Tutorial setup

If you have not done the prior sections, you’ll need to set Spack up like this:

git clone https://github.com/spack/spack
. spack/share/spack/setup-env.sh
spack tutorial

See the Basic Installation Tutorial for full details on setup. For more help join us in the #tutorial channel on Slack – get an invitation at spackpm.herokuapp.com

Module Files Tutorial¶

This tutorial illustrates how Spack can be used to generate module files for the software that has been installed. Both hierarchical and non-hierarchical deployments will be discussed in details and we will show how to customize the content and naming of each module file.

At the end of the tutorial readers should have a clear understanding of:

What module files are and how they are used on HPC clusters

How Spack generates module files for the software it installs

Which Spack commands can be used to manage module files

How module files generated by Spack can be customized

and be confident that Spack can deal with all of the common use cases that occur when maintaining software installations on HPC clusters.

Setup for the Tutorial¶

To prepare for this tutorial we are going to install a small but representative set of software that includes different configurations of the same packages and some external packages. To keep the installations manageable, let’s start by uninstalling everything from earlier in the tutorial:

$ spack uninstall -ay

Build a module tool¶

The first thing that we need is the module tool itself. In the tutorial we will use lmod because it can work with both hierarchical and non-hierarchical layouts.

$ spack install lmod

Once the module tool is installed we need to have it available in the current shell. Installation directories in Spack’s store are definitely not easy to remember, but they can be retrieved with the spack location command:

$ . $(spack location -i lmod)/lmod/lmod/init/bash

Now we can re-source the setup file and Spack modules will be put in our module path.

$ . share/spack/setup-env.sh

Add a new compiler¶

The second step is to build a recent compiler. On first use, Spack scans the environment and automatically locates the compiler(s) already available on the system. For this tutorial, however, we want to use gcc@8.3.0.

$ spack install gcc@8.3.0

You can get this in your environment using spack load gcc@8.3.0:

$ spack load gcc@8.3.0
$ which gcc
/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gcc

Now, gcc is in your PATH, and you can add it to the list of compilers with spack compiler add:

$ spack compiler add
==> Added 1 new compiler to /home/spack/.spack/linux/compilers.yaml
    gcc@8.3.0
==> Compilers are defined in the following files:
    /home/spack/.spack/linux/compilers.yaml

$ spack compiler list
==> Available compilers
-- clang ubuntu18.04-x86_64 -------------------------------------
clang@6.0.0

-- gcc ubuntu18.04-x86_64 ---------------------------------------
gcc@8.3.0  gcc@7.5.0  gcc@6.5.0

Build the software that will be used in the tutorial¶

Finally, we will use Spack to install the packages used in the examples:

$ spack install netlib-scalapack ^openmpi ^openblas
$ spack install netlib-scalapack ^mpich ^openblas
$ spack install netlib-scalapack ^openmpi ^netlib-lapack
$ spack install netlib-scalapack ^mpich ^netlib-lapack
$ spack install py-scipy ^openblas

What are Module Files?¶

Module files are an easy way to modify your environment in a controlled manner during a shell session. In general, they contain the information needed to run an application or use a library. The module command is used to interpret and execute module files. For example, module show tells you what a module will do when loaded:

$ module show zlib
----------------------------------------------------------------------------------------------------------------------------------------------
   /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/zlib/1.2.11-gcc-8.3.0:
----------------------------------------------------------------------------------------------------------------------------------------------
whatis("A free, general-purpose, legally unencumbered lossless data-compression library. ")
conflict("zlib")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/share/man")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/lib")
prepend_path("INCLUDE","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/include")
prepend_path("PKG_CONFIG_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/lib/pkgconfig")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/")
help([[A free, general-purpose, legally unencumbered lossless data-compression
library.
]])

$ echo $LD_LIBRARY_PATH

module load will execute all of the changes shown above:

$ module load zlib
$ echo $LD_LIBRARY_PATH
/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/zlib-1.2.11-2icaxiyy5rrqdavfv7jbojdq36r6u37n/lib

and to undo the modifications, you can use module unload:

$ module unload zlib
$ echo $LD_LIBRARY_PATH

$

Module Systems¶

There are two main module systems used in HPC, both installable by Spack. In this tutorial we will be working with lmod and be showing examples with both Tcl and Lua.

Environment Modules¶

This is the original modules tool. It can be installed with Spack using the following command:

$ spack install environment-modules

It was first coded in C in the early 1990s and was later rewritten entirely in Tcl. Long stagnant, the project has been revived in the past few years by Xavier Delaruelle at CEA, and it is now very actively developed. For further details we refer to its documentation.

Lmod¶

Lmod is a module system written in Lua, originally created at the “Texas Advanced Computing Center” (TACC) by Robert McLay. You can get it with:

$ spack install lmod

as shown in the Setup for the Tutorial section. It is a drop-in replacement for Environment Modules, and it works with both Tcl and Lua module files. It is fully compatible with Environment Modules, but it also has many distinguishing features of its own. The main one is the module hierarchy, which simplifies the module UI by only showing modules built with the currently loaded compiler and/or MPI. There are also some unique safety features.

How does Spack generate module files?¶

Before we dive into the hands-on sections it’s worth explaining how module files are generated by Spack. The following diagram provides a high-level view of the process:

Modules in Spack are generated using configuration files (config.yaml and modules.yaml), information from Spack’s package recipes, and Jinja2 templates. Spack comes with Jinja2, an external template engine, so you do not need to install it yourself.

Modules vs `spack load`¶

You may have noticed that we used spack load in the Setup for the Tutorial section above. This is a built-in mechanism of Spack’s – it’s designed so that users on a cluster or a laptop can quickly get a package into their path, and it understands Spack’s spec syntax. It does not require modules, as Spack needs to work regardless of whether modules are set up on the system.

As you might expect, you can see what is loaded via spack load using spack find:

$ spack find --loaded
==> 6 installed packages
-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
gcc@8.3.0  gmp@6.1.2  isl@0.18	mpc@1.1.0  mpfr@3.1.6  zlib@1.2.11

Because Spack is designed to be run on HPC systems, it also generates a module file for every installed package. This allows users unfamiliar with Spack’s interface to see things through the module system they’re used to. To see this, try:

