Software Modules Lmod

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Software Module System - Lmod

1 PREFACE

This guide describes the software environment and tools used to run applications on JUSTUS 2 system. It is intended as a general overview and introduction to the software system management on JUSTUS 2 for new users as well as for experienced users coming, e.g. from sites planted with different Environment modules package, as for example JUSTUS 1 system.

2 Essential "JUSTUS 1 to JUSTUS 2" migration guide

There exist several software implementations for a dynamical management of environmental variables throughout the HPC world. JUSTUS 1 hosted Environment Modules package based on Tcl, while there is a Lua based module system Lmod (https://lmod.readthedocs.io/en/latest/#) installed on JUSTUS 2. Despite of the various software solutions, the difference in handling of the modules from users' perspective of view stays tiny. The biggest change lies in the introducing of the partial software hierarchy implemented in modules system on JUSTUS 2.

2.1 Lmod commnads

The much of module commands and its functionality has remained same on JUSTUS 2, although Lmod offers new functions as for example module spider as an extension of "old" module avail functionality.
Thus, the default Gaussian module is initialized by 

$ module load chem/gaussian

or with using of the shorthand version 

$ ml chem/gaussian


Full list of the Lmod module commands is available online on https://lmod.readthedocs.io/en/latest/010_user.html

Rather than the divergence of module commands, JUSTUS 1 users has to get a grasp of the modulefile system hierarchy built-in JUSTUS 2 software layout. The layout is no more flat as on JUSTUS 1, however JUSTUS 2 adopts a partial module hierarchy for mpi modules.

2.2 Consequences of the partial module hierarchy for mpi modules

Due the flat layout of software modules on JUSTUS 1 module avail command showed all pre-installed software packages including those directly depended on another modules. This is no more true on JUSTUS 2, in particular for mpi modules. mpi modules remains invisible for a user (prompted module avail) until some compiler module has been loaded. Once the compiler module has been activated corresponding mpi modules, i.e. built with the particular compiler, become visible.

E.g., with the originally empty list of the loaded modules, the module command 

$ module avail

or its shorthand analogue 

 
$ ml av

displays no mpi module available. After running 

ml compiler/intel/19.1
ml av

mpi packages compatible with the intel 19.1 compiler becomes visible 

--------------------------------------------------------------- /opt/bwhpc/common/modulefiles/Compiler/intel/19.1 ---------------------------------------------------------------
   mpi/impi/2019.7    mpi/openmpi/4.0

in the list of the available software.

3 MINIMALISTIC DESCRIPTION OF LMOD MODULE SYSTEM ON JUSTUS 2

JUSTUS 2 system uses Lmod (the Lua Based Module System) environment management package to support dynamical modification of the user environment via modulefiles. Each modulefile contains information needed to configure the shell, i.e. its environmental variables, required to run a particular software application. To make major changes in the users' environment, such as modifications of PATH, LD_LIBRARY_PATH, CC or FC variables for, e.g. a switching to a different compiler, use the appropriate single or sequence of modules commands instead of a reconfiguration of the shell by hand.

E.g. in order to activate the default vasp module run a single command: 

$ module load chem/vasp

or its shorthand variant 

$ml chem/vasp

For an activation of the module of intel mpi built with the corresponding intel compiler a sequence of two module commands 

$ module load compiler/intel
$ module load mpi/impi

has to be run.

3.1 Online user guide of Lmod

The complete user guide can be found on Lmod websites https://lmod.readthedocs.io/en/latest/010_user.html

3.2 Which shells supports module commands?

So far Bash is only supported shell on JUSTUS 2 to interpret module commands.

3.3 Most basic tasks for Module System

Lmod offers more than 25 sub-commands plus various options to manage the modulefile system installed on JUSTUS 2. See, e.g. output of "module --help" command. Large majority of users will use only couple of them. A complete list of module sub-commands can be displayed by entering "module --help" command or in Lmod online documentation. The following text lists only a couple of them.

