Use Cases for Sites¶

Sites can use mkmod in build scripts or within rpm spec files for modulefile generation. However, the component that inserts the module use <dir> command in startup scripts must be turned off, and the site name (abbreviation) must be specified for the convenience environment variables (e.g. TACC_PHDF5_DOC, etc.).

Package specific variables can be set, and non-standard pathnames can be added to PATH-type variables, as explained above in the use cases for HPC users, by setting environment variables and PATH-type list variables (e.g. ENV1, …, ENVn, and PATH_LIST, MANPATH_LIST, etc.)

For site-wide modulefiles the SITE_INSTALL variable should be set to the site name (e.g. TACC, PSC, SDSC, NERSC). This sets the modulefile-name prefix to “”; the information environment variables are prefixed with the site name and an underscore (e.g. TACC_, PSC_, etc.); and no insertion of module use <dir> is attempted in startup scripts. The MODULEFILES_DIR variable is set to the site-wide modulesfile directory for the application.

Often site installers are interested in including whatis and help information. There are several ways to have mkmod “ingest” this information.

Use Case 1¶

In this example SITE_INSTALL and MODULEFILES_DIR are set for site installation.

Also, NAME, VER and TOPDIR variables are set as usual; and the ENV1 variable is set to a name=value pair (REMORA_BIN=$TOPDIR/bin) for mkmod to set the REMORA_BIN environment variable to $TOPDIR/bin in the modulefile:

# finished installing remora, with compiler and mpi module loaded

$ export SITE_INSTALL=TACC
$ export MODULEFILES_DIR=/opt/apps/modulefiles

$ export NAME=remora VER=1.8.2 TOPDIR=/opt/apps/$NAME/$VER

$ export ENV1="REMORA_BIN=$TOPDIR/bin"

$ mkmod

The compiler and MPI modules loaded at this time (for the remora install, and subsequently seen by the mkmod execution) are set as prerequisites.

Use Case 2¶

The following example is a script for installing a modulefile for MOOSE.

Compiler and MPI modules are explicitly loaded in the script, and the subsequent mkmod execution will put these module prerequisites in the modulefile (gcc/7.1.0 and impi/17.0).

The SITE_INSTALL and MODULEFILES_DIR mkmod variables are set for site installation. For a site with a hierarchical module structure the MODULEFILES_DIR and TOPDIR may contain compiler and MPI path components, and may even be in different directory trees, as shown in this example.

Here, the whatis information is included through the WHATIS mkmod environment variable, and modulefile help-text is contained in the HELP_MESSAGE mkmod variable. Also, the environment variables MOOSE_DIR and MOOSE_ARCH are set in the modulefile as specified by the mkmod ENV1 and ENV2 variables:

#!/bin/bash

module load gcc/7.1.0 impi/17.0

export SITE_INSTALL=TACC
export MODULEFILES_DIR=/opt/apps/gcc7_1/impi17_0/modulefiles

export NAME=moose
export VER=git.20170622
export TOPDIR=/home1/apps/gcc7_1/impi17_0/$NAME/$VER


export ENV1="MOOSE_DIR=$TOPDIR"
export ENV2="MOOSE_ARCH=\"\""    # set to blank, ""

export WHATIS="
  Name: Moose
  @ Version: $VER
  @ Version-notes: external packages installed:
  @ Category: library, mathematics
  @ URL: https://mooseframework.inl.gov
  @ Description: Numerical library for sparse linear algebra
"
export HELP_MESSAGE="
 Compile with: -I\$PHDF5_INC
 Link with:    -Wl,-rpath,\$PHDF5_LIB -L\$PHDF5_LIB -lhdf5 -lz
"
mkmod

The WHATIS variable contains a @-separated list of whatis key:value pairs separated by colons. (Above, each key:value type pair is entered on a separate line, and includes a @ separator where appropriate.) Optionally, each key:value pair can be entered as a WHATIS# variable, like this:

export WHATIS1="Name: Moose"
export WHATIS2="Version: $VER"
export WHATIS3="Version-notes: external packages installed"
export WHATIS4="Category: library, mathematics"
export WHATIS5="URL: https://mooseframework.inl.gov"
export WHATIS6="Description: Numerical library for sparse linear algebra"

Note: the installation tree is in /home1/apps, while the modulefile is in /opt/apps. The site hierarchical structure is indicated in the pathnames.