$ module avail

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   autoconf-2.69-gcc-7.5.0-nwb3bf5	libiconv-1.16-gcc-7.5.0-jearpk4 	       ncurses-6.2-gcc-7.5.0-crhlefo
   automake-1.16.2-gcc-7.5.0-wdflovn	libidn2-2.1.1a-gcc-7.5.0-gcbfo3a	       openssl-1.1.1g-gcc-7.5.0-4dj34yw
   bzip2-1.0.8-gcc-7.5.0-fvfpt26	libsigsegv-2.12-gcc-7.5.0-lbrx7ln	       patchelf-0.10-gcc-7.5.0-2nj3vxx
   curl-7.68.0-gcc-7.5.0-e4rrsab	libtool-2.4.6-gcc-7.5.0-jdxbjft 	       pcre2-10.35-gcc-7.5.0-xyujt3h
   diffutils-3.7-gcc-7.5.0-otkkten	libunistring-0.9.10-gcc-7.5.0-dyq3apq	       perl-5.30.3-gcc-7.5.0-hyrsxn4
   expat-2.2.9-gcc-7.5.0-3f3kkbl	libxml2-2.9.10-gcc-7.5.0-m3l53bh	       pkgconf-1.7.3-gcc-7.5.0-4sh6pym
   gcc-8.3.0-gcc-7.5.0-6hbkzol		lmod-8.3-gcc-7.5.0-kqbszrm		       readline-8.0-gcc-7.5.0-t54jzdy
   gdbm-1.18.1-gcc-7.5.0-4av4gyw	lua-5.3.5-gcc-7.5.0-n37jedg		       tar-1.32-gcc-7.5.0-uwe6tb5
   gettext-0.20.2-gcc-7.5.0-p4xwlyy	lua-luafilesystem-1_7_0_2-gcc-7.5.0-tk7fdik    tcl-8.6.8-gcc-7.5.0-aszidzn
   git-2.27.0-gcc-7.5.0-pzqvpp2 	lua-luaposix-33.4.0-gcc-7.5.0-sas2uzg	       unzip-6.0-gcc-7.5.0-2ozim4d
   gmp-6.1.2-gcc-7.5.0-3ol3tld		m4-1.4.18-gcc-7.5.0-mkc3u4x		       xz-5.2.5-gcc-7.5.0-6nxes4r
   isl-0.18-gcc-7.5.0-4lkvfkv		mpc-1.1.0-gcc-7.5.0-uur2dd6		       zlib-1.2.11-gcc-7.5.0-smoyzzo
   libbsd-0.10.0-gcc-7.5.0-u6ue7vw	mpfr-3.1.6-gcc-7.5.0-nwsubsw

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

You can module load any of these. By default, Spack generates modules named by package-version-compiler-version-hash, which is a bit hard to read. We’ll show you how to customize this in the following sections.

Non-hierarchical Module Files¶

If you arrived to this point you should have an environment that looks similar to:

$ module avail

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   autoconf-2.69-gcc-7.5.0-nwb3bf5	libidn2-2.1.1a-gcc-7.5.0-gcbfo3a	       openssl-1.1.1g-gcc-7.5.0-4dj34yw
   autoconf-2.69-gcc-8.3.0-c7fxiuu	libpciaccess-0.13.5-gcc-8.3.0-rqqclxg	       openssl-1.1.1g-gcc-8.3.0-yygx7ht
   automake-1.16.2-gcc-7.5.0-wdflovn	libsigsegv-2.12-gcc-7.5.0-lbrx7ln	       patchelf-0.10-gcc-7.5.0-2nj3vxx
   automake-1.16.2-gcc-8.3.0-25eawip	libsigsegv-2.12-gcc-8.3.0-oaiujfn	       patchelf-0.10-gcc-8.3.0-35lyjgt
   bzip2-1.0.8-gcc-7.5.0-fvfpt26	libtool-2.4.6-gcc-7.5.0-jdxbjft 	       pcre2-10.35-gcc-7.5.0-xyujt3h
   bzip2-1.0.8-gcc-8.3.0-jx7bite	libtool-2.4.6-gcc-8.3.0-too4ft7 	       perl-5.30.3-gcc-7.5.0-hyrsxn4
   cmake-3.17.3-gcc-8.3.0-7otuah5	libunistring-0.9.10-gcc-7.5.0-dyq3apq	       perl-5.30.3-gcc-8.3.0-xmhlmqr
   curl-7.68.0-gcc-7.5.0-e4rrsab	libxml2-2.9.10-gcc-7.5.0-m3l53bh	       pkgconf-1.7.3-gcc-7.5.0-4sh6pym
   diffutils-3.7-gcc-7.5.0-otkkten	libxml2-2.9.10-gcc-8.3.0-u5khonr	       pkgconf-1.7.3-gcc-8.3.0-oo4jobp
   diffutils-3.7-gcc-8.3.0-5fvw3jh	lmod-8.3-gcc-7.5.0-kqbszrm		       py-cython-0.29.16-gcc-8.3.0-mbnkbhv
   expat-2.2.9-gcc-7.5.0-3f3kkbl	lua-5.3.5-gcc-7.5.0-n37jedg		       py-numpy-1.19.0-gcc-8.3.0-3s3aj6y
   expat-2.2.9-gcc-8.3.0-xrk7vwz	lua-luafilesystem-1_7_0_2-gcc-7.5.0-tk7fdik    py-pybind11-2.5.0-gcc-8.3.0-mjmujjo
   findutils-4.6.0-gcc-8.3.0-gxxeusv	lua-luaposix-33.4.0-gcc-7.5.0-sas2uzg	       py-scipy-1.5.0-gcc-8.3.0-6f5vgp6
   gcc-8.3.0-gcc-7.5.0-6hbkzol		m4-1.4.18-gcc-7.5.0-mkc3u4x		       py-setuptools-46.1.3-gcc-8.3.0-4dcvntv
   gdbm-1.18.1-gcc-7.5.0-4av4gyw	m4-1.4.18-gcc-8.3.0-65odbgi		       python-3.7.7-gcc-8.3.0-4uojybm
   gdbm-1.18.1-gcc-8.3.0-alz6ery	mpc-1.1.0-gcc-7.5.0-uur2dd6		       readline-8.0-gcc-7.5.0-t54jzdy
   gettext-0.20.2-gcc-7.5.0-p4xwlyy	mpfr-3.1.6-gcc-7.5.0-nwsubsw		       readline-8.0-gcc-8.3.0-l33t67c
   gettext-0.20.2-gcc-8.3.0-euuxtvr	mpich-3.3.2-gcc-8.3.0-focol2k		       sqlite-3.31.1-gcc-8.3.0-vz4awtk
   git-2.27.0-gcc-7.5.0-pzqvpp2 	ncurses-6.2-gcc-7.5.0-crhlefo		       tar-1.32-gcc-7.5.0-uwe6tb5
   gmp-6.1.2-gcc-7.5.0-3ol3tld		ncurses-6.2-gcc-8.3.0-klfkayd		       tar-1.32-gcc-8.3.0-fk4qp4i
   hwloc-1.11.11-gcc-8.3.0-lz2i2dd	netlib-lapack-3.8.0-gcc-8.3.0-kbk7dg3	       tcl-8.6.8-gcc-7.5.0-aszidzn
   hwloc-2.2.0-gcc-8.3.0-4otoxex	netlib-scalapack-2.1.0-gcc-8.3.0-h2amar2       texinfo-6.5-gcc-8.3.0-7t62l5t
   isl-0.18-gcc-7.5.0-4lkvfkv		netlib-scalapack-2.1.0-gcc-8.3.0-kt5c5on       unzip-6.0-gcc-7.5.0-2ozim4d
   libbsd-0.10.0-gcc-7.5.0-u6ue7vw	netlib-scalapack-2.1.0-gcc-8.3.0-qsewiuz       util-macros-1.19.1-gcc-8.3.0-obeg5kx
   libbsd-0.10.0-gcc-8.3.0-nr46ju6	netlib-scalapack-2.1.0-gcc-8.3.0-uf4ynvq       xz-5.2.5-gcc-7.5.0-6nxes4r
   libffi-3.3-gcc-8.3.0-lo4lv3d 	numactl-2.0.12-gcc-8.3.0-tusy4nf	       xz-5.2.5-gcc-8.3.0-72wq5od
   libiconv-1.16-gcc-7.5.0-jearpk4	openblas-0.3.10-gcc-8.3.0-x32w5jn	       zlib-1.2.11-gcc-7.5.0-smoyzzo
   libiconv-1.16-gcc-8.3.0-brkkjge	openmpi-3.1.6-gcc-8.3.0-4twpso3 	       zlib-1.2.11-gcc-8.3.0-2icaxiy