3.3.1 Loading and unloading modulefiles

To load and unload a module of a specific package use "module load category/package" and "module unload category/package", respectively. Thus, e.g, to load default version of VASP which belongs into category chem, enter 

$ module load chem/VASP

and for unloading of the package use 

$ module unload chem/VASP

3.3.2 Complete unloading of all modulefiles

To clean the environment from all entries set by lmod use "module purge" command. 

$ module purge

Beware that the "module purge" does not always restore the environmental variables that existed prior entering first "module load" command. I.e., some of the entries in PATH, or environmental variables, etc. originally existed in the environment might be cleaned by "module purge" if those would be duplicates of the variables set by any modulefiles that was loaded.

3.3.3 What is Loaded Now?

To see which modules are currently loaded in your environment, enter the command "module list". 

$ module list

3.3.4 Which modulefiles/software is available?

To see what modulefiles are available on JUSTUS 2, you can enter the following command: 

$ module avail

or alternatively 

$ ml av

which comes with lmod to save typewriting.

3.3.5 Module specific help

To access the module specific help, use the "module help" command. For example, to see the module help associated with the default VASP module, enter this command: 

$ module help chem/vasp

It is always a good practice to read through all the info provided by a specific module help since this serves as an important communication channel between a user and the person who install the piece of a software.

3.4 Semi hierarchical layout of modules on JUSTUS 2

3.4.1 Module hierarchy in Lmod

The structure of software modules on JUSTUS 2 exploits a "semi" hierarchical structure. This is slightly different from what can be seen on another HPC systems with "full" hierarchical structure. The typical systems with full hierarchy put compiler modules (i.e., intel, gcc) in the uppermost (Core) level, depending libraries (e.g., MPI) on the second level, and more depending libraries on a third level. As a consequence, not all the modules contained in the module system are initially visible, namely the modules putted in the second and third layer. Only after a loading a compiler module, the modules of the second layer directly depending on the particular compiler will become available. And similarly, loading an MPI module will make the modules of the third layer depending on the loaded MPI library visible.

=== Semi hierarchy on JUSTUS 2 JUSTUS 2 adopted the hierarchical structure of the modules layout only partially. In particular, there is only "Core" and the "second" level presented and there are only mpi modules contained in the second level. All other modules, i.e. for example those from the "chem" sub-cathegory such as vasp, turbomole, or gaussian, or those located in the "numlib" sub-cathegory such as mkl or python_numpy, are embodied in the "Core" level.

Many modules depends on another modules. Except the modules in compiler category, it is the case for almost all software modules installed on JUSTUS 2. In another words, for a correct functioning of the most modules another modules must be simultaneously activated. Most of the modules manage that automatically or the user is instructed to reload a particular module/s to fulfill a specific module dependency.

4 General Introduction

Environment Modules, or short Modules are the means by which most of the installed scientific software is provided on JUSTUS 2.
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. JUSTUS 2 provides users with the possibility to load and unload complete environments for compilers, libraries and software packages by a single command.

5 General 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 JUSTUS 2 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.
If you want to see which modules are loaded you must execute 'module list'. 

$ module list
Currently Loaded Modules:
  1) compiler/intel/19.1   2) mpi/impi/2019   3) numlib/mkl/2019


6 Usage

Lmod on JUSTUS 2: A New Environment Module System from http://lmod.readthedocs.org/en/latest/ is installed.

6.1 Documentation

Execute 'module help' or 'man module' for help on how to use Modules software. 

$ module help
Usage: module [options] sub-command [args ...]

