Tutorial setup
If you have not done the prior sections, you’ll need to start the docker image:
docker run -it ghcr.io/spack/tutorial:isc23
and then set Spack up like this:
git clone --depth=100 --branch=releases/v0.20 https://github.com/spack/spack
. spack/share/spack/setup-env.sh
spack tutorial -y
spack bootstrap now
spack compiler find
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 slack.spack.io
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
and by enabling tcl module files, which are disabled by default since Spack v0.20:
$ spack config add "modules:default:enable:[tcl]"
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.
$ . spack/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@12.1.0.
$ spack install gcc@12.1.0
You can get this in your environment using spack load gcc@12.1.0:
$ spack load gcc@12.1.0
$ which gcc
/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gcc
Now, gcc is in your PATH. 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@=12.1.0
==> Compilers are defined in the following files:
/home/spack/.spack/linux/compilers.yaml
To check which compilers are available you can use spack compiler list:
$ spack compiler list
==> Available compilers
-- clang ubuntu22.04-x86_64 -------------------------------------
clang@=14.0.0
-- gcc ubuntu22.04-x86_64 ---------------------------------------
gcc@=12.1.0 gcc@=11.3.0 gcc@=10.4.0
Finally, when you confirmed gcc@12.1.0 is properly registered, clean the environment
with spack unload:
$ spack unload --all
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:
spack@a7c82535d8c9:~$ module show zlib-1.2.13-gcc-11.3.0-mntflxr
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/zlib-1.2.13-gcc-11.3.0-mntflxr:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("A free, general-purpose, legally unencumbered lossless data-compression library.")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/zlib-1.2.13-mntflxrgekkm5lbpbl5r66lh2ieted4y/share/man")
prepend_path("PKG_CONFIG_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/zlib-1.2.13-mntflxrgekkm5lbpbl5r66lh2ieted4y/lib/pkgconfig")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/zlib-1.2.13-mntflxrgekkm5lbpbl5r66lh2ieted4y/.")
help([[Name : zlib
Version: 1.2.13
Target : x86_64_v3
A free, general-purpose, legally unencumbered lossless data-compression
module.
]])
$ echo $PKG_CONFIG_PATH
module load will execute all of the changes shown above:
spack@a7c82535d8c9:~$ module load gcc-12.1.0-gcc-11.3.0-s5e5zwr
spack@a7c82535d8c9:~$ echo $PKG_CONFIG_PATH
/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/zstd-1.5.5-qoo4rlopj4vqbc6k633cu3tzawtfjjvh/lib/pkgconfig:/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/zlib-1.2.13-mntflxrgekkm5lbpbl5r66lh2ieted4y/lib/pkgconfig:/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/mpfr-4.2.0-aiys7vci7zwuci5phi5yje7ql3des4jw/lib/pkgconfig:/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gmp-6.2.1-7kxi3rr3qduvmao43tjigamo2eqdme4q/lib/pkgconfig
and to undo the modifications, you can use module unload:
$ module unload zlib
$ echo $PKG_CONFIG_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
-- linux-ubuntu22.04-x86_64_v3 / gcc@=11.3.0 --------------------
autoconf@2.69 automake@1.16.5 bzip2@1.0.8 gawk@5.2.1 gdbm@1.23 gmake@4.4.1 libiconv@1.17 libtool@2.4.7 m4@1.4.19 mpfr@4.2.0 perl@5.36.0 pkgconf@1.9.5 tar@1.34 xz@5.4.1 zstd@1.5.5
autoconf-archive@2023.02.20 berkeley-db@18.1.40 diffutils@3.9 gcc@12.1.0 gettext@0.21.1 gmp@6.2.1 libsigsegv@2.14 libxml2@2.10.3 mpc@1.3.1 ncurses@6.4 pigz@2.7 readline@8.2 texinfo@7.0.3 zlib@1.2.13
==> 29 loaded packages
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-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
autoconf-2.69-gcc-11.3.0-t4nuen3 curl-8.0.1-gcc-11.3.0-4cec7ab gmake-4.4.1-gcc-11.3.0-guaj3kb lua-5.4.4-gcc-11.3.0-l5jkvce openssl-1.1.1t-gcc-11.3.0-w2by2b2 texinfo-7.0.3-gcc-11.3.0-tcpqkls
autoconf-archive-2023.02.20-gcc-11.3.0-5wwl7c6 diffutils-3.9-gcc-11.3.0-zdl3dic gmp-6.2.1-gcc-11.3.0-7kxi3rr lua-luafilesystem-1_8_0-gcc-11.3.0-23tvtrc perl-5.36.0-gcc-11.3.0-j5tavds unzip-6.0-gcc-11.3.0-ttovk4w
automake-1.16.5-gcc-11.3.0-oa3w4kf ed-1.4-gcc-11.3.0-yru5brp libiconv-1.17-gcc-11.3.0-7wr75ce lua-luaposix-36.1-gcc-11.3.0-zebno4c pigz-2.7-gcc-11.3.0-aln73eo xz-5.4.1-gcc-11.3.0-4kpkw5a
bc-1.07.1-gcc-11.3.0-ekfwavo gawk-5.2.1-gcc-11.3.0-6lk2khk libsigsegv-2.14-gcc-11.3.0-okig24f m4-1.4.19-gcc-11.3.0-llbjfk2 pkgconf-1.9.5-gcc-11.3.0-mh73nkp zlib-1.2.13-gcc-11.3.0-mntflxr