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

The non-hierarchical module files that have been generated so far follow Spack’s default rules for module generation. Taking a look at the gcc module you’ll see, for example:

$ module show gcc-8.3.0-gcc-7.5.0-6hbkzol
----------------------------------------------------------------------------------------------------------------------------------------------
   /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/gcc-8.3.0-gcc-7.5.0-6hbkzol:
----------------------------------------------------------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/share/man")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib")
prepend_path("LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib64")
prepend_path("LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib64")
prepend_path("C_INCLUDE_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/include")
prepend_path("CPLUS_INCLUDE_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/include")
prepend_path("INCLUDE","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/include")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Ada, and Go, as well as libraries for these languages.
]])

As expected, a few environment variables representing paths will be modified by the module file according to the default prefix inspection rules.

Filter unwanted modifications to the environment¶

Now consider the case that your site has decided that C_INCLUDE_PATH, CPLUS_INCLUDE_PATH, and LIBRARY_PATH modifications should not be present in module files. What you can do to abide by the rules is to create a configuration file ${SPACK_ROOT}/etc/spack/modules.yaml with the following content:

modules:
  tcl:
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"

Next you should regenerate all the module files:

$ spack module tcl refresh
y

==> You are about to regenerate tcl module files for:

-- linux-ubuntu18.04-x86_64 / gcc@7.5.0 -------------------------
nwb3bf5 autoconf@2.69
wdflovn automake@1.16.2
fvfpt26 bzip2@1.0.8
e4rrsab curl@7.68.0
otkkten diffutils@3.7
3f3kkbl expat@2.2.9
6hbkzol gcc@8.3.0
4av4gyw gdbm@1.18.1
p4xwlyy gettext@0.20.2
pzqvpp2 git@2.27.0
3ol3tld gmp@6.1.2
4lkvfkv isl@0.18
u6ue7vw libbsd@0.10.0
jearpk4 libiconv@1.16
gcbfo3a libidn2@2.1.1a
lbrx7ln libsigsegv@2.12
jdxbjft libtool@2.4.6
dyq3apq libunistring@0.9.10
m3l53bh libxml2@2.9.10
kqbszrm lmod@8.3
n37jedg lua@5.3.5
tk7fdik lua-luafilesystem@1_7_0_2
sas2uzg lua-luaposix@33.4.0
mkc3u4x m4@1.4.18
uur2dd6 mpc@1.1.0
nwsubsw mpfr@3.1.6
crhlefo ncurses@6.2
4dj34yw openssl@1.1.1g
2nj3vxx patchelf@0.10
xyujt3h pcre2@10.35
hyrsxn4 perl@5.30.3
4sh6pym pkgconf@1.7.3
t54jzdy readline@8.0
uwe6tb5 tar@1.32
aszidzn tcl@8.6.8
2ozim4d unzip@6.0
6nxes4r xz@5.2.5
smoyzzo zlib@1.2.11

-- linux-ubuntu18.04-x86_64 / gcc@8.3.0 -------------------------
c7fxiuu autoconf@2.69
25eawip automake@1.16.2
jx7bite bzip2@1.0.8
7otuah5 cmake@3.17.3
5fvw3jh diffutils@3.7
xrk7vwz expat@2.2.9
gxxeusv findutils@4.6.0
alz6ery gdbm@1.18.1
euuxtvr gettext@0.20.2
lz2i2dd hwloc@1.11.11
4otoxex hwloc@2.2.0
nr46ju6 libbsd@0.10.0
lo4lv3d libffi@3.3
brkkjge libiconv@1.16
rqqclxg libpciaccess@0.13.5
oaiujfn libsigsegv@2.12
too4ft7 libtool@2.4.6
u5khonr libxml2@2.9.10
65odbgi m4@1.4.18
focol2k mpich@3.3.2
klfkayd ncurses@6.2
kbk7dg3 netlib-lapack@3.8.0
h2amar2 netlib-scalapack@2.1.0
uf4ynvq netlib-scalapack@2.1.0
qsewiuz netlib-scalapack@2.1.0
kt5c5on netlib-scalapack@2.1.0
tusy4nf numactl@2.0.12
x32w5jn openblas@0.3.10
4twpso3 openmpi@3.1.6
yygx7ht openssl@1.1.1g
35lyjgt patchelf@0.10
xmhlmqr perl@5.30.3
oo4jobp pkgconf@1.7.3
mbnkbhv py-cython@0.29.16
3s3aj6y py-numpy@1.19.0
mjmujjo py-pybind11@2.5.0
6f5vgp6 py-scipy@1.5.0
4dcvntv py-setuptools@46.1.3
4uojybm python@3.7.7
l33t67c readline@8.0
vz4awtk sqlite@3.31.1
fk4qp4i tar@1.32
7t62l5t texinfo@6.5
obeg5kx util-macros@1.19.1
72wq5od xz@5.2.5
2icaxiy zlib@1.2.11

==> Do you want to proceed? [y/n] ==> Regenerating tcl module files

If you take a look now at the module for gcc you’ll see that the unwanted paths have disappeared:

$ module show gcc-8.3.0-gcc-7.5.0-6hbkzol
----------------------------------------------------------------------------------------------------------------------------------------------
   /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/gcc-8.3.0-gcc-7.5.0-6hbkzol:
----------------------------------------------------------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/share/man")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib64")
prepend_path("INCLUDE","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/include")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Ada, and Go, as well as libraries for these languages.
]])

Prevent some module files from being generated¶

Another common request at many sites is to avoid exposing software that is only needed as an intermediate step when building a newer stack. Let’s try to prevent the generation of module files for anything that is compiled with gcc@7.5.0 (the OS provided compiler).

To do this you should add a blacklist keyword to ${SPACK_ROOT}/etc/spack/modules.yaml:

modules:
  tcl:
    blacklist:
      -  '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"

and regenerate the module files. This time we’ll pass the option --delete-tree so that Spack will delete the existing module tree and regenerate a new one, instead of overwriting the files in the existing directory.