Options:
  -h -? -H --help                   This help message
  -s availStyle --style=availStyle  Site controlled avail style: system (default: system)
  --regression_testing              Lmod regression testing
  -D                                Program tracing written to stderr
  --debug=dbglvl                    Program tracing written to stderr (where dbglvl is a number 1,2,3)
  --pin_versions=pinVersions        When doing a restore use specified version, do not follow defaults
  -d --default                      List default modules only when used with avail
  -q --quiet                        Do not print out warnings
  --expert                          Expert mode
  -t --terse                        Write out in machine readable format for commands: list, avail, spider, savelist
  --initial_load                    loading Lmod for first time in a user shell
  --latest                          Load latest (ignore default)
  --ignore_cache                    Treat the cache file(s) as out-of-date
  --novice                          Turn off expert and quiet flag
  --raw                             Print modulefile in raw output when used with show
  -w twidth --width=twidth          Use this as max term width
  -v --version                      Print version info and quit
  -r --regexp                       use regular expression match
  --gitversion                      Dump git version in a machine readable way and quit
  --dumpversion                     Dump version in a machine readable way and quit
  --check_syntax --checkSyntax      Checking module command syntax: do not load
  --config                          Report Lmod Configuration
  --config_json                     Report Lmod Configuration in json format
  --mt                              Report Module Table State
  --timer                           report run times
  --force                           force removal of a sticky module or save an empty collection
  --redirect                        Send the output of list, avail, spider to stdout (not stderr)
  --no_redirect                     Force output of list, avail and spider to stderr
  --show_hidden                     Avail and spider will report hidden modules
  --spider_timeout=timeout          a timeout for spider
  -T --trace                       

module [options] sub-command [args ...]

Help sub-commands:
------------------
  help                              prints this message
  help                module [...]  print help message from module(s)

Loading/Unloading sub-commands:
-------------------------------
  load | add          module [...]  load module(s)
  try-load | try-add  module [...]  Add module(s), do not complain if not found
  del | unload        module [...]  Remove module(s), do not complain if not found
  swap | sw | switch  m1 m2         unload m1 and load m2
  purge                             unload all modules
  refresh                           reload aliases from current list of modules.
  update                            reload all currently loaded modules.

Listing / Searching sub-commands:
---------------------------------
  list                              List loaded modules
  list                s1 s2 ...     List loaded modules that match the pattern
  avail | av                        List available modules
  avail | av          string        List available modules that contain "string".
  spider                            List all possible modules
  spider              module        List all possible version of that module file
  spider              string        List all module that contain the "string".
  spider              name/version  Detailed information about that version of the module.
  whatis              module        Print whatis information about module
  keyword | key       string        Search all name and whatis that contain "string".

Searching with Lmod:
--------------------
  All searching (spider, list, avail, keyword) support regular expressions:


  -r spider           '^p'          Finds all the modules that start with `p' or `P'
  -r spider           mpi           Finds all modules that have "mpi" in their name.
  -r spider           'mpi$         Finds all modules that end with "mpi" in their name.

Handling a collection of modules:
--------------------------------
  save | s                          Save the current list of modules to a user defined "default" collection.
  save | s            name          Save the current list of modules to "name" collection.
  reset                             The same as "restore system"
  restore | r                       Restore modules from the user's "default" or system default.
  restore | r         name          Restore modules from "name" collection.
  restore             system        Restore module state to system defaults.
  savelist                          List of saved collections.
  describe | mcc      name          Describe the contents of a module collection.
  disable             name          Disable (i.e. remove) a collection.

Deprecated commands:
--------------------
  getdefault          [name]        load name collection of modules or user's "default" if no name given.
                                    ===> Use "restore" instead  <====
  setdefault          [name]        Save current list of modules to name if given, otherwise save as the default list for you the user.
                                    ===> Use "save" instead. <====

Miscellaneous sub-commands:
---------------------------
  is-loaded           modulefile    return a true status if module is loaded
  is-avail            modulefile    return a true status if module can be loaded
  show                modulefile    show the commands in the module file.
  use [-a]            path          Prepend or Append path to MODULEPATH.
  unuse               path          remove path from MODULEPATH.
  tablelist                         output list of active modules as a lua table.

Important Environment Variables:
--------------------------------
  LMOD_COLORIZE                     If defined to be "YES" then Lmod prints properties and warning in color.

