Environment Modules: Difference between revisions

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Revision as of 17:31, 9 January 2016

Description Content
module load category/name | category/name/version (optional)
Availability bwUniCluster | BwForCluster_Chemistry | bwGRiD_tu
Links Environment Modules Project | Environment Modules
License GNU General Public License


Introduction

Environment Modules, or short Modules are the means by which most of the installed scientific software is provided on the bwHPC clusters.
The use of different compilers, libraries and software packages requires users to set up a specific session environment suited for the program they want to run. The bwHPC clusters provide users with the possibility to load and unload complete environments for compilers, libraries and software packages by a single command.

Description

The Environment Modules package enables dynamic modification of your environment by the use of so-called modulefiles. A modulefile contains information to configure the shell for a program/software . Typically, a modulefile contains instructions that alter or set shell environment variables, such as PATH and MANPATH, to enable access to various installed software.
One of the key features of using the Environment Modules software is to allow multiple versions of the same software to be used in your environment in a controlled manner. For example, two different versions of the Intel C compiler can be installed on the system at the same time - the version used is based upon which Intel C compiler modulefile is loaded.
The software stack of bwHPC clusters provides a number of modulefiles. You can also create your own modulefiles. Modulefiles may be shared by many users on a system, and users may have their own collection of modulefiles to supplement or replace the shared modulefiles.
A modulefile does not provide configuration of your environment until it is explicitly loaded, i.e., the specific modulefile for a software product or application must be loaded in your environment before the configuration information in the modulefile is effective.
For instance loading the default Intel C and Fortran compiler you must execute 'module load compiler/intel'. 

$ module load compiler/intel
$ module list
Currently Loaded Modulefiles:
  1) compiler/pgi/12.10(default)    2) compiler/intel/15.0(default)
$ : Display all Intel related environments now
$ env | grep INTEL
INTEL_LICENSE_FILE=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/licenses
INTEL_LIB_MICMPI=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/mpirt/lib/mic
INTEL_HOME=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187
INTEL_VERSION=15.0.3
INTEL_MAN_DIR=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/man/en_US
INTEL_INC_DIR=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/compiler/include
INTEL_BIN_DIR=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/bin/intel64
INTEL_DOC_DIR=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/Documentation/en_US
INTEL_LIB_DIR=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/compiler/lib/intel64
INTEL_LIB_MIC=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/compiler/lib/mic
INTEL_PYTHONHOME=/opt/bwhpc/common/compiler/intel/compxe.2015.3.187/composer_xe_2015.3.187/debugger/python/intel64


Usage

Documentation

For help on how to use Modules software, i.e., the command module, execute 'module help'. 

$ module help
Modules Release 3.2.10 2012-12-21 (Copyright GNU GPL v2 1991):

  Usage: module [ switches ] [ subcommand ] [subcommand-args ]

Switches:
	-H|--help		this usage info
	-V|--version		modules version & configuration options
	-f|--force		force active dependency resolution
	-t|--terse		terse    format avail and list format
	-l|--long		long     format avail and list format
	-h|--human		readable format avail and list format
	-v|--verbose		enable  verbose messages
	-s|--silent		disable verbose messages
	-c|--create		create caches for avail and apropos
	-i|--icase		case insensitive
	-u|--userlvl <lvl>	set user level to (nov[ice],exp[ert],adv[anced])
  Available SubCommands and Args:
	+ add|load		modulefile [modulefile ...]
	+ rm|unload		modulefile [modulefile ...]
	+ switch|swap		[modulefile1] modulefile2
	+ display|show		modulefile [modulefile ...]
	+ avail			[modulefile [modulefile ...]]
	+ use [-a|--append]	dir [dir ...]
	+ unuse			dir [dir ...]
	+ update
	+ refresh
	+ purge
	+ list
	+ clear
	+ help			[modulefile [modulefile ...]]
	+ whatis		[modulefile [modulefile ...]]
	+ apropos|keyword	string
	+ initadd		modulefile [modulefile ...]
	+ initprepend		modulefile [modulefile ...]
	+ initrm		modulefile [modulefile ...]
	+ initswitch		modulefile1 modulefile2
	+ initlist
	+ initclear

or 'man module'. 

MODULE(1)                       Modules package                      MODULE(1)

NAME
       module - command interface to the Modules package

SYNOPSIS
       module [ switches ] [ sub-command ] [ sub-command-args ]

DESCRIPTION
       module is a user interface to the Modules package.  The Modules package
       provides for the dynamic modification of  the  user's  environment  via
       modulefiles.

       Each  modulefile contains the information needed to configure the shel
[...]

For help on particular version of Module, e.g. Intel compiler version X.Y, execute 'module help compiler/intel'. 

$ module help compiler/intel
----------- Module Specific Help for 'compiler/intel/15.0' --------
This module provides the Intel(R) compiler suite version 15.0.3 via
commands 'icc', 'icpc' and 'ifort' (version 15.0.3), the debugger 'gdb-ia' (version
7.8.3) as well as the Intel(R) Threading Building Blocks TBB (version 4.3.5)
and the Integrated Performance Primitives IPP libraries (version 8.2.2)
(for details see also 'http://software.intel.com/en-us/intel-compilers/').