Case 3¶

This HDF5 modulefile site installation is similar to those in the above scripts, but it extracts the whatis and help information from files specified in the WHATIS_FILE and HELP_FILE environment variables.

The whatis key:value pairs are in the site_phdf_modules_whatis file, and the help information text is in the site_phdf5_modules_help file.

#!/bin/bash

module load intel/18.0.2 impi/18.0.2

BASE_DIR=/opt/apps/intel18/impi18_0

export SITE_INSTALL=TACC
export MODULEFILES_DIR=$BASE_DIR/modulefiles

          NAME=phdf5
           VER=1.8.16
        TOPDIR=$BASE_DIR/phdf5/1.8.16

export NAME VER TOPDIR PREFIX

export WHATIS_FILE=site_phdf5_modules_whatis
export   HELP_FILE=site_phdf5_modules_help

mkmod

The contents of the files are shown below. (If a whatis or help file is specified, then the WHATIS or HELP_MESSAGE environment variable is ignored.)

Variable substitution is performed for the file content. Hence it may be necessary to escape (protect) the dollar ($) character at times, as is done in the help file below. (Substitution is only for externally defined variables; internal (convenience) variables, such as TACC_PHDF5_LIB, TACC_PHDF5_DOC, etc. holding directory names, are not available for evaluation). The two information files are listed here:

$ cat my_local_whatis_file

   Name:        PHDF5
   Version:     $VER
   Category:    library, runtime support
   Keywords:    I/O, Library
   URL:         http://www.hdfgroup.org/HDF5/
   Description: file format library for storing data (Parallel Version)

$ cat my_local_help_file

   Compile the source code with the option:

       -I\$PHDF5_INC

   and add the following options to the link step:

       -Wl,-rpath,\$PHDF5_LIB -L\$PHDF5_LIB -lhdf5 -lz

Mkmod also searches, relative to $TOPDIR, for files named modules_help and modules_whatis. It appends the content of modules_help to the automatic modulefile help-message, and uses the key:value pairs in the modules_whatis file for the modulefile whatis entries. The precedence is presented in the following table:

HELP:

File/Env. Var. Location/Value Modulefile Help Message Contribution

modules_help file name, found relative to $TOPDIR search Appends content to modulefile help message.

HELP_FILE =pathname (file) Don’t search for modules_help file. Append content of this fileto modulefile help message.

HELP_FILE =none Don’t search for modules_help file.

HELP_MESSAGE =”some text” Append text to module help message, if no help file is being used.

WHATIS:

File/Env. Var. Location/Value whatis

modules_whatis file name, found relative to $TOPDIR search Read each line as a whatis key:value formatted pair.

WHATIS_FILE =pathname (file) Don’t search for modules_whatis file. Read each line as a whatis key:value format.

WHATIS_FILE =none Don’t search for modules_whatis file.

WHATIS_MESSAGE =”list of key:value pairs” (@-separated list) Only uses these as whatis values if no whatis file is being used.

Use Cases for Sites¶

Use Case 1¶

Use Case 2¶

Case 3¶

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File/Env. Var.	Location/Value	Modulefile Help Message Contribution
modules_help	file name, found relative to $TOPDIR search	Appends content to modulefile help message.
HELP_FILE	=pathname (file)	Don’t search for modules_help file. Append content of this fileto modulefile help message.
HELP_FILE	=none	Don’t search for modules_help file.
HELP_MESSAGE	=”some text”	Append text to module help message, if no help file is being used.

File/Env. Var.	Location/Value	whatis
modules_whatis	file name, found relative to $TOPDIR search	Read each line as a whatis key:value formatted pair.
WHATIS_FILE	=pathname (file)	Don’t search for modules_whatis file. Read each line as a whatis key:value format.
WHATIS_FILE	=none	Don’t search for modules_whatis file.
WHATIS_MESSAGE	=”list of key:value pairs” (@-separated list)	Only uses these as whatis values if no whatis file is being used.