modules.md

Environment modules

---

This section describes the setting up of "environment modules" on Mojave. There are no macports for "modules". We will build this from scratch. The build process on OS X has changed slightly since modules v4. The instructions below are from the latest version (4.2.4 as on 2019-06-01).

1. Download modules from here: https://sourceforge.net/projects/modules/

2. Note that you will need the macports installation done before you start with modules.

3. If you don't have ggrep via the coreutils port, create soft link as shown below (modules developers use homebrew and look for ggrep)

   • sudo ln -s /usr/bin/grep /opt/local/bin/ggrep

4. "sed" on OS X does not support some options. So, we need to replace it with "gsed" for auto-complete to work.

   • Edit the init/bash_completion.in in the untarred directory and replace "sed" with "gsed" in functions _module_avail(), _module_savelist() and _module_not_yet_loaded()

5. In the untarred directory:

   • ./configure --prefix=/usr/local/Modules --with-tcl=/opt/local/lib
   • make
   • sudo make install

6. Modify .bash_profile as shown below. If using another shell, adapt the commands as needed:

export CLICOLOR=1
export PS1="\h:\w>: "

##
# Your previous /Users/agram/.bash_profile file was backed up as /Users/agram/.bash_profile.macports-saved_2013-03-04_at_11:21:37
##

# MacPorts Installer addition on 2013-03-04_at_11:21:37: adding an appropriate PATH variable for use with MacPorts.
export PATH=/opt/local/bin:/opt/local/sbin:$PATH
# Finished adapting your PATH environment variable for use with MacPorts.

export MANPATH=/opt/local/share/man:$MANPATH

###Add these two lines to setup modules
##If using another shell use that instead of bash
source /usr/local/Modules/init/bash
module load use.own   #This allows module files in your /Users/agram/privatemodules to be used
module load basic     #Replacement for adding stuff to .bashrc/.bash_profile/.profile

Create the "basic" module

---

We move all the stuff that we usually put in the .bashrc / .bash_profile /.profile to a basic module files located at /Users/agram/privatemodules/basic. We load this module by default in .bashrc / .bash_profile / .profile.

Remember to close the terminal and reopen a fresh one for further work after you setup this file. This will ensure that the basic module will be loaded by default.

#%Module1.0#####################################################################
##
## basic modulefile
##
## privatemodules/basic. Generated from dot.in by configure.
##
proc ModulesHelp { } {
        global version

        puts stderr "\t Sets up basic environment"
        puts stderr "\n\tVersion $version\n"
}

module-whatis   "Sets up basic environment on the machine"

# for Tcl script use only
set     version      3.2.10

set-alias       "rm"    "rm -i"   #I'm paranoid. This will ask for confirmation
set-alias       "cp"    "cp -i"
set-alias       "mv"    "mv -i"
set-alias       "gvim"  "mvim"    #Same name as on a linux machine
setenv          GDAL_DATA       /opt/local/share/gdal #Needed for GDAL ancillary data
#setenv          GDAL_DRIVER_PATH    /opt/local/lib/gdalplugins #Uncomment if you want kealib support