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Lmod Web Sites

  Documentation:    http://lmod.readthedocs.org
  Github:           https://github.com/TACC/Lmod
  Sourceforge:      https://lmod.sf.net
  TACC Homepage:    https://www.tacc.utexas.edu/research-development/tacc-projects/lmod

  To report a bug please read http://lmod.readthedocs.io/en/latest/075_bug_reporting.html
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Modules based on Lua: Version 8.2 (8.2-1-g9c98036c) 2019-10-30 11:17 -05:00
    by Robert McLay mclay@tacc.utexas.edu

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

$ module help compiler/intel
---------------------- Module Specific Help for "compiler/intel/19.1" ----------------------
Intel(R) Compilers 19.1 for Linux*
For details see: https://software.intel.com/en-us/intel-compilers
In case of problems, please contact: Hartmut Häfner <hartmut.haefner@kit.edu>
SCC support end: 2022-12-31


6.1.1 Online Documentation

Lmod: A New Environment Module System

6.2 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

Some modules may not be available right now, because their requirements are not met. To get a complete list of all possible modules use the module spider command.

6.3 Module categories, versions and defaults

The ForHLR clusters 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 all versions of the Intel compiler belong to the category of compilers, thus the corresponding modulefiles are 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


6.4 Finding software Modules

Currently all JUSTUS 2 software packages are assigned to the following Module categories (???):

  • chem
  • compiler
  • devel
  • lib
  • numlib
  • phys
  • system
  • vis

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


6.5 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.

6.5.1 Loading conflicts

You can not load different versions of the same software at the same time! Loading the Intel compiler in version X while Intel compiler in version Y is loaded leads to an automatic unloading of Intel compiler in version Y.

6.5.2 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.

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
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
   /opt/bwhpc/common/modulefiles/Core/compiler/intel/19.1.lua:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
setenv("INTEL_LICENSE_FILE","28518@scclic1.scc.kit.edu")
setenv("AR","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/xiar")
setenv("CC","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/icc")
setenv("CXX","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/icpc")
setenv("F77","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/ifort")
setenv("FC","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64/ifort")
setenv("CFLAGS","-O2 -xCORE-AVX2")
setenv("CXXFLAGS","-O2 -xCORE-AVX2")
setenv("FFLAGS","-O2 -xCORE-AVX2")
setenv("FCFLAGS","-O2 -xCORE-AVX2")
setenv("INTEL_VERSION","19.1.0.166")
setenv("INTEL_HOME","/opt/intel/compilers_and_libraries_2020/linux")
setenv("INTEL_BIN_DIR","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64")
setenv("INTEL_LIB_DIR","/opt/intel/compilers_and_libraries_2020/linux/lib/intel64")
setenv("INTEL_INC_DIR","/opt/intel/compilers_and_libraries_2020/linux/include")
setenv("INTEL_MAN_DIR","/opt/intel/compilers_and_libraries_2020/linux/man/common")
setenv("INTEL_DOC_DIR","/opt/intel/compilers_and_libraries_2020/linux/documentation/en")
setenv("GDB_VERSION","19.1.0.166")
setenv("GDB_HOME","/opt/intel/debugger_2020/gdb/intel64")
setenv("GDB_BIN_DIR","/opt/intel/debugger_2020/gdb/intel64/bin")
setenv("GDB_LIB_DIR","/opt/intel/debugger_2020/libipt/intel64/lib")
setenv("GDB_INC_DIR","/opt/intel/debugger_2020/gdb/intel64/include")
setenv("GDB_INF_DIR","/opt/intel/documentation_2020/en/debugger/gdb-ia/info")
setenv("GDB_MAN_DIR","/opt/intel/documentation_2020/en/debugger/gdb-ia/man")
setenv("KMP_AFFINITY","noverbose,granularity=core,respect,warnings,compact,1")
prepend_path("PATH","/opt/intel/compilers_and_libraries_2020/linux/bin/intel64")
prepend_path("MANPATH","/opt/intel/compilers_and_libraries_2020/linux/man/common")
prepend_path("LD_LIBRARY_PATH","/opt/intel/compilers_and_libraries_2020/linux/lib/intel64")
whatis("Sets up Intel C/C++ and Fortran compiler version 19.1 (Intel(R) Compilers 19.1 for Linux*) - supported by SCC till 2022-12-31!")
help([[Intel(R) Compilers 19.1 for Linux*
For details see: https://software.intel.com/en-us/intel-compilers
In case of problems, please contact: Hartmut Häfner <hartmut.haefner@kit.edu>
SCC support end: 2022-12-31]])
prepend_path("MODULEPATH","/software/bwhpc/common/modulefiles/Compiler/intel/19.1")
family("compiler")



6.5.3 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.