$ spack module tcl refresh --delete-tree -y
==> Regenerating tcl module files

$ module avail

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   autoconf-2.69-gcc-8.3.0-c7fxiuu	    libtool-2.4.6-gcc-8.3.0-too4ft7		pkgconf-1.7.3-gcc-8.3.0-oo4jobp
   automake-1.16.2-gcc-8.3.0-25eawip	    libxml2-2.9.10-gcc-8.3.0-u5khonr		py-cython-0.29.16-gcc-8.3.0-mbnkbhv
   bzip2-1.0.8-gcc-8.3.0-jx7bite	    m4-1.4.18-gcc-8.3.0-65odbgi 		py-numpy-1.19.0-gcc-8.3.0-3s3aj6y
   cmake-3.17.3-gcc-8.3.0-7otuah5	    mpich-3.3.2-gcc-8.3.0-focol2k		py-pybind11-2.5.0-gcc-8.3.0-mjmujjo
   diffutils-3.7-gcc-8.3.0-5fvw3jh	    ncurses-6.2-gcc-8.3.0-klfkayd		py-scipy-1.5.0-gcc-8.3.0-6f5vgp6
   expat-2.2.9-gcc-8.3.0-xrk7vwz	    netlib-lapack-3.8.0-gcc-8.3.0-kbk7dg3	py-setuptools-46.1.3-gcc-8.3.0-4dcvntv
   findutils-4.6.0-gcc-8.3.0-gxxeusv	    netlib-scalapack-2.1.0-gcc-8.3.0-h2amar2	python-3.7.7-gcc-8.3.0-4uojybm
   gdbm-1.18.1-gcc-8.3.0-alz6ery	    netlib-scalapack-2.1.0-gcc-8.3.0-kt5c5on	readline-8.0-gcc-8.3.0-l33t67c
   gettext-0.20.2-gcc-8.3.0-euuxtvr	    netlib-scalapack-2.1.0-gcc-8.3.0-qsewiuz	sqlite-3.31.1-gcc-8.3.0-vz4awtk
   hwloc-1.11.11-gcc-8.3.0-lz2i2dd	    netlib-scalapack-2.1.0-gcc-8.3.0-uf4ynvq	tar-1.32-gcc-8.3.0-fk4qp4i
   hwloc-2.2.0-gcc-8.3.0-4otoxex	    numactl-2.0.12-gcc-8.3.0-tusy4nf		texinfo-6.5-gcc-8.3.0-7t62l5t
   libbsd-0.10.0-gcc-8.3.0-nr46ju6	    openblas-0.3.10-gcc-8.3.0-x32w5jn		util-macros-1.19.1-gcc-8.3.0-obeg5kx
   libffi-3.3-gcc-8.3.0-lo4lv3d 	    openmpi-3.1.6-gcc-8.3.0-4twpso3		xz-5.2.5-gcc-8.3.0-72wq5od
   libiconv-1.16-gcc-8.3.0-brkkjge	    openssl-1.1.1g-gcc-8.3.0-yygx7ht		zlib-1.2.11-gcc-8.3.0-2icaxiy
   libpciaccess-0.13.5-gcc-8.3.0-rqqclxg    patchelf-0.10-gcc-8.3.0-35lyjgt
   libsigsegv-2.12-gcc-8.3.0-oaiujfn	    perl-5.30.3-gcc-8.3.0-xmhlmqr

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

if you look closely you’ll see though that we went too far in blacklisting modules: the module for gcc@8.3.0 disappeared as it was bootstrapped with gcc@7.5.0. To specify exceptions to the blacklist rules you can use whitelist:

modules:
  tcl:
    whitelist:
      -  gcc
    blacklist:
      -  '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"

whitelist rules always have precedence over blacklist rules. If you regenerate the modules again:

$ spack module tcl refresh -y
==> Regenerating tcl module files

you’ll see that now the module for gcc@8.3.0 has reappeared:

$ module avail gcc-8.3.0-gcc-7.5.0-6hbkzol

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   gcc-8.3.0-gcc-7.5.0-6hbkzol

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

An additional feature that you can leverage to unclutter the environment is to skip the generation of module files for implicitly installed packages. In this case you only need to add the following line:

modules:
  tcl:
    blacklist_implicits: true
    whitelist:
      -  gcc
    blacklist:
      -  '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"

to modules.yaml and regenerate the module file tree as above.

Change module file naming¶

The next step in making module files more user-friendly is to improve their naming scheme. To reduce the length of the hash or remove it altogether you can use the hash_length keyword in the configuration file:

modules:
  tcl:
    hash_length: 0
    whitelist:
      -  gcc
    blacklist:
      -  '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"

If you try to regenerate the module files now you will get an error:

$ spack module tcl refresh --delete-tree -y
==> Error: Name clashes detected in module files:

file: /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/netlib-scalapack-2.1.0-gcc-8.3.0
spec: netlib-scalapack@2.1.0%gcc@8.3.0~pic+shared build_type=RelWithDebInfo patches=f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-ubuntu18.04-x86_64
spec: netlib-scalapack@2.1.0%gcc@8.3.0~pic+shared build_type=RelWithDebInfo patches=f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-ubuntu18.04-x86_64
spec: netlib-scalapack@2.1.0%gcc@8.3.0~pic+shared build_type=RelWithDebInfo patches=f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-ubuntu18.04-x86_64
spec: netlib-scalapack@2.1.0%gcc@8.3.0~pic+shared build_type=RelWithDebInfo patches=f2baedde688ffe4c20943c334f580eb298e04d6f35c86b90a1f4e8cb7ae344a2 arch=linux-ubuntu18.04-x86_64

==> Error: Operation aborted

Note

We try to check for errors up front!

In Spack we check for errors upfront whenever possible, so don’t worry about your module files: as a name clash was detected nothing has been changed on disk.

The problem here is that without the hashes the four different flavors of netlib-scalapack map to the same module file name. We can change how the names are formatted to differentiate them:

modules:
  tcl:
    hash_length: 0
    whitelist:
      -  gcc
    blacklist:
      -  '%gcc@7.5.0'
    all:
      conflict:
        - '{name}'
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
    projections:
      all:               '{name}/{version}-{compiler.name}-{compiler.version}'
      netlib-scalapack:  '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}-{^mpi.name}'
      ^python^lapack:    '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}'

As you can see it is possible to specify rules that apply only to a restricted set of packages using anonymous specs like ^mpi^lapack. Here we declare a conflict between any two modules with the same name, so they cannot be loaded together. We also format the names of modules according to compiler, compiler version, and MPI version using the spec format syntax. This allows us to match specs by their dependencies, and format them based on their DAGs.

$ spack module tcl refresh --delete-tree -y
==> Regenerating tcl module files

$ module avail

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   autoconf/2.69-gcc-8.3.0		libsigsegv/2.12-gcc-8.3.0				      perl/5.30.3-gcc-8.3.0
   automake/1.16.2-gcc-8.3.0		libtool/2.4.6-gcc-8.3.0 				      pkgconf/1.7.3-gcc-8.3.0
   bzip2/1.0.8-gcc-8.3.0		libxml2/2.9.10-gcc-8.3.0				      py-cython/0.29.16-gcc-8.3.0
   cmake/3.17.3-gcc-8.3.0		m4/1.4.18-gcc-8.3.0					      py-numpy/1.19.0-gcc-8.3.0-openblas
   diffutils/3.7-gcc-8.3.0		mpich/3.3.2-gcc-8.3.0					      py-pybind11/2.5.0-gcc-8.3.0
   expat/2.2.9-gcc-8.3.0		ncurses/6.2-gcc-8.3.0					      py-scipy/1.5.0-gcc-8.3.0-openblas
   findutils/4.6.0-gcc-8.3.0		netlib-lapack/3.8.0-gcc-8.3.0				      py-setuptools/46.1.3-gcc-8.3.0
   gcc/8.3.0-gcc-7.5.0			netlib-scalapack/2.1.0-gcc-8.3.0-netlib-lapack-mpich	      python/3.7.7-gcc-8.3.0
   gdbm/1.18.1-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-netlib-lapack-openmpi	      readline/8.0-gcc-8.3.0
   gettext/0.20.2-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-openblas-mpich 	      sqlite/3.31.1-gcc-8.3.0
   hwloc/1.11.11-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-openblas-openmpi      (D)    tar/1.32-gcc-8.3.0
   hwloc/2.2.0-gcc-8.3.0	 (D)	numactl/2.0.12-gcc-8.3.0				      texinfo/6.5-gcc-8.3.0
   libbsd/0.10.0-gcc-8.3.0		openblas/0.3.10-gcc-8.3.0				      util-macros/1.19.1-gcc-8.3.0
   libffi/3.3-gcc-8.3.0 		openmpi/3.1.6-gcc-8.3.0 				      xz/5.2.5-gcc-8.3.0
   libiconv/1.16-gcc-8.3.0		openssl/1.1.1g-gcc-8.3.0				      zlib/1.2.11-gcc-8.3.0
   libpciaccess/0.13.5-gcc-8.3.0	patchelf/0.10-gcc-8.3.0