The related Math Kernel Library MKL module is 'numlib/mkl/11.2.3'.
The related Intel MPI module is 'mpi/impi/5.0.3-intel-15.0'.
The Intel 'icpc' should work well with GNU compiler version 4.4 to 4.8.
Before using TBB or IPP setup the corresponding environment, e.g. for 64bit+bash
  source $INTEL_HOME/tbb/bin/tbbvars.sh intel64
  source $INTEL_HOME/ipp/bin/ippvars.sh intel64

Commands:
  icc           # Intel(R) C compiler
  icpc          # Intel(R) C++ compiler
  ifort         # Intel(R) Fortran compiler
  gdb-ia        # Intel version of GNU debugger
  # idb is not available anymore in Intel compiler suite 2015.

Local documentation:
  Man pages: man icc; man icpc; man ifort; man gdb-ia
  firefox $INTEL_DOC_DIR/beginusing_lc.htm
  firefox $INTEL_DOC_DIR/beginusing_lf.htm
  The html-pages are very detailed and cover TBB and IPP as well as MKL.

For some Intel(R) compiler option examples, hints on how to compile 32bit code
and solutions for less common problems see the tips and troubleshooting doc:
  $INTEL_DOC_DIR/intel-compiler-tips-and-troubleshooting.txt

For details on library and include dirs please call
    module show compiler/intel/15.0
[...]

Online Documentation

Frequently Asked Questions (FAQ)

Display all available Modules

Available Module are modulefiles that can be loaded by the user. A Module must be loaded before it provides changes to your environment, as described in the introduction to this section. You can display all available Modules on the system by executing: 

$ module avail

The short form the command is: 

$ module av

Available Modules can be also displayed in different modes, such as

  • each Module per one line
$ module -t avail
  • long
$ module -l avail

bwHPC CLuster Information System (CIS)

A GUI-Version of all available and scheduled modules is available with our
CIS (Cluster Information System).
Software Admins are able to announce new modules, versions and complete new software, too.
Academic users and other interested parties can get a summay of all installed modules and module-help informations.
CIS: Cluster Information System

Cis.jpg

Module categories, versions and defaults

The bwHPC clusters (such as bwUniCluster) traditionally provide a large variety of software and software versions. Therefore Module are divided in category folders containing subfolders of modulefiles again containing modulefile versions, and must be addressed as follows: 

category/softwarename/version

For instance the Intel compiler X.Y belongs to the category of compilers, therefore the modulefile X.Y is placed under the category compiler and intel.
In case of multiple software versions, one version will be always defined as the default version. The Module of the default can be addressed by simply omitting the version number: 

category/softwarename

Finding software Modules

Currently all bwHPC software packages are assigned to the following Module categories:

You can selectively list software in one of those categories using, e.g. for the category "compiler" 

$ module avail compiler/

Searches are looking for a substring starting at the begin of the name, so this would list all software in categories starting with a "c" 

$ module avail c

while this would find nothing 

$ module avail hem

Loading Modules

You can load a Module software in to your environment to enable easier access to software that you want to use by executing: 

$ module load category/softwarename/version

or 

$ module add category/softwarename/version

Loading a Module in this manner affects ONLY your environment for the current session.

Loading conflicts

By default you can not load different versions of same software Module in same session. Loading for example Intel compiler version X while Intel compiler version Y is loaded results in error message as follows: 

Module 'compiler/intel/X' conflicts with the currently loaded module(s) 'compiler/intel/Y'

The solution is unloading or switching Modules.

Showing the changes introduced by a Module

Loading a Module will change the environment of the current shell session. For instance the $PATH variable will be expanded by the software's binary directory. Other Module variables may even change the behavior of the current shell session or the software program(s) in a more drastic way.
Loaded Modules may also invoke an additional set of environment variables, which e.g. point to directories or destinations of documentation and examples. Their nomenclature is systematic:

Variable Pointing to
$SWN_HOME Root directory of the software package
$SWN_DOC_DIR Documentation
$SWN_EXA_DIR Examples
$SWN_BPR_URL URL of software's Wiki article
and many many more...  

with SWN being the place holder of the software Module name.
All the changes to the current shell session to be invoked by loading the Module can be reviewed using 'module show category/softwarename/version'.
Example (Intel compiler) 

