereq or always_load will succeed if the version of gnuplot is 5.0 or greater.

Assigning Properties

Modules can have properties that will be displayed in a module list or module avail. Properties can be anything but they must be specified in the lmodrc.lua file. You are free to add to the list. For example, to specify a module to be experimental all you need to do is:

add_property("state","experimental")

Any properties you set must be defined in the lmodrc.lua file. In the source tree the properties are in init/lmodrc.lua. A more detailed discussion of the lmodrc.lua file can be found at The Properties File: lmodrc.lua

Pushenv

Lmod allows you to save the state in a stack hidden in the environment. So if you want to set the CC environment variable to contain the name of the compiler.:

-- gcc --
pushenv("CC","gcc")

-- mpich --
pushenv("CC","mpicc")

If the user executes the following:

#                                      SETENV         PUSHENV
$ export CC=cc;         echo $CC  # -> CC=cc          CC=cc
$ module load   gcc;    echo $CC  # -> CC=gcc         CC=gcc
$ module load   mpich;  echo $CC  # -> CC=mpicc       CC=mpicc
$ module unload mpich;  echo $CC  # -> CC is unset    CC=gcc
$ module unload gcc;    echo $CC  # -> CC is unset    CC=cc

We see that the value of CC is maintained as a stack variable when we use pushenv but not when we use setenv.

Setting aliases and shell functions

Sometimes you want to set an alias as part of a module. For example the visit program requires the version to be specified when running it. So for version 2.9 of visit, the alias is set:

set_alias("visit","visit -v 2.9")

Whether this will expand correctly depends on the shell. While C-shell allows argument expansion in aliases, Bash and Zsh do not. Bash and Zsh use shell functions instead. For example the ml shell function can be set like this:

local bashStr = 'eval $($LMOD_DIR/ml_cmd "$@")'
local cshStr  = "eval `$LMOD_DIR/ml_cmd $*`"
set_shell_function("ml",bashStr,cshStr)

Please note that aliases in bash are not expanded for non-interactive shells. This means that it won’t work in bash shell scripts. Please change the shell alias to use the set_shell_function instead. Shell functions do work in both interactive and non-interactive shells.