  Where:
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Note

The conflict directive is Tcl-specific and can’t be used in the lmod section of the configuration file.

Add custom environment modifications¶

At many sites it is customary to set an environment variable in a package’s module file that points to the folder in which the package is installed. You can achieve this with Spack by adding an environment directive to the configuration file:

modules:
  tcl:
    hash_length: 0
    naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
    whitelist:
      -  gcc
    blacklist:
      -  '%gcc@7.5.0'
    all:
      conflict:
        - '{name}'
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    projections:
      all:               '{name}/{version}-{compiler.name}-{compiler.version}'
      netlib-scalapack:  '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}-{^mpi.name}'
      ^python^lapack:    '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}'

Under the hood Spack uses the format() API to substitute tokens in either environment variable names or values. There are two caveats though:

The set of allowed tokens in variable names is restricted to name, version, compiler, compiler.name, compiler.version, architecture
Any token expanded in a variable name is made uppercase, but other than that case sensitivity is preserved

Regenerating the module files results in something like:

$ spack module tcl refresh -y
==> Regenerating tcl module files

$ module show gcc
----------------------------------------------------------------------------------------------------------------------------------------------
   /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/gcc/8.3.0-gcc-7.5.0:
----------------------------------------------------------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages. ")
conflict("gcc")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/share/man")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/lib64")
prepend_path("INCLUDE","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/include")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl/bin/gfortran")
setenv("'GCC_ROOT'","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.5.0/gcc-8.3.0-6hbkzolzshktgws6mz3f4s23v6sbkgnl")
help([[The GNU Compiler Collection includes front ends for C, C++, Objective-C,
Fortran, Ada, and Go, as well as libraries for these languages.
]])

As you can see, the gcc module has the environment variable GCC_ROOT set.

Sometimes it’s also useful to apply environment modifications selectively and target only certain packages. You can for instance apply modifications to the openmpi module as follows:

modules:
  tcl:
    hash_length: 0
    naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
    whitelist:
      - gcc
    blacklist:
      - '%gcc@7.5.0'
    all:
      conflict:
        - '{name}'
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    projections:
      all:               '{name}/{version}-{compiler.name}-{compiler.version}'
      netlib-scalapack:  '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}-{^mpi.name}'
      ^python^lapack:    '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}'

This time we will be more selective and regenerate only the openmpi module file:

$ spack module tcl refresh -y openmpi
==> Regenerating tcl module files

$ module show openmpi
----------------------------------------------------------------------------------------------------------------------------------------------
   /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64/openmpi/3.1.6-gcc-8.3.0:
----------------------------------------------------------------------------------------------------------------------------------------------
whatis("An open source Message Passing Interface implementation. ")
conflict("openmpi")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/share/man")
prepend_path("LD_LIBRARY_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/lib")
prepend_path("INCLUDE","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/include")
prepend_path("PKG_CONFIG_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/lib/pkgconfig")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/")
setenv("MPICC","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/bin/mpicc")
setenv("MPICXX","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/bin/mpic++")
setenv("MPIF77","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/bin/mpif77")
setenv("MPIF90","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky/bin/mpif90")
setenv("'OPENMPI_ROOT'","/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/openmpi-3.1.6-4twpso3kn2f3z6oa527snqvn7fsridky")
setenv("SLURM_MPI_TYPE","pmi2")
setenv("OMPI_MCA_btl_openib_warn_default_git_prefix","0")
help([[An open source Message Passing Interface implementation. The Open MPI
Project is an open source Message Passing Interface implementation that
is developed and maintained by a consortium of academic, research, and
industry partners. Open MPI is therefore able to combine the expertise,
technologies, and resources from all across the High Performance
Computing community in order to build the best MPI library available.
Open MPI offers advantages for system and software vendors, application
developers and computer science researchers.
]])

Autoload dependencies¶

Spack can also generate module files that contain code to load the dependencies automatically. You can, for instance generate python modules that load their dependencies by adding the autoload directive and assigning it the value direct:

modules:
  tcl:
    verbose: True
    hash_length: 0
    naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
    whitelist:
      - gcc
    blacklist:
      - '%gcc@7.5.0'
    all:
      conflict:
        - '{name}'
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    gcc:
      environment:
        set:
          CC: gcc
          CXX: g++
          FC: gfortran
          F90: gfortran
          F77: gfortran
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    projections:
      all:               '{name}/{version}-{compiler.name}-{compiler.version}'
      netlib-scalapack:  '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}-{^mpi.name}'
      ^python^lapack:    '{name}/{version}-{compiler.name}-{compiler.version}-{^lapack.name}'
    ^python:
      autoload:  direct

and regenerating the module files for every package that depends on python:

$ spack module tcl refresh -y ^python
==> Regenerating tcl module files

and will contain code to autoload all the dependencies:

$ module load py-scipy
Autoloading openblas/0.3.10-gcc-8.3.0
Autoloading py-numpy/1.19.0-gcc-8.3.0-openblas
Autoloading python/3.7.7-gcc-8.3.0
Autoloading python/3.7.7-gcc-8.3.0

In case messages are unwanted during the autoload procedure, it will be sufficient to omit the line setting verbose: True in the configuration file above.

Hierarchical Module Files¶

So far we worked with non-hierarchical module files, i.e. with module files that are all generated in the same root directory and don’t attempt to dynamically modify the MODULEPATH. This results in a flat module structure where all the software is visible at the same time:

