Providing A Standard Set Of Modules for all Users
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Users can be provided with an initial set of modulefiles as part of
the login procedure.  Once a list of modulefiles have been installed,
please create a file called ``StdEnv.lua`` and place it in the ``$MODULEPATH``
list of directories, typically
``/opt/apps/modulefiles/Core/StdEnv.lua``. The name is your choice,
the purpose is provide a standard list of modules that get loaded during
login. In ``StdEnv.lua`` is something like: ::

    load("name1","name2","name3")

Using the /etc/profile.d directory system described earlier to create a
file called ``z00_StdEnv.sh`` ::

    if [ -z "$__Init_Default_Modules" ]; then
       export __Init_Default_Modules=1;

       ## ability to predefine elsewhere the default list
       LMOD_SYSTEM_DEFAULT_MODULES=${LMOD_SYSTEM_DEFAULT_MODULES:-"StdEnv"} 
       export LMOD_SYSTEM_DEFAULT_MODULES
       module --initial_load restore
    else
       module refresh
    fi

Similar for z00_StdEnv.csh::

    if ( ! $?__Init_Default_Modules )  then
      setenv __Init_Default_Modules 1
      if ( ! $?LMOD_SYSTEM_DEFAULT_MODULES ) then
        setenv LMOD_SYSTEM_DEFAULT_MODULES "StdEnv"
      endif
      module --initial_load restore
    else
      module refresh
    endif

The z00_Stdenv.* names are chosen because the files in /etc/profile.d
are sourced in alphabetical order. These names guarantee they will run
after the module command is defined.

The first time these files are sourced by a shell they will set
``LMOD_SYSTEM_DEFAULT_MODULES`` to ``StdEnv`` and then execute
``module restore``.  Any subshells will instead call ``module
refresh``.  Both of these statements are important to get the
correct behavior out of Lmod.

The ``module restore`` tries to restore the user's default
collection.  If that doesn't exist, it then uses contents of the variable
``LMOD_SYSTEM_DEFAULT_MODULES`` to find a colon separated list of
Modules to load.


The ``module refresh`` solves an interesting problem.  Sub shells
inherit the environment variables of the parent but do not normally
inherit the shell aliases and functions.  This statement fixes this.
Under a "``refresh``", all the currently loaded modules are reloaded
but in a special way. Only the functions which define alias and shell
functions are active, all others functions are ignored.

The above is an example of how a site might provide a default set of
modules that a user can override with a default collection. Site are,
of course, free to setup Lmod any way they like. The
minimum required setup (for bash with z00_StdEnv.sh ) would be::

    if [ -z "$__Init_Default_Modules" ]; then
       export __Init_Default_Modules=1;

       module --initial_load restore   
    else
       module refresh
    fi

The module restore command still depends on the environment variable
LMOD_SYSTEM_DEFAULT_MODULES but that can be set somewhere else.


Lmod, LD_LIBRARY_PATH and screen
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In general, it is probably better to NOT use ``screen`` and use
``tmux`` instead.  The problem with ``screen`` is that it guid
program (``tmux`` is not).  That means it uses the group associated
with the executable and not the user's group.  The main consequence of
this is that the operating system removes LD_LIBRARY_PATH from the
environment.  This is a security feature built into the operating
system.

A site could change z00_StdEnv.sh to have::

    if [ -z "$__Init_Default_Modules" -o -z "$LD_LIBRARY_PATH" ]; then
       export __Init_Default_Modules=1;

       module --initial_load restore   
    else
       module refresh
    fi

to help with the situation.  This will force Lmod restore the initial
set of modules (or the user's default collection).  This works fine as
long as the initial set of modules actually sets LD_LIBRARY_PATH.  If
it doesn't every interactive sub-shell will do a module restore, which
is probably not what you want.  For example, if you see the following
then you probably want to remove the test for an empty LD_LIBRARY_PATH::

    $ module list
    Currently Loaded Modules:
       1) gcc/5.2     2) StdEnv

    $ module load bowtie
    $ bash
    $ module list
    Currently Loaded Modules:
       1) gcc/5.2     2) StdEnv

Running the bash shell caused the module restore to run which unloaded
all modules and restored the modules back to the initial set.