HPC/Module Setup: Difference between revisions

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* Most application software is installed under <code>'''/opt/soft/'''</code>
* Most application software is installed under <code>'''/opt/soft/'''</code>
* Package directories are named <code>''' ''name-version-build'' '''</code>, e.g. <code>/opt/soft/jmol-12.1.37-1</code>.
* Package directories are named <code>''' ''name-version-build'' '''</code>, e.g. <code>/opt/soft/jmol-12.1.37-1</code>.
* Module names are organized by a mostly version-less name, with the version following after a slash: <code>''' ''name/version-build'' '''</code>. Using the <code>''name''</code> alone is possible and will select a default version for a SubCommand to act upon.
* Module names are organized by a mostly version-less name, with the version following after a slash: <code>''' ''name/version-build'' '''</code>. Using the <code>''name''</code> 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.
* <code>module help</code> briefly describes a package and will usually contain a link to its home page.
* <code>module help</code> briefly describes a package and will usually contain a link to its home page.
  $ '''module help jmol'''
  $ '''module help jmol'''

Revision as of 21:56, May 18, 2011

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 …

Modules – Introduction

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

Modules general introductions can be found at many other sites, such as:

On Carbon:

$ 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/