$ module avail

----------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu18.04-x86_64 -----------------------------------------
   autoconf/2.69-gcc-8.3.0		libsigsegv/2.12-gcc-8.3.0				      perl/5.30.3-gcc-8.3.0
   automake/1.16.2-gcc-8.3.0		libtool/2.4.6-gcc-8.3.0 				      pkgconf/1.7.3-gcc-8.3.0
   bzip2/1.0.8-gcc-8.3.0		libxml2/2.9.10-gcc-8.3.0				      py-cython/0.29.16-gcc-8.3.0
   cmake/3.17.3-gcc-8.3.0		m4/1.4.18-gcc-8.3.0					      py-numpy/1.19.0-gcc-8.3.0-openblas
   diffutils/3.7-gcc-8.3.0		mpich/3.3.2-gcc-8.3.0					      py-pybind11/2.5.0-gcc-8.3.0
   expat/2.2.9-gcc-8.3.0		ncurses/6.2-gcc-8.3.0					      py-scipy/1.5.0-gcc-8.3.0-openblas
   findutils/4.6.0-gcc-8.3.0		netlib-lapack/3.8.0-gcc-8.3.0				      py-setuptools/46.1.3-gcc-8.3.0
   gcc/8.3.0-gcc-7.5.0			netlib-scalapack/2.1.0-gcc-8.3.0-netlib-lapack-mpich	      python/3.7.7-gcc-8.3.0
   gdbm/1.18.1-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-netlib-lapack-openmpi	      readline/8.0-gcc-8.3.0
   gettext/0.20.2-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-openblas-mpich 	      sqlite/3.31.1-gcc-8.3.0
   hwloc/1.11.11-gcc-8.3.0		netlib-scalapack/2.1.0-gcc-8.3.0-openblas-openmpi      (D)    tar/1.32-gcc-8.3.0
   hwloc/2.2.0-gcc-8.3.0	 (D)	numactl/2.0.12-gcc-8.3.0				      texinfo/6.5-gcc-8.3.0
   libbsd/0.10.0-gcc-8.3.0		openblas/0.3.10-gcc-8.3.0				      util-macros/1.19.1-gcc-8.3.0
   libffi/3.3-gcc-8.3.0 		openmpi/3.1.6-gcc-8.3.0 				      xz/5.2.5-gcc-8.3.0
   libiconv/1.16-gcc-8.3.0		openssl/1.1.1g-gcc-8.3.0				      zlib/1.2.11-gcc-8.3.0
   libpciaccess/0.13.5-gcc-8.3.0	patchelf/0.10-gcc-8.3.0

  Where:
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

This layout is quite simple to deploy, but you can see from the above snippet that nothing prevents users from loading incompatible sets of modules:

$ module purge
$ module load netlib-lapack openblas
$ module list

Currently Loaded Modules:
  1) netlib-lapack/3.8.0-gcc-8.3.0   2) openblas/0.3.10-gcc-8.3.0

Even if conflicts directives are carefully placed in module files, they:

won’t enforce a consistent environment, but will just report an error

need constant updates, for instance as soon as a new compiler or MPI library is installed

Hierarchical module files try to overcome these shortcomings by showing at start-up only a restricted view of what is available on the system: more specifically only the software that has been installed with OS provided compilers. Among this software there will be other - usually more recent - compilers that, once loaded, will prepend new directories to MODULEPATH unlocking all the software that was compiled with them. This “unlocking” idea can then be extended arbitrarily to virtual dependencies, as we’ll see in the following section.

Core/Compiler/MPI¶

The most widely used hierarchy is the so called Core/Compiler/MPI where, on top of the compilers, different MPI libraries also unlock software linked to them. There are just a few steps needed to adapt the modules.yaml file we used previously:

enable the lmod file generator

change the tcl tag to lmod

remove the tcl specific conflict directive

declare which compilers are considered core_compilers

remove the mpi related suffixes in projections (as they will be substituted by hierarchies)

After these modifications your configuration file should look like:

modules:
  enable::
    - lmod
  lmod:
    core_compilers:
      - 'gcc@7.5.0'
    hierarchy:
      - mpi
    hash_length: 0
    whitelist:
      - gcc
    blacklist:
      - '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    projections:
      all:          '{name}/{version}'
      ^lapack:      '{name}/{version}-{^lapack.name}'

Note

Double colon in configuration files: The double colon after enable is intentional and it serves the purpose of overriding the default list of enabled generators so that only lmod will be active (see Overriding entire sections for more details).

The directive core_compilers accepts a list of compilers. Everything built using these compilers will create a module in the Core part of the hierarchy, which is the entry point for hierarchical module files. It is common practice to put the OS provided compilers in the list and only build common utilities and other compilers with them.

If we now regenerate the module files:

$ spack module lmod refresh --delete-tree -y
==> Regenerating lmod module files

and update MODULEPATH to point to the Core:

$ module purge
$ module unuse $HOME/spack/share/spack/modules/linux-ubuntu18.04-x86_64
$ module use $HOME/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core

asking for the available modules will return:

$ module avail

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Unsurprisingly, the only visible module is gcc. Loading that we’ll unlock the Compiler part of the hierarchy:

$ module load gcc
$ module avail

------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/gcc/8.3.0 --------------------------------------
   autoconf/2.69      gdbm/1.18.1	    libpciaccess/0.13.5    netlib-lapack/3.8.0	  pkgconf/1.7.3 	      readline/8.0
   automake/1.16.2    gettext/0.20.2	    libsigsegv/2.12	   numactl/2.0.12	  py-cython/0.29.16	      sqlite/3.31.1
   bzip2/1.0.8	      hwloc/1.11.11	    libtool/2.4.6	   openblas/0.3.10	  py-numpy/1.19.0-openblas    tar/1.32
   cmake/3.17.3       hwloc/2.2.0    (D)    libxml2/2.9.10	   openmpi/3.1.6	  py-pybind11/2.5.0	      texinfo/6.5
   diffutils/3.7      libbsd/0.10.0	    m4/1.4.18		   openssl/1.1.1g	  py-scipy/1.5.0-openblas     util-macros/1.19.1
   expat/2.2.9	      libffi/3.3	    mpich/3.3.2 	   patchelf/0.10	  py-setuptools/46.1.3	      xz/5.2.5
   findutils/4.6.0    libiconv/1.16	    ncurses/6.2 	   perl/5.30.3		  python/3.7.7		      zlib/1.2.11

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0 (L)

  Where:
   D:  Default Module
   L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

The same holds true also for the MPI part, that you can enable by loading either mpich or openmpi. Let’s start by loading mpich:

$ module load mpich
$ module avail

--------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/mpich/3.3.2-focol2k/gcc/8.3.0 ----------------------------
   netlib-scalapack/2.1.0-netlib-lapack    netlib-scalapack/2.1.0-openblas (D)

------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/gcc/8.3.0 --------------------------------------
   autoconf/2.69      gdbm/1.18.1	    libpciaccess/0.13.5        netlib-lapack/3.8.0    pkgconf/1.7.3		  readline/8.0
   automake/1.16.2    gettext/0.20.2	    libsigsegv/2.12	       numactl/2.0.12	      py-cython/0.29.16 	  sqlite/3.31.1
   bzip2/1.0.8	      hwloc/1.11.11	    libtool/2.4.6	       openblas/0.3.10	      py-numpy/1.19.0-openblas	  tar/1.32
   cmake/3.17.3       hwloc/2.2.0    (D)    libxml2/2.9.10	       openmpi/3.1.6	      py-pybind11/2.5.0 	  texinfo/6.5
   diffutils/3.7      libbsd/0.10.0	    m4/1.4.18		       openssl/1.1.1g	      py-scipy/1.5.0-openblas	  util-macros/1.19.1
   expat/2.2.9	      libffi/3.3	    mpich/3.3.2 	(L)    patchelf/0.10	      py-setuptools/46.1.3	  xz/5.2.5
   findutils/4.6.0    libiconv/1.16	    ncurses/6.2 	       perl/5.30.3	      python/3.7.7		  zlib/1.2.11

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0 (L)

  Where:
   D:  Default Module
   L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

$ module load openblas netlib-scalapack/2.1.0-openblas
$ module list

Currently Loaded Modules:
  1) gcc/8.3.0	 2) mpich/3.3.2   3) openblas/0.3.10   4) netlib-scalapack/2.1.0-openblas

At this point we can showcase the improved consistency that a hierarchical layout provides over a non-hierarchical one:

$ export LMOD_AUTO_SWAP=yes
$ module load openmpi

Lmod is automatically replacing "mpich/3.3.2" with "openmpi/3.1.6".