$ module show compiler/intel/14.0
-------------------------------------------------------------------
/opt/bwhpc/common/modulefiles/compiler/intel/14.0:
module-whatis	 Intel(R) compiler suite (icc, icpc, ifort), debugger (idb), IPP and TBB ver 14.0.4 
setenv		 INTEL_VERSION 14.0.4 
setenv		 INTEL_HOME /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211 
setenv		 INTEL_BIN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/bin/intel64 
setenv		 INTEL_LIB_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
setenv		 INTEL_LIB_MIC /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/mic 
setenv		 INTEL_INC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/include 
setenv		 INTEL_MAN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/man/en_US 
setenv		 INTEL_DOC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/Documentation/en_US 
setenv		 ICC_VERSION 14.0.4 
setenv		 ICC_HOME /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211 
setenv		 ICC_BIN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/bin/intel64 
setenv		 ICC_LIB_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
setenv		 ICC_INC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/include 
setenv		 ICC_MAN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/man/en_US 
setenv		 ICC_DOC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/Documentation/en_US 
setenv		 IFORT_VERSION 14.0.4 
setenv		 IFORT_HOME /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211 
setenv		 IFORT_BIN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/bin/intel64 
setenv		 IFORT_LIB_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
setenv		 IFORT_INC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/include 
setenv		 IFORT_MAN_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/man/en_US 
setenv		 IFORT_DOC_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/Documentation/en_US 
setenv		 IDB_VERSION 14.0.4 
setenv		 IDB_HOME /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211 
setenv		 IDB_LIB_DIR /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/debugger/lib/intel64 
setenv		 LANGUAGE_TERRITORY en_US 
prepend-path	 PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/bin/intel64 
prepend-path	 LD_LIBRARY_PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
prepend-path	 LD_RUN_PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
prepend-path	 MIC_LD_LIBRARY_PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/mic 
prepend-path	 LIBRARY_PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64 
prepend-path	 MANPATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/man/en_US 
prepend-path	 NLSPATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/compiler/lib/intel64/locale/%l_%t/%N 
prepend-path	 LD_LIBRARY_PATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/debugger/lib/intel64 
prepend-path	 NLSPATH /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/debugger/intel64/locale/%l_%t/%N 
prepend-path	 INTEL_LICENSE_FILE /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/composer_xe_2013_sp1.4.211/licenses 
setenv		 IDB_JAVA_ARGUMENTS -Xms512m -Xmx1024m 
setenv		 CC icc 
setenv		 CXX icpc 
setenv		 F77 ifort 
setenv		 FC ifort 
setenv		 F90 ifort 
setenv		 TEST_MODULE_SCRIPT /opt/bwhpc/common/compiler/intel/compxe.2013.sp1.4.211/install-doc/test-compiler-intel.sh 
setenv		 TEST_MODULE_NAME compiler/intel/14.0 
conflict	 compiler/intel 
conflict	 compiler/gnu/4.9 
-------------------------------------------------------------------

'module show' does not load the Module!

Modules depending on Modules

Some program Modules depend on libraries to be loaded to the user environment. Therefore the corresponding Modules of the software must be loaded together with the Modules of the libraries.
By default such software Modules try to load required Modules and corresponding versions automatically. However, automatic loading might fail if a different version of that required Module is already loaded (cf. Loading conflicts).

Unloading Modules

To unload or to remove a software Module execute: 

$ module unload category/softwarename/version

or 

$ module remove category/softwarename/version

Unloading all loaded modules

Purge

Unloading a Module that has been loaded by default makes it inactive for the current session only - it will be reloaded the next time you log in.
In order to remove all previously loaded software modules from your environment issue the command 'module purge'.
Example 

$ module list
Currently Loaded Modulefiles:
  1) devel/gdb/7.7
  2) compiler/intel/14.0
  3) mpi/openmpi/1.8-intel-14.0(default)
$
$ module purge
$ module list
No Modulefiles Currently Loaded.
$

Beware!
'module purge' is working without any further inquiry.

Clear

Use 'module clear' and confirm with "y" to unload all loaded module, too.
Example 

$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/14.0
  2) mpi/openmpi/1.8-intel-14.0(default)
  3) devel/gdb/7.7
$ 
$ module clear
Are you sure you want to clear all loaded modules!? [n] y
$
$ module list
No Modulefiles Currently Loaded.

Display your loaded Modules

All Modules that are currently loaded for you can be displayed by the command 'module list'. See example above.
Note: You only have to load further Modules, if you want to use additional software packages or to change the version of an already loaded software.

Software job examples

The Modules installed on bwHPC systems provide job examples to help you get started using the software or submitting jobs with this software. Examples can be found via a convenient variable $SWN_EXA_DIR (for a Module called SWN). It is advisable to copy the whole example folder to your $HOME directory, so you can edit those job examples.
For copying the entire job examples folder of software swn to your working directory, execute: 

$ module load catogory/softwarename
$ cp -R $SWN_EXA_DIR .


How do Modules work?

The default shell on the bwHPC clusters is bash, so explanations and examples will be shown for bash. In general, programs cannot modify the environment of the shell they are being run from, so how can the module command do exactly that?
The module command is not a program, but a bash-function. You can view its content using 

$ type module

and you will get a result like this: 

$ type module
module is a function
module () 
{ 
    eval `/usr/bin/modulecmd bash $*`
}

In this function, modulecmd is called. Its output to stdout is then executed inside your current shell using the bash-internal eval command. As a consequence, all output that you see from the module is transmitted via stderr (output handle 2) or in some cases even stdin (output handle 0).

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