berkeley-db-18.1.40-gcc-11.3.0-7sohpaz gcc-12.1.0-gcc-11.3.0-s5e5zwr libtool-2.4.7-gcc-11.3.0-qkvj7am mpc-1.3.1-gcc-11.3.0-3qvnliw readline-8.2-gcc-11.3.0-tddm2ff zstd-1.5.5-gcc-11.3.0-qoo4rlo
bzip2-1.0.8-gcc-11.3.0-dca2qyg gdbm-1.23-gcc-11.3.0-ba4juc3 libxml2-2.10.3-gcc-11.3.0-pcbenki mpfr-4.2.0-gcc-11.3.0-aiys7vc tar-1.34-gcc-11.3.0-e77cf6a
ca-certificates-mozilla-2023-01-10-gcc-11.3.0-5pxkrf4 gettext-0.21.1-gcc-11.3.0-p4obvgx lmod-8.7.24-gcc-11.3.0-hrwwlqa ncurses-6.4-gcc-11.3.0-4dokmxj tcl-8.6.12-gcc-11.3.0-6afnoet
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
autoconf-2.69-gcc-11.3.0-t4nuen3 gdbm-1.23-gcc-12.1.0-febzyvz libxml2-2.10.3-gcc-12.1.0-sbbiixp openssl-1.1.1t-gcc-11.3.0-w2by2b2 py-scipy-1.10.1-gcc-12.1.0-ol3w546
autoconf-2.69-gcc-12.1.0-mr5osqp gettext-0.21.1-gcc-11.3.0-p4obvgx lmod-8.7.24-gcc-11.3.0-hrwwlqa openssl-1.1.1t-gcc-12.1.0-7dyvgor py-setuptools-63.4.3-gcc-12.1.0-wujb6fw
autoconf-archive-2023.02.20-gcc-11.3.0-5wwl7c6 gettext-0.21.1-gcc-12.1.0-7qnn3pi lua-5.4.4-gcc-11.3.0-l5jkvce perl-5.36.0-gcc-11.3.0-j5tavds py-tomli-2.0.1-gcc-12.1.0-ivq3gn7
automake-1.16.5-gcc-11.3.0-oa3w4kf gmake-4.4.1-gcc-11.3.0-guaj3kb lua-luafilesystem-1_8_0-gcc-11.3.0-23tvtrc perl-5.36.0-gcc-12.1.0-fq7gb4a py-wheel-0.37.1-gcc-12.1.0-kbelzwq
automake-1.16.5-gcc-12.1.0-yyzuikk gmake-4.4.1-gcc-12.1.0-74omm4b lua-luaposix-36.1-gcc-11.3.0-zebno4c pigz-2.7-gcc-11.3.0-aln73eo python-3.10.10-gcc-12.1.0-nvcwpz4
bc-1.07.1-gcc-11.3.0-ekfwavo gmp-6.2.1-gcc-11.3.0-7kxi3rr m4-1.4.19-gcc-11.3.0-llbjfk2 pigz-2.7-gcc-12.1.0-i2azy7n re2c-2.2-gcc-12.1.0-622aruu
berkeley-db-18.1.40-gcc-11.3.0-7sohpaz hwloc-2.9.1-gcc-12.1.0-sd6g5bq m4-1.4.19-gcc-12.1.0-s6ky5ld pkgconf-1.9.5-gcc-11.3.0-mh73nkp readline-8.2-gcc-11.3.0-tddm2ff
berkeley-db-18.1.40-gcc-12.1.0-vtjcxzc krb5-1.20.1-gcc-12.1.0-n5v3tug meson-1.1.0-gcc-12.1.0-s5rzrue pkgconf-1.9.5-gcc-12.1.0-gbfssja readline-8.2-gcc-12.1.0-qypmr5g
bison-3.8.2-gcc-12.1.0-fjc7p57 libbsd-0.11.7-gcc-12.1.0-kqphoxb mpc-1.3.1-gcc-11.3.0-3qvnliw pmix-4.2.3-gcc-12.1.0-ouqw26w sqlite-3.40.1-gcc-12.1.0-at2vwsu
bzip2-1.0.8-gcc-11.3.0-dca2qyg libedit-3.1-20210216-gcc-12.1.0-xkjcqre mpfr-4.2.0-gcc-11.3.0-aiys7vc py-beniget-0.4.1-gcc-12.1.0-s6swsfi tar-1.34-gcc-11.3.0-e77cf6a
bzip2-1.0.8-gcc-12.1.0-ecute7q libevent-2.1.12-gcc-12.1.0-2y2whk4 mpich-4.1.1-gcc-12.1.0-fb4tt65 py-build-0.10.0-gcc-12.1.0-uhboysx tar-1.34-gcc-12.1.0-2r7rutu
ca-certificates-mozilla-2023-01-10-gcc-11.3.0-5pxkrf4 libfabric-1.18.0-gcc-12.1.0-er4rpyd ncurses-6.4-gcc-11.3.0-4dokmxj py-cython-0.29.33-gcc-12.1.0-ny2lq6w tcl-8.6.12-gcc-11.3.0-6afnoet
ca-certificates-mozilla-2023-01-10-gcc-12.1.0-7u553me libffi-3.4.4-gcc-12.1.0-u2ztzc2 ncurses-6.4-gcc-12.1.0-yugzpgp py-flit-core-3.7.1-gcc-12.1.0-ihmiu27 texinfo-7.0.3-gcc-11.3.0-tcpqkls
cmake-3.26.3-gcc-12.1.0-cb3vkyk libiconv-1.17-gcc-11.3.0-7wr75ce netlib-lapack-3.11.0-gcc-12.1.0-fjlwowf py-gast-0.5.3-gcc-12.1.0-xg26gxl unzip-6.0-gcc-11.3.0-ttovk4w
curl-8.0.1-gcc-11.3.0-4cec7ab libiconv-1.17-gcc-12.1.0-ojujfjj netlib-scalapack-2.2.0-gcc-12.1.0-75u5574 py-meson-python-0.12.0-gcc-12.1.0-rosemhn util-linux-uuid-2.38.1-gcc-12.1.0-gbfbnoj
diffutils-3.9-gcc-11.3.0-zdl3dic libmd-1.0.4-gcc-12.1.0-a4ofctm netlib-scalapack-2.2.0-gcc-12.1.0-ea7dxfb py-numpy-1.24.3-gcc-12.1.0-54s3ofo util-macros-1.19.3-gcc-12.1.0-imbmumc
diffutils-3.9-gcc-12.1.0-csiltjm libpciaccess-0.17-gcc-12.1.0-4voenez netlib-scalapack-2.2.0-gcc-12.1.0-qmna5re py-packaging-23.0-gcc-12.1.0-yoamuqz xz-5.4.1-gcc-11.3.0-4kpkw5a
ed-1.4-gcc-11.3.0-yru5brp libsigsegv-2.14-gcc-11.3.0-okig24f netlib-scalapack-2.2.0-gcc-12.1.0-yq5hsff py-pip-23.0-gcc-12.1.0-khveatv xz-5.4.1-gcc-12.1.0-dat54qr
expat-2.5.0-gcc-12.1.0-upevc4c libsigsegv-2.14-gcc-12.1.0-oyzxg5g ninja-1.11.1-gcc-12.1.0-2zgsglc py-ply-3.11-gcc-12.1.0-ovxjh5h yaksa-0.2-gcc-12.1.0-5mplopl
findutils-4.9.0-gcc-12.1.0-hgvmfon libtool-2.4.7-gcc-11.3.0-qkvj7am numactl-2.0.14-gcc-12.1.0-45xq3wr py-pybind11-2.10.1-gcc-12.1.0-2hmi7rq zlib-1.2.13-gcc-11.3.0-mntflxr
gawk-5.2.1-gcc-11.3.0-6lk2khk libtool-2.4.7-gcc-12.1.0-owrdqyk openblas-0.3.23-gcc-12.1.0-5hvwk3g py-pyproject-hooks-1.0.0-gcc-12.1.0-udgbusq zlib-1.2.13-gcc-12.1.0-oboyaa5
gcc-12.1.0-gcc-11.3.0-s5e5zwr libxcrypt-4.4.33-gcc-12.1.0-uq4wpnl openmpi-4.1.5-gcc-12.1.0-ekmi64f py-pyproject-metadata-0.7.1-gcc-12.1.0-lrhcey2 zstd-1.5.5-gcc-11.3.0-qoo4rlo
gdbm-1.23-gcc-11.3.0-ba4juc3 libxml2-2.10.3-gcc-11.3.0-pcbenki openssh-9.3p1-gcc-12.1.0-vu4ehmb py-pythran-0.12.0-gcc-12.1.0-s6iwj3a zstd-1.5.5-gcc-12.1.0-a5p5yob