Due to MODULEPATH changes, the following have been reloaded:
  1) netlib-scalapack/2.1.0-openblas

Lmod took care of swapping the MPI provider for us, and it also substituted the netlib-scalapack module to conform to the change in the MPI. In this way we can’t accidentally pull-in two different MPI providers at the same time or load a module file for a package linked to openmpi when mpich is also loaded. Consistency for compilers and MPI is ensured by the tool.

Add LAPACK to the hierarchy¶

The hierarchy just shown is already a great improvement over non-hierarchical layouts, but it still has an asymmetry: LAPACK providers cover the same semantic role as MPI providers, but yet they are not part of the hierarchy.

To be more practical, this means that although we have gained an improved consistency in our environment when it comes to MPI, we still have the same problems as we had before for LAPACK implementations:

$ module list

Currently Loaded Modules:
  1) gcc/8.3.0	 2) openblas/0.3.10   3) openmpi/3.1.6	 4) netlib-scalapack/2.1.0-openblas



$ module avail

-------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/openmpi/3.1.6-4twpso3/gcc/8.3.0 ---------------------------
   netlib-scalapack/2.1.0-netlib-lapack    netlib-scalapack/2.1.0-openblas (L,D)

------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/gcc/8.3.0 --------------------------------------
   autoconf/2.69      gdbm/1.18.1	    libpciaccess/0.13.5    netlib-lapack/3.8.0	      pkgconf/1.7.3		  readline/8.0
   automake/1.16.2    gettext/0.20.2	    libsigsegv/2.12	   numactl/2.0.12	      py-cython/0.29.16 	  sqlite/3.31.1
   bzip2/1.0.8	      hwloc/1.11.11	    libtool/2.4.6	   openblas/0.3.10     (L)    py-numpy/1.19.0-openblas	  tar/1.32
   cmake/3.17.3       hwloc/2.2.0    (D)    libxml2/2.9.10	   openmpi/3.1.6       (L)    py-pybind11/2.5.0 	  texinfo/6.5
   diffutils/3.7      libbsd/0.10.0	    m4/1.4.18		   openssl/1.1.1g	      py-scipy/1.5.0-openblas	  util-macros/1.19.1
   expat/2.2.9	      libffi/3.3	    mpich/3.3.2 	   patchelf/0.10	      py-setuptools/46.1.3	  xz/5.2.5
   findutils/4.6.0    libiconv/1.16	    ncurses/6.2 	   perl/5.30.3		      python/3.7.7		  zlib/1.2.11

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0 (L)

  Where:
   D:  Default Module
   L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".


$ module load netlib-scalapack/2.1.0-netlib-lapack

The following have been reloaded with a version change:
  1) netlib-scalapack/2.1.0-openblas => netlib-scalapack/2.1.0-netlib-lapack

$ module list

Currently Loaded Modules:
  1) gcc/8.3.0	 2) openblas/0.3.10   3) openmpi/3.1.6	 4) netlib-scalapack/2.1.0-netlib-lapack

Hierarchies that are deeper than Core/Compiler/MPI are probably still considered “unusual” or “impractical” at many sites, mainly because module files are written manually and keeping track of the combinations among multiple providers quickly becomes quite involved.

For instance, having both MPI and LAPACK in the hierarchy means we must classify software into one of four categories:

Software that doesn’t depend on MPI or LAPACK

Software that depends only on MPI

Software that depends only on LAPACK

Software that depends on both

to decide when to show it to the user. The situation becomes more involved as the number of virtual dependencies in the hierarchy increases.

We can take advantage of the DAG that Spack maintains for the installed software and solve this combinatorial problem in a clean and automated way. In some sense Spack’s ability to manage this combinatorial complexity makes deeper hierarchies feasible.

Coming back to our example, let’s add lapack to the hierarchy and remove the remaining suffix projection for lapack:

modules:
  enable::
    - lmod
  lmod:
    core_compilers:
      - 'gcc@7.5.0'
    hierarchy:
      - mpi
      - lapack
    hash_length: 0
    whitelist:
      - gcc
    blacklist:
      - '%gcc@7.5.0'
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    projections:
      all:          '{name}/{version}'

After module files have been regenerated as usual:

$ module purge
$ spack module lmod refresh --delete-tree -y
==> Regenerating lmod module files

we can see that now we have additional components in the hierarchy:

$ module load gcc

Inactive Modules:
  1) netlib-scalapack/2.1.0-netlib-lapack

$ module load openblas
$ module avail

-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/openmpi/3.1.6-4twpso3/openblas/0.3.10-x32w5jn/gcc/8.3.0 ---------------
   netlib-scalapack/2.1.0

------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/openblas/0.3.10-x32w5jn/gcc/8.3.0 --------------------------
   py-numpy/1.19.0    py-scipy/1.5.0

------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/gcc/8.3.0 --------------------------------------
   autoconf/2.69      gdbm/1.18.1	    libpciaccess/0.13.5    netlib-lapack/3.8.0	      pkgconf/1.7.3	      tar/1.32
   automake/1.16.2    gettext/0.20.2	    libsigsegv/2.12	   numactl/2.0.12	      py-cython/0.29.16       texinfo/6.5
   bzip2/1.0.8	      hwloc/1.11.11	    libtool/2.4.6	   openblas/0.3.10     (L)    py-pybind11/2.5.0       util-macros/1.19.1
   cmake/3.17.3       hwloc/2.2.0    (D)    libxml2/2.9.10	   openmpi/3.1.6       (L)    py-setuptools/46.1.3    xz/5.2.5
   diffutils/3.7      libbsd/0.10.0	    m4/1.4.18		   openssl/1.1.1g	      python/3.7.7	      zlib/1.2.11
   expat/2.2.9	      libffi/3.3	    mpich/3.3.2 	   patchelf/0.10	      readline/8.0
   findutils/4.6.0    libiconv/1.16	    ncurses/6.2 	   perl/5.30.3		      sqlite/3.31.1

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0 (L)

  Where:
   D:  Default Module
   L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".