6.6 Unloading Modules

To unload or remove a software Module execute: 

$ module unload category/softwarename/version

or 

$ module remove category/softwarename/version


6.6.1 Unloading all loaded modules

6.6.1.1 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 Modules:
  1) compiler/intel/19.1   2) mpi/impi/2019   3) numlib/mkl/2019
$
$ module purge
$ module list
No modules loaded
$

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

6.7 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.

6.8 Display all possible Modules

Modulefiles can be searched by the user. You can dipslay all possible modules by executing: 

$ module spider

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
The following is a list of the modules and extensions currently available:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  cae/abaqus: cae/abaqus/2018, cae/abaqus/2019

  cae/adina: cae/adina/9.1.2

  cae/ansys: cae/ansys/19.2, cae/ansys/2019R3, cae/ansys/2020R1

  cae/comsol: cae/comsol/5.4, cae/comsol/5.5

  cae/cst: cae/cst/2018

  cae/lsdyna: cae/lsdyna/901

  cae/openfoam: cae/openfoam/v1912, cae/openfoam/2.4.x, cae/openfoam/6, cae/openfoam/7

  cae/paraview: cae/paraview/5.8

  cae/starccm+: cae/starccm+/14.02.010, cae/starccm+/2019.2.1

  cae/starcd: cae/starcd/4.28

  compiler/clang: compiler/clang/9.0

  compiler/gnu: compiler/gnu/9.2

  compiler/intel: compiler/intel/18.0, compiler/intel/19.0, compiler/intel/19.1

  compiler/pgi: compiler/pgi/2019

  devel/cmake: devel/cmake/3.16

  devel/cuda: devel/cuda/9.2, devel/cuda/10.0, devel/cuda/10.2

  devel/gdb: devel/gdb/9.1

  devel/python: devel/python/3.7.4_gnu_9.2, devel/python/3.8.1_gnu_9.2, devel/python/3.8.1_intel_19.1

  math/R: math/R/3.6.3

  math/julia: math/julia/1.3.1

  mpi/impi: mpi/impi/2018, mpi/impi/2019, mpi/impi/2020

  mpi/openmpi: mpi/openmpi/4.0

  numlib/mkl: numlib/mkl/2018, numlib/mkl/2019, numlib/mkl/2020

  numlib/python_numpy: numlib/python_numpy/1.17.2_python_3.7.4_gnu_9.2

  numlib/python_scipy: numlib/python_scipy/1.3.1_numpy_1.17.2_python_3.7.4_gnu_9.2

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

To learn more about a package execute:

   $ module spider Foo

where "Foo" is the name of a module.

To find detailed information about a particular package you
must specify the version if there is more than one version:

   $ module spider Foo/11.1

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

'module spider name/version' : If you search the full name and version of the module, the search gives detailed information about that module version. 

$ module spider devel/cmake

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  devel/cmake: devel/cmake/3.16
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    This module can be loaded directly: module load devel/cmake/3.16

    Help:
      Home page:            https://www.cmake.org
      Online Documentation: https://www.cmake.org/HTML/Documentation.html
      Local Documentation:  /opt/bwhpc/common/devel/cmake/3.16.4/docFAQ:                  https://gitlab.kitware.com/cmake/community/wikis/FAQ

Moreover, you can see the dependencies of the module with using the same command. For example, if the following is executed, you can see which modules need to be loaded before loading the module mpi/impi/2019 

$ module spider mpi/impi/2019

------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  mpi/impi: mpi/impi/2019
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

    You will need to load all module(s) on any one of the lines below before the "mpi/impi/2019" module is available to load.

      compiler/clang/9.0
      compiler/gnu/9.2
      compiler/intel/18.0
      compiler/intel/19.0
      compiler/intel/19.1

    Help:
      Intel(R) MPI Library


7 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 the following result: 

$ type module
module is a function
module ()
{
    eval $($LMOD_CMD bash "$@");
    [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}

In this function, lmod 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 so

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