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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-12.1.0-gcc-11.3.0-s5e5zwr
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0-gcc-11.3.0-s5e5zwr:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
load("gmp-6.2.1-gcc-11.3.0-7kxi3rr")
load("mpc-1.3.1-gcc-11.3.0-3qvnliw")
load("mpfr-4.2.0-gcc-11.3.0-aiys7vc")
load("zlib-1.2.13-gcc-11.3.0-mntflxr")
load("zstd-1.5.5-gcc-11.3.0-qoo4rlo")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/.")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
help([[Name : gcc
Version: 12.1.0
Target : x86_64_v3
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 CC,
CXX, FC and F77 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:
default:
tcl:
all:
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
Next you should regenerate all the module files:
$ spack module tcl refresh -y
==> 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-12.1.0-gcc-11.3.0-s5e5zwr
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0-gcc-11.3.0-s5e5zwr:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
load("gmp-6.2.1-gcc-11.3.0-7kxi3rr")
load("mpc-1.3.1-gcc-11.3.0-3qvnliw")
load("mpfr-4.2.0-gcc-11.3.0-aiys7vc")
load("zlib-1.2.13-gcc-11.3.0-mntflxr")
load("zstd-1.5.5-gcc-11.3.0-qoo4rlo")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/.")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
help([[Name : gcc
Version: 12.1.0
Target : x86_64_v3
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@11.3.0 (the OS provided compiler).
To do this you should add the exclude keyword to ${SPACK_ROOT}/etc/spack/modules.yaml:
modules:
default:
tcl:
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "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-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
autoconf-2.69-gcc-12.1.0-mr5osqp libbsd-0.11.7-gcc-12.1.0-kqphoxb ncurses-6.4-gcc-12.1.0-yugzpgp pmix-4.2.3-gcc-12.1.0-ouqw26w py-scipy-1.10.1-gcc-12.1.0-ol3w546
automake-1.16.5-gcc-12.1.0-yyzuikk libedit-3.1-20210216-gcc-12.1.0-xkjcqre netlib-lapack-3.11.0-gcc-12.1.0-fjlwowf py-beniget-0.4.1-gcc-12.1.0-s6swsfi py-setuptools-63.4.3-gcc-12.1.0-wujb6fw
berkeley-db-18.1.40-gcc-12.1.0-vtjcxzc libevent-2.1.12-gcc-12.1.0-2y2whk4 netlib-scalapack-2.2.0-gcc-12.1.0-75u5574 py-build-0.10.0-gcc-12.1.0-uhboysx py-tomli-2.0.1-gcc-12.1.0-ivq3gn7
bison-3.8.2-gcc-12.1.0-fjc7p57 libfabric-1.18.0-gcc-12.1.0-er4rpyd netlib-scalapack-2.2.0-gcc-12.1.0-ea7dxfb py-cython-0.29.33-gcc-12.1.0-ny2lq6w py-wheel-0.37.1-gcc-12.1.0-kbelzwq
bzip2-1.0.8-gcc-12.1.0-ecute7q libffi-3.4.4-gcc-12.1.0-u2ztzc2 netlib-scalapack-2.2.0-gcc-12.1.0-qmna5re py-flit-core-3.7.1-gcc-12.1.0-ihmiu27 python-3.10.10-gcc-12.1.0-nvcwpz4
ca-certificates-mozilla-2023-01-10-gcc-12.1.0-7u553me libiconv-1.17-gcc-12.1.0-ojujfjj netlib-scalapack-2.2.0-gcc-12.1.0-yq5hsff py-gast-0.5.3-gcc-12.1.0-xg26gxl re2c-2.2-gcc-12.1.0-622aruu
cmake-3.26.3-gcc-12.1.0-cb3vkyk libmd-1.0.4-gcc-12.1.0-a4ofctm ninja-1.11.1-gcc-12.1.0-2zgsglc py-meson-python-0.12.0-gcc-12.1.0-rosemhn readline-8.2-gcc-12.1.0-qypmr5g
diffutils-3.9-gcc-12.1.0-csiltjm libpciaccess-0.17-gcc-12.1.0-4voenez numactl-2.0.14-gcc-12.1.0-45xq3wr py-numpy-1.24.3-gcc-12.1.0-54s3ofo sqlite-3.40.1-gcc-12.1.0-at2vwsu
expat-2.5.0-gcc-12.1.0-upevc4c libsigsegv-2.14-gcc-12.1.0-oyzxg5g openblas-0.3.23-gcc-12.1.0-5hvwk3g py-packaging-23.0-gcc-12.1.0-yoamuqz tar-1.34-gcc-12.1.0-2r7rutu
findutils-4.9.0-gcc-12.1.0-hgvmfon libtool-2.4.7-gcc-12.1.0-owrdqyk openmpi-4.1.5-gcc-12.1.0-ekmi64f py-pip-23.0-gcc-12.1.0-khveatv util-linux-uuid-2.38.1-gcc-12.1.0-gbfbnoj
gdbm-1.23-gcc-12.1.0-febzyvz libxcrypt-4.4.33-gcc-12.1.0-uq4wpnl openssh-9.3p1-gcc-12.1.0-vu4ehmb py-ply-3.11-gcc-12.1.0-ovxjh5h util-macros-1.19.3-gcc-12.1.0-imbmumc
gettext-0.21.1-gcc-12.1.0-7qnn3pi libxml2-2.10.3-gcc-12.1.0-sbbiixp openssl-1.1.1t-gcc-12.1.0-7dyvgor py-pybind11-2.10.1-gcc-12.1.0-2hmi7rq xz-5.4.1-gcc-12.1.0-dat54qr
gmake-4.4.1-gcc-12.1.0-74omm4b m4-1.4.19-gcc-12.1.0-s6ky5ld perl-5.36.0-gcc-12.1.0-fq7gb4a py-pyproject-hooks-1.0.0-gcc-12.1.0-udgbusq yaksa-0.2-gcc-12.1.0-5mplopl
hwloc-2.9.1-gcc-12.1.0-sd6g5bq meson-1.1.0-gcc-12.1.0-s5rzrue pigz-2.7-gcc-12.1.0-i2azy7n py-pyproject-metadata-0.7.1-gcc-12.1.0-lrhcey2 zlib-1.2.13-gcc-12.1.0-oboyaa5
krb5-1.20.1-gcc-12.1.0-n5v3tug mpich-4.1.1-gcc-12.1.0-fb4tt65 pkgconf-1.9.5-gcc-12.1.0-gbfssja py-pythran-0.12.0-gcc-12.1.0-s6iwj3a zstd-1.5.5-gcc-12.1.0-a5p5yob