$ module load openmpi
$ module avail

-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/openmpi/3.1.6-4twpso3/openblas/0.3.10-x32w5jn/gcc/8.3.0 ---------------
   netlib-scalapack/2.1.0

------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/openblas/0.3.10-x32w5jn/gcc/8.3.0 --------------------------
   py-numpy/1.19.0    py-scipy/1.5.0

------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/gcc/8.3.0 --------------------------------------
   autoconf/2.69      gdbm/1.18.1	    libpciaccess/0.13.5    netlib-lapack/3.8.0	      pkgconf/1.7.3	      tar/1.32
   automake/1.16.2    gettext/0.20.2	    libsigsegv/2.12	   numactl/2.0.12	      py-cython/0.29.16       texinfo/6.5
   bzip2/1.0.8	      hwloc/1.11.11	    libtool/2.4.6	   openblas/0.3.10     (L)    py-pybind11/2.5.0       util-macros/1.19.1
   cmake/3.17.3       hwloc/2.2.0    (D)    libxml2/2.9.10	   openmpi/3.1.6       (L)    py-setuptools/46.1.3    xz/5.2.5
   diffutils/3.7      libbsd/0.10.0	    m4/1.4.18		   openssl/1.1.1g	      python/3.7.7	      zlib/1.2.11
   expat/2.2.9	      libffi/3.3	    mpich/3.3.2 	   patchelf/0.10	      readline/8.0
   findutils/4.6.0    libiconv/1.16	    ncurses/6.2 	   perl/5.30.3		      sqlite/3.31.1

---------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu18.04-x86_64/Core ----------------------------------------
   gcc/8.3.0 (L)

  Where:
   D:  Default Module
   L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

Both MPI and LAPACK providers will now benefit from the same safety features:

$ module load py-numpy netlib-scalapack

Activating Modules:
  1) netlib-scalapack/2.1.0

$ module load mpich

Lmod is automatically replacing "openmpi/3.1.6" with "mpich/3.3.2".

Due to MODULEPATH changes, the following have been reloaded:
  1) netlib-scalapack/2.1.0

$ module load netlib-lapack

Lmod is automatically replacing "openblas/0.3.10" with "netlib-lapack/3.8.0".

Inactive Modules:
  1) py-numpy

Due to MODULEPATH changes, the following have been reloaded:
  1) netlib-scalapack/2.1.0

Because we only compiled py-numpy with openblas the module is made inactive when we switch the LAPACK provider. The user environment is now consistent by design!

Working with Templates¶

As briefly mentioned in the introduction, Spack uses Jinja2 to generate each individual module file. This means that you have all of its flexibility and power when it comes to customizing what gets generated!

Module file templates¶

The templates that Spack uses to generate module files are stored in the share/spack/templates/module directory within the Spack prefix, and they all share the same common structure. Usually, they start with a header that identifies the type of module being generated. In the case of hierarchical module files it’s:

-- -*- lua -*-
-- Module file created by spack (https://github.com/spack/spack) on {{ timestamp }}
--
-- {{ spec.short_spec }}
--

The statements within double curly brackets {{ ... }} denote expressions that will be evaluated and substituted at module generation time. The rest of the file is then divided into blocks that can be overridden or extended by users, if need be. Control structures , delimited by {% ... %}, are also permitted in the template language:

{% block environment %}
{% for command_name, cmd in environment_modifications %}
{% if command_name == 'PrependPath' %}
prepend_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name == 'AppendPath' %}
append_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name == 'RemovePath' %}
remove_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name == 'SetEnv' %}
setenv("{{ cmd.name }}", "{{ cmd.value }}")
{% elif command_name == 'UnsetEnv' %}
unsetenv("{{ cmd.name }}")
{% endif %}
{% endfor %}
{% endblock %}

The locations where Spack looks for templates are specified in config.yaml:

    projections:
      all: "${ARCHITECTURE}/${COMPILERNAME}-${COMPILERVER}/${PACKAGE}-${VERSION}-${HASH}"
    # install_tree can include an optional padded length (int or boolean)
    # default is False (do not pad)

and can be extended by users to employ custom templates, as we’ll see next.

Extend the default templates¶

Let’s assume one of our software is protected by group membership: allowed users belong to the same linux group, and access is granted at group level. Wouldn’t it be nice if people that are not yet entitled to use it could receive a helpful message at module load time that tells them who to contact in your organization to be inserted in the group?

To automate the generation of module files with such site-specific behavior we’ll start by extending the list of locations where Spack looks for module files. Let’s create the file ${SPACK_ROOT}/etc/spack/config.yaml with the content:

config:
  template_dirs:
    - $HOME/.spack/templates

This tells Spack to also search another location when looking for template files. Next, we need to create our custom template extension in the folder listed above:

{% extends "modules/modulefile.lua" %}
{% block footer %}
-- Access is granted only to specific groups
if not isDir("{{ spec.prefix }}") then
    LmodError (
        "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
        "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
    )
end
{% endblock %}

Let’s name this file group-restricted.lua. The line:

{% extends "modules/modulefile.lua" %}

tells Jinja2 that we are reusing the standard template for hierarchical module files. The section:

{% block footer %}
-- Access is granted only to specific groups
if not isDir("{{ spec.prefix }}") then
    LmodError (
        "You don't have the necessary rights to run \"{{ spec.name }}\".\n\n",
        "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
    )
end
{% endblock %}

overrides the footer block. Finally, we need to add a couple of lines in modules.yaml to tell Spack which specs need to use the new custom template. For the sake of illustration let’s assume it’s netlib-scalapack:

modules:
  enable::
    - lmod
  lmod:
    core_compilers:
      - 'gcc@7.5.0'
    hierarchy:
      - mpi
      - lapack
    hash_length: 0
    whitelist:
      - gcc
    blacklist:
      - '%gcc@7.5.0'
      - readline
    all:
      filter:
        environment_blacklist:
          - "C_INCLUDE_PATH"
          - "CPLUS_INCLUDE_PATH"
          - "LIBRARY_PATH"
      environment:
        set:
          '{name}_ROOT': '{prefix}'
    openmpi:
      environment:
        set:
          SLURM_MPI_TYPE: pmi2
          OMPI_MCA_btl_openib_warn_default_gid_prefix: '0'
    netlib-scalapack:
      template: 'group-restricted.lua'

If we regenerate the module files one last time:

$ spack module lmod refresh -y netlib-scalapack
==> Regenerating lmod module files

we’ll find the following at the end of each netlib-scalapack module file:

-- Access is granted only to specific groups
if not isDir("/home/spack/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-8.3.0/netlib-scalapack-2.0.2-2p75lzqjbsnev7d2j2osgpkz7ib33oca") then
    LmodError (
        "You don't have the necessary rights to run \"netlib-scalapack\".\n\n",
        "\tPlease write an e-mail to 1234@foo.com if you need further information on how to get access to it.\n"
    )
end

and every user that doesn’t have access to the software will now be redirected to the right e-mail address where to ask for it!

Restore settings for future sections¶

For future sections of the tutorial, we will not use the gcc@8.3.0 compiler. Since it is currently the default compiler (our current defualt is the most recent version of gcc available), we will remove it now.

$ spack compiler rm gcc@8.3.0

This will ensure the rest of the tutorial goes smoothly for you.

Module Files Tutorial¶

Setup for the Tutorial¶

Build a module tool¶

Add a new compiler¶

Build the software that will be used in the tutorial¶

What are Module Files?¶

Module Systems¶

Environment Modules¶

Lmod¶

How does Spack generate module files?¶

Modules vs spack load¶

Non-hierarchical Module Files¶

Filter unwanted modifications to the environment¶

Prevent some module files from being generated¶

Change module file naming¶

Add custom environment modifications¶

Autoload dependencies¶

Hierarchical Module Files¶

Core/Compiler/MPI¶

Add LAPACK to the hierarchy¶

Working with Templates¶

Module file templates¶

Extend the default templates¶

Restore settings for future sections¶

Modules vs `spack load`¶