HPC/Module Setup

Shell startup files

• The default login shell on Carbon is bash
• Place customizations in your file ~/.bashrc

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
fi

export PATH=$HOME/mypackage/bin:$PATH
module load name1 name2 … 

• tcsh only if you insist. It is not supported. In fact: “csh programming considered harmful” – Tom Christiansen

Modules – Introduction

Carbon uses the Environment Modules package to dynamically provision software. The package primarily modifies your $PATH and other environment variables.

• Current Carbon module catalog
• A general introduction to modules can be found at many other sites, such as:
  • NERSC
  • PITT
  • NCI (AU)

$ module help
…
  Usage: module [ switches ] [ subcommand ] [subcommand-args ]
…

  Available SubCommands and Args:

+ load		modulefile [modulefile ...]
+ unload	modulefile [modulefile ...]
+ switch	[modulefile1] modulefile2.]
+ list

+ avail		[modulefile [modulefile ...]]
+ whatis	[modulefile [modulefile ...]]
+ help		[modulefile [modulefile ...]]
+ show		modulefile [modulefile ..]

For full documentation, consult the manual page:

$ man module

Module Conventions on Carbon

• Most application software is installed under /opt/soft/
• Package directories are named name-version-build , e.g. /opt/soft/jmol-12.1.37-1.
• Module names are organized by a mostly version-less name, with the version following after a slash: name/version-build . Using the name alone is possible and will select a default version for a SubCommand to act upon. Some packages carry a major version number in their name, notably fftw3 and vasp5.
• module help briefly describes a package and will usually contain a link to its home page.

$ module help jmol

----------- Module Specific Help for 'jmol/12.0.34-1' -------------

	Jmol is a molecule viewer platform for researchers in chemistry and
	biochemistry, implemented in Java for multi-platform use.  This is the
	standalone application.  It offers high-performance 3D rendering with
	no hardware requirements and supports many popular file formats.

	http://jmol.sourceforge.net/
	http://wiki.jmol.org/

• Home dirs: Most modules will set a convenience variable NAME_HOME which points to the toplevel directory. This is mostly useful to inspect documentation and auxiliary files:

$ module load jmol
$ ls -l $JMOL_HOME/doc
total 488
-rw-r--r-- 1 stern stern 369786 Feb 25 12:59 CHANGES.txt
-rw-r--r-- 1 stern stern   2841 Feb 25 12:59 COPYRIGHT.txt
…

… and to specifcy link paths in makefiles:

$ module load fftw3

LDFLAGS += -L$FFTW3_HOME/lib/

• Default modules are loaded by /etc/profile.d/zz-moduleuse.sh. (The strange name form ensures this profile segment is loaded last.)

$ module list
Currently Loaded Modulefiles:
  1) moab/6.0.3-1              4) icc/11/11.1.073
  2) gold/2.1.11.0-4           5) ifort/11/11.1.073
  3) openmpi/1.4.3-intel11-1   6) mkl/10.2.6.038