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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
excluding modules: the module for gcc@12.1.0 disappeared as it was
bootstrapped with gcc@11.3.0. To specify exceptions to the exclude
rules you can use include:
modules:
default:
tcl:
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "C_INCLUDE_PATH"
- "CPLUS_INCLUDE_PATH"
- "LIBRARY_PATH"
include rules always have precedence over exclude 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@12.1.0 has reappeared:
$ module avail gcc-12.1.0-gcc-11.3.0-s5e5zwr
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
gcc-12.1.0-gcc-11.3.0-s5e5zwr
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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:
default:
tcl:
exclude_implicits: true
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "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:
default:
tcl:
hash_length: 0
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "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-ubuntu22.04-x86_64_v3/netlib-scalapack-2.2.0-gcc-12.1.0
spec: netlib-scalapack@=2.2.0%gcc@=12.1.0~ipo~pic+shared build_system=cmake build_type=Release generator=make patches=072b006,1c9ce5f,244a9aa arch=linux-ubuntu22.04-x86_64_v3
spec: netlib-scalapack@=2.2.0%gcc@=12.1.0~ipo~pic+shared build_system=cmake build_type=Release generator=make patches=072b006,1c9ce5f,244a9aa arch=linux-ubuntu22.04-x86_64_v3
spec: netlib-scalapack@=2.2.0%gcc@=12.1.0~ipo~pic+shared build_system=cmake build_type=Release generator=make patches=072b006,1c9ce5f,244a9aa arch=linux-ubuntu22.04-x86_64_v3
spec: netlib-scalapack@=2.2.0%gcc@=12.1.0~ipo~pic+shared build_system=cmake build_type=Release generator=make patches=072b006,1c9ce5f,244a9aa arch=linux-ubuntu22.04-x86_64_v3
==> 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:
default:
tcl:
hash_length: 0
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "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-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
autoconf/2.69-gcc-12.1.0 gmake/4.4.1-gcc-12.1.0 libxcrypt/4.4.33-gcc-12.1.0 openblas/0.3.23-gcc-12.1.0 py-meson-python/0.12.0-gcc-12.1.0 python/3.10.10-gcc-12.1.0
automake/1.16.5-gcc-12.1.0 hwloc/2.9.1-gcc-12.1.0 libxml2/2.10.3-gcc-12.1.0 openmpi/4.1.5-gcc-12.1.0 py-numpy/1.24.3-gcc-12.1.0-openblas re2c/2.2-gcc-12.1.0
berkeley-db/18.1.40-gcc-12.1.0 krb5/1.20.1-gcc-12.1.0 m4/1.4.19-gcc-12.1.0 openssh/9.3p1-gcc-12.1.0 py-packaging/23.0-gcc-12.1.0 readline/8.2-gcc-12.1.0
bison/3.8.2-gcc-12.1.0 libbsd/0.11.7-gcc-12.1.0 meson/1.1.0-gcc-12.1.0 openssl/1.1.1t-gcc-12.1.0 py-pip/23.0-gcc-12.1.0 sqlite/3.40.1-gcc-12.1.0
bzip2/1.0.8-gcc-12.1.0 libedit/3.1-20210216-gcc-12.1.0 mpich/4.1.1-gcc-12.1.0 perl/5.36.0-gcc-12.1.0 py-ply/3.11-gcc-12.1.0 tar/1.34-gcc-12.1.0
ca-certificates-mozilla/2023-01-10-gcc-12.1.0 libevent/2.1.12-gcc-12.1.0 ncurses/6.4-gcc-12.1.0 pigz/2.7-gcc-12.1.0 py-pybind11/2.10.1-gcc-12.1.0 util-linux-uuid/2.38.1-gcc-12.1.0
cmake/3.26.3-gcc-12.1.0 libfabric/1.18.0-gcc-12.1.0 netlib-lapack/3.11.0-gcc-12.1.0 pkgconf/1.9.5-gcc-12.1.0 py-pyproject-hooks/1.0.0-gcc-12.1.0 util-macros/1.19.3-gcc-12.1.0
diffutils/3.9-gcc-12.1.0 libffi/3.4.4-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-netlib-lapack-mpich pmix/4.2.3-gcc-12.1.0 py-pyproject-metadata/0.7.1-gcc-12.1.0 xz/5.4.1-gcc-12.1.0
expat/2.5.0-gcc-12.1.0 libiconv/1.17-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-netlib-lapack-openmpi py-beniget/0.4.1-gcc-12.1.0 py-pythran/0.12.0-gcc-12.1.0-openblas yaksa/0.2-gcc-12.1.0
findutils/4.9.0-gcc-12.1.0 libmd/1.0.4-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-openblas-mpich py-build/0.10.0-gcc-12.1.0 py-scipy/1.10.1-gcc-12.1.0-openblas zlib/1.2.13-gcc-12.1.0
gcc/12.1.0-gcc-11.3.0 libpciaccess/0.17-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-openblas-openmpi (D) py-cython/0.29.33-gcc-12.1.0 py-setuptools/63.4.3-gcc-12.1.0 zstd/1.5.5-gcc-12.1.0
gdbm/1.23-gcc-12.1.0 libsigsegv/2.14-gcc-12.1.0 ninja/1.11.1-gcc-12.1.0 py-flit-core/3.7.1-gcc-12.1.0 py-tomli/2.0.1-gcc-12.1.0
gettext/0.21.1-gcc-12.1.0 libtool/2.4.7-gcc-12.1.0 numactl/2.0.14-gcc-12.1.0 py-gast/0.5.3-gcc-12.1.0 py-wheel/0.37.1-gcc-12.1.0
Where:
D: Default Module
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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:
default:
tcl:
hash_length: 0
naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "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-ubuntu22.04-x86_64_v3/gcc/12.1.0-gcc-11.3.0:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/.")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx/bin/gfortran")
setenv("GCC_ROOT","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.3.0/gcc-12.1.0-s5e5zwrzqozb5e6liaz3tjm6achptgzx")
help([[Name : gcc
Version: 12.1.0
Target : x86_64_v3
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:
default:
tcl:
hash_length: 0
naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "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-ubuntu22.04-x86_64_v3/openmpi/4.1.5-gcc-12.1.0:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
whatis("An open source Message Passing Interface implementation.")
load("hwloc/2.9.1-gcc-12.1.0")
load("numactl/2.0.14-gcc-12.1.0")
load("openssh/9.3p1-gcc-12.1.0")
load("pmix/4.2.3-gcc-12.1.0")
load("zlib/1.2.13-gcc-12.1.0")
conflict("openmpi")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/share/man")
prepend_path("PKG_CONFIG_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/lib/pkgconfig")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/.")
setenv("MPICC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/bin/mpicc")
setenv("MPICXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/bin/mpic++")
setenv("MPIF77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/bin/mpif77")
setenv("MPIF90","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx/bin/mpif90")
setenv("OPENMPI_ROOT","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.1.0/openmpi-4.1.5-ekmi64fdx3jcorwo3irbmlxza6f4atkx")
setenv("SLURM_MPI_TYPE","pmi2")
setenv("OMPI_MCA_btl_openib_warn_default_git_prefix","0")
help([[Name : openmpi
Version: 4.1.5
Target : x86_64_v3
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:
default:
tcl:
verbose: True
hash_length: 0
naming_scheme: '{name}/{version}-{compiler.name}-{compiler.version}'
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "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
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-ubuntu22.04-x86_64_v3 -------------------------------------------------------------------------------------------------------
autoconf/2.69-gcc-12.1.0 gmake/4.4.1-gcc-12.1.0 libxcrypt/4.4.33-gcc-12.1.0 openblas/0.3.23-gcc-12.1.0 py-meson-python/0.12.0-gcc-12.1.0 python/3.10.10-gcc-12.1.0
automake/1.16.5-gcc-12.1.0 hwloc/2.9.1-gcc-12.1.0 libxml2/2.10.3-gcc-12.1.0 openmpi/4.1.5-gcc-12.1.0 py-numpy/1.24.3-gcc-12.1.0-openblas re2c/2.2-gcc-12.1.0
berkeley-db/18.1.40-gcc-12.1.0 krb5/1.20.1-gcc-12.1.0 m4/1.4.19-gcc-12.1.0 openssh/9.3p1-gcc-12.1.0 py-packaging/23.0-gcc-12.1.0 readline/8.2-gcc-12.1.0
bison/3.8.2-gcc-12.1.0 libbsd/0.11.7-gcc-12.1.0 meson/1.1.0-gcc-12.1.0 openssl/1.1.1t-gcc-12.1.0 py-pip/23.0-gcc-12.1.0 sqlite/3.40.1-gcc-12.1.0
bzip2/1.0.8-gcc-12.1.0 libedit/3.1-20210216-gcc-12.1.0 mpich/4.1.1-gcc-12.1.0 perl/5.36.0-gcc-12.1.0 py-ply/3.11-gcc-12.1.0 tar/1.34-gcc-12.1.0
ca-certificates-mozilla/2023-01-10-gcc-12.1.0 libevent/2.1.12-gcc-12.1.0 ncurses/6.4-gcc-12.1.0 pigz/2.7-gcc-12.1.0 py-pybind11/2.10.1-gcc-12.1.0 util-linux-uuid/2.38.1-gcc-12.1.0
cmake/3.26.3-gcc-12.1.0 libfabric/1.18.0-gcc-12.1.0 netlib-lapack/3.11.0-gcc-12.1.0 pkgconf/1.9.5-gcc-12.1.0 py-pyproject-hooks/1.0.0-gcc-12.1.0 util-macros/1.19.3-gcc-12.1.0
diffutils/3.9-gcc-12.1.0 libffi/3.4.4-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-netlib-lapack-mpich pmix/4.2.3-gcc-12.1.0 py-pyproject-metadata/0.7.1-gcc-12.1.0 xz/5.4.1-gcc-12.1.0
expat/2.5.0-gcc-12.1.0 libiconv/1.17-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-netlib-lapack-openmpi py-beniget/0.4.1-gcc-12.1.0 py-pythran/0.12.0-gcc-12.1.0-openblas yaksa/0.2-gcc-12.1.0
findutils/4.9.0-gcc-12.1.0 libmd/1.0.4-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-openblas-mpich py-build/0.10.0-gcc-12.1.0 py-scipy/1.10.1-gcc-12.1.0-openblas zlib/1.2.13-gcc-12.1.0
gcc/12.1.0-gcc-11.3.0 libpciaccess/0.17-gcc-12.1.0 netlib-scalapack/2.2.0-gcc-12.1.0-openblas-openmpi (D) py-cython/0.29.33-gcc-12.1.0 py-setuptools/63.4.3-gcc-12.1.0 zstd/1.5.5-gcc-12.1.0
gdbm/1.23-gcc-12.1.0 libsigsegv/2.14-gcc-12.1.0 ninja/1.11.1-gcc-12.1.0 py-flit-core/3.7.1-gcc-12.1.0 py-tomli/2.0.1-gcc-12.1.0
gettext/0.21.1-gcc-12.1.0 libtool/2.4.7-gcc-12.1.0 numactl/2.0.14-gcc-12.1.0 py-gast/0.5.3-gcc-12.1.0 py-wheel/0.37.1-gcc-12.1.0
Where:
D: Default Module
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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/3.11.0-gcc-12.1.0 2) openblas/0.3.23-gcc-12.1.0
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
lmodfile generator- change the
tcltag tolmod- remove the
tclspecificconflictdirective- declare which compilers are considered
core_compilers- remove the
mpirelated suffixes in projections (as they will be substituted by hierarchies)
After these modifications your configuration file should look like:
modules:
default:
enable::
- lmod
lmod:
core_compilers:
- 'gcc@11'
hierarchy:
- mpi
hash_length: 0
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "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
enableis intentional and it serves the purpose of overriding the default list of enabled generators so that onlylmodwill 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-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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-ubuntu22.04-x86_64/gcc/12.1.0 -----------------------------------------------------------------------------------------------------
autoconf/2.69 diffutils/3.9 krb5/1.20.1 libmd/1.0.4 meson/1.1.0 openmpi/4.1.5 py-beniget/0.4.1 py-packaging/23.0 py-scipy/1.10.1-openblas sqlite/3.40.1 zstd/1.5.5
automake/1.16.5 expat/2.5.0 libbsd/0.11.7 libpciaccess/0.17 mpich/4.1.1 openssh/9.3p1 py-build/0.10.0 py-pip/23.0 py-setuptools/63.4.3 tar/1.34
berkeley-db/18.1.40 findutils/4.9.0 libedit/3.1-20210216 libsigsegv/2.14 ncurses/6.4 openssl/1.1.1t py-cython/0.29.33 py-ply/3.11 py-tomli/2.0.1 util-linux-uuid/2.38.1
bison/3.8.2 gdbm/1.23 libevent/2.1.12 libtool/2.4.7 netlib-lapack/3.11.0 perl/5.36.0 py-flit-core/3.7.1 py-pybind11/2.10.1 py-wheel/0.37.1 util-macros/1.19.3
bzip2/1.0.8 gettext/0.21.1 libfabric/1.18.0 libxcrypt/4.4.33 ninja/1.11.1 pigz/2.7 py-gast/0.5.3 py-pyproject-hooks/1.0.0 python/3.10.10 xz/5.4.1
ca-certificates-mozilla/2023-01-10 gmake/4.4.1 libffi/3.4.4 libxml2/2.10.3 numactl/2.0.14 pkgconf/1.9.5 py-meson-python/0.12.0 py-pyproject-metadata/0.7.1 re2c/2.2 yaksa/0.2
cmake/3.26.3 hwloc/2.9.1 libiconv/1.17 m4/1.4.19 openblas/0.3.23 pmix/4.2.3 py-numpy/1.24.3-openblas py-pythran/0.12.0-openblas readline/8.2 zlib/1.2.13
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0 (L)
Where:
L: Module is loaded
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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-ubuntu22.04-x86_64/mpich/4.1.1-fb4tt65/gcc/12.1.0 -------------------------------------------------------------------------------------------
netlib-scalapack/2.2.0-netlib-lapack netlib-scalapack/2.2.0-openblas (D)
---------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.1.0 -----------------------------------------------------------------------------------------------------
autoconf/2.69 expat/2.5.0 libedit/3.1-20210216 libtool/2.4.7 ninja/1.11.1 pkgconf/1.9.5 py-numpy/1.24.3-openblas py-scipy/1.10.1-openblas tar/1.34
automake/1.16.5 findutils/4.9.0 libevent/2.1.12 libxcrypt/4.4.33 numactl/2.0.14 pmix/4.2.3 py-packaging/23.0 py-setuptools/63.4.3 util-linux-uuid/2.38.1
berkeley-db/18.1.40 gdbm/1.23 libfabric/1.18.0 (L) libxml2/2.10.3 (L) openblas/0.3.23 py-beniget/0.4.1 py-pip/23.0 py-tomli/2.0.1 util-macros/1.19.3
bison/3.8.2 gettext/0.21.1 libffi/3.4.4 m4/1.4.19 openmpi/4.1.5 py-build/0.10.0 py-ply/3.11 py-wheel/0.37.1 xz/5.4.1 (L)
bzip2/1.0.8 gmake/4.4.1 libiconv/1.17 (L) meson/1.1.0 openssh/9.3p1 py-cython/0.29.33 py-pybind11/2.10.1 python/3.10.10 yaksa/0.2 (L)
ca-certificates-mozilla/2023-01-10 hwloc/2.9.1 (L) libmd/1.0.4 mpich/4.1.1 (L) openssl/1.1.1t py-flit-core/3.7.1 py-pyproject-hooks/1.0.0 re2c/2.2 zlib/1.2.13 (L)
cmake/3.26.3 krb5/1.20.1 libpciaccess/0.17 (L) ncurses/6.4 (L) perl/5.36.0 py-gast/0.5.3 py-pyproject-metadata/0.7.1 readline/8.2 zstd/1.5.5
diffutils/3.9 libbsd/0.11.7 libsigsegv/2.14 netlib-lapack/3.11.0 pigz/2.7 py-meson-python/0.12.0 py-pythran/0.12.0-openblas sqlite/3.40.1
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0 (L)
Where:
D: Default Module
L: Module is loaded
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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/2.2.0-openblas
$ module list
Currently Loaded Modules:
1) gcc/12.1.0 2) libpciaccess/0.17 3) libiconv/1.17 4) xz/5.4.1 5) zlib/1.2.13 6) libxml2/2.10.3 7) ncurses/6.4 8) hwloc/2.9.1 9) libfabric/1.18.0 10) yaksa/0.2 11) mpich/4.1.1 12) openblas/0.3.23 13) netlib-scalapack/2.2.0-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/4.1.1" with "openmpi/4.1.5".
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.2.0-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/12.1.0 3) libpciaccess/0.17 5) xz/5.4.1 7) libxml2/2.10.3 9) hwloc/2.9.1 11) bzip2/1.0.8 13) zstd/1.5.5 15) gettext/0.21.1 17) krb5/1.20.1 19) libxcrypt/4.4.33 21) libevent/2.1.12 23) openmpi/4.1.5
2) openblas/0.3.23 4) libiconv/1.17 6) zlib/1.2.13 8) ncurses/6.4 10) numactl/2.0.14 12) pigz/2.7 14) tar/1.34 16) openssl/1.1.1t 18) libedit/3.1-20210216 20) openssh/9.3p1 22) pmix/4.2.3 24) netlib-scalapack/2.2.0-openblas
$ module avail
----------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openmpi/4.1.5-ekmi64f/gcc/12.1.0 ------------------------------------------------------------------------------------------
netlib-scalapack/2.2.0-netlib-lapack netlib-scalapack/2.2.0-openblas (L,D)
---------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.1.0 -----------------------------------------------------------------------------------------------------
autoconf/2.69 expat/2.5.0 libedit/3.1-20210216 (L) libtool/2.4.7 ninja/1.11.1 pkgconf/1.9.5 py-numpy/1.24.3-openblas py-scipy/1.10.1-openblas tar/1.34 (L)
automake/1.16.5 findutils/4.9.0 libevent/2.1.12 (L) libxcrypt/4.4.33 (L) numactl/2.0.14 (L) pmix/4.2.3 (L) py-packaging/23.0 py-setuptools/63.4.3 util-linux-uuid/2.38.1
berkeley-db/18.1.40 gdbm/1.23 libfabric/1.18.0 libxml2/2.10.3 (L) openblas/0.3.23 (L) py-beniget/0.4.1 py-pip/23.0 py-tomli/2.0.1 util-macros/1.19.3
bison/3.8.2 gettext/0.21.1 (L) libffi/3.4.4 m4/1.4.19 openmpi/4.1.5 (L) py-build/0.10.0 py-ply/3.11 py-wheel/0.37.1 xz/5.4.1 (L)
bzip2/1.0.8 (L) gmake/4.4.1 libiconv/1.17 (L) meson/1.1.0 openssh/9.3p1 (L) py-cython/0.29.33 py-pybind11/2.10.1 python/3.10.10 yaksa/0.2
ca-certificates-mozilla/2023-01-10 hwloc/2.9.1 (L) libmd/1.0.4 mpich/4.1.1 openssl/1.1.1t (L) py-flit-core/3.7.1 py-pyproject-hooks/1.0.0 re2c/2.2 zlib/1.2.13 (L)
cmake/3.26.3 krb5/1.20.1 (L) libpciaccess/0.17 (L) ncurses/6.4 (L) perl/5.36.0 py-gast/0.5.3 py-pyproject-metadata/0.7.1 readline/8.2 zstd/1.5.5 (L)
diffutils/3.9 libbsd/0.11.7 libsigsegv/2.14 netlib-lapack/3.11.0 pigz/2.7 (L) py-meson-python/0.12.0 py-pythran/0.12.0-openblas sqlite/3.40.1
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0 (L)
Where:
D: Default Module
L: Module is loaded
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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/2.2.0-netlib-lapack
The following have been reloaded with a version change:
1) netlib-scalapack/2.2.0-openblas => netlib-scalapack/2.2.0-netlib-lapack
$ module list
Currently Loaded Modules:
1) gcc/12.1.0 4) libiconv/1.17 7) libxml2/2.10.3 10) numactl/2.0.14 13) zstd/1.5.5 16) openssl/1.1.1t 19) libxcrypt/4.4.33 22) pmix/4.2.3 25) netlib-scalapack/2.2.0-netlib-lapack
2) openblas/0.3.23 5) xz/5.4.1 8) ncurses/6.4 11) bzip2/1.0.8 14) tar/1.34 17) krb5/1.20.1 20) openssh/9.3p1 23) openmpi/4.1.5
3) libpciaccess/0.17 6) zlib/1.2.13 9) hwloc/2.9.1 12) pigz/2.7 15) gettext/0.21.1 18) libedit/3.1-20210216 21) libevent/2.1.12 24) netlib-lapack/3.11.0
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
MPIorLAPACK- 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:
default:
enable::
- lmod
lmod:
core_compilers:
- 'gcc@11'
hierarchy:
- mpi
- lapack
hash_length: 0
include:
- gcc
exclude:
- '%gcc@11.3.0'
all:
filter:
exclude_env_vars:
- "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
Lmod is automatically replacing "openblas/0.3.23" with "netlib-lapack/3.11.0".
Inactive Modules:
1) netlib-scalapack/2.2.0-netlib-lapack 2) openblas
$ module load openblas
Lmod is automatically replacing "netlib-lapack/3.11.0" with "openblas/0.3.23".
Activating Modules:
1) openblas/0.3.23
$ module avail
----------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openmpi/4.1.5-ekmi64f/openblas/0.3.23-5hvwk3g/gcc/12.1.0 ------------------------------------------------------------------------------
netlib-scalapack/2.2.0
---------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openblas/0.3.23-5hvwk3g/gcc/12.1.0 -----------------------------------------------------------------------------------------
py-numpy/1.24.3 py-pythran/0.12.0 py-scipy/1.10.1
---------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.1.0 -----------------------------------------------------------------------------------------------------
autoconf/2.69 expat/2.5.0 libedit/3.1-20210216 (L) libtool/2.4.7 ninja/1.11.1 pkgconf/1.9.5 py-packaging/23.0 py-wheel/0.37.1 xz/5.4.1 (L)
automake/1.16.5 findutils/4.9.0 libevent/2.1.12 (L) libxcrypt/4.4.33 (L) numactl/2.0.14 (L) pmix/4.2.3 (L) py-pip/23.0 python/3.10.10 yaksa/0.2
berkeley-db/18.1.40 gdbm/1.23 libfabric/1.18.0 libxml2/2.10.3 (L) openblas/0.3.23 (L) py-beniget/0.4.1 py-ply/3.11 re2c/2.2 zlib/1.2.13 (L)
bison/3.8.2 gettext/0.21.1 (L) libffi/3.4.4 m4/1.4.19 openmpi/4.1.5 (L) py-build/0.10.0 py-pybind11/2.10.1 readline/8.2 zstd/1.5.5 (L)
bzip2/1.0.8 (L) gmake/4.4.1 libiconv/1.17 (L) meson/1.1.0 openssh/9.3p1 (L) py-cython/0.29.33 py-pyproject-hooks/1.0.0 sqlite/3.40.1
ca-certificates-mozilla/2023-01-10 hwloc/2.9.1 (L) libmd/1.0.4 mpich/4.1.1 openssl/1.1.1t (L) py-flit-core/3.7.1 py-pyproject-metadata/0.7.1 tar/1.34 (L)
cmake/3.26.3 krb5/1.20.1 (L) libpciaccess/0.17 (L) ncurses/6.4 (L) perl/5.36.0 py-gast/0.5.3 py-setuptools/63.4.3 util-linux-uuid/2.38.1
diffutils/3.9 libbsd/0.11.7 libsigsegv/2.14 netlib-lapack/3.11.0 pigz/2.7 (L) py-meson-python/0.12.0 py-tomli/2.0.1 util-macros/1.19.3
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0 (L)
Where:
L: Module is loaded
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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-ubuntu22.04-x86_64/openmpi/4.1.5-ekmi64f/openblas/0.3.23-5hvwk3g/gcc/12.1.0 ------------------------------------------------------------------------------
netlib-scalapack/2.2.0
---------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openblas/0.3.23-5hvwk3g/gcc/12.1.0 -----------------------------------------------------------------------------------------
py-numpy/1.24.3 py-pythran/0.12.0 py-scipy/1.10.1
---------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.1.0 -----------------------------------------------------------------------------------------------------
autoconf/2.69 expat/2.5.0 libedit/3.1-20210216 (L) libtool/2.4.7 ninja/1.11.1 pkgconf/1.9.5 py-packaging/23.0 py-wheel/0.37.1 xz/5.4.1 (L)
automake/1.16.5 findutils/4.9.0 libevent/2.1.12 (L) libxcrypt/4.4.33 (L) numactl/2.0.14 (L) pmix/4.2.3 (L) py-pip/23.0 python/3.10.10 yaksa/0.2
berkeley-db/18.1.40 gdbm/1.23 libfabric/1.18.0 libxml2/2.10.3 (L) openblas/0.3.23 (L) py-beniget/0.4.1 py-ply/3.11 re2c/2.2 zlib/1.2.13 (L)
bison/3.8.2 gettext/0.21.1 (L) libffi/3.4.4 m4/1.4.19 openmpi/4.1.5 (L) py-build/0.10.0 py-pybind11/2.10.1 readline/8.2 zstd/1.5.5 (L)
bzip2/1.0.8 (L) gmake/4.4.1 libiconv/1.17 (L) meson/1.1.0 openssh/9.3p1 (L) py-cython/0.29.33 py-pyproject-hooks/1.0.0 sqlite/3.40.1
ca-certificates-mozilla/2023-01-10 hwloc/2.9.1 (L) libmd/1.0.4 mpich/4.1.1 openssl/1.1.1t (L) py-flit-core/3.7.1 py-pyproject-metadata/0.7.1 tar/1.34 (L)
cmake/3.26.3 krb5/1.20.1 (L) libpciaccess/0.17 (L) ncurses/6.4 (L) perl/5.36.0 py-gast/0.5.3 py-setuptools/63.4.3 util-linux-uuid/2.38.1
diffutils/3.9 libbsd/0.11.7 libsigsegv/2.14 netlib-lapack/3.11.0 pigz/2.7 (L) py-meson-python/0.12.0 py-tomli/2.0.1 util-macros/1.19.3
------------------------------------------------------------------------------------------------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------------------------------------------------------------------------------------------------
gcc/12.1.0 (L)
Where:
L: Module is loaded
If the avail list is too long consider trying:
"module --default avail" or "ml -d av" to just list the default modules.
"module overview" or "ml ov" to display the number of modules for each name.
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/2.2.0
$ module load mpich
Lmod is automatically replacing "openmpi/4.1.5" with "mpich/4.1.1".
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.2.0
$ module load netlib-lapack
Lmod is automatically replacing "openblas/0.3.23" with "netlib-lapack/3.11.0".
Inactive Modules:
1) bzip2/1.0.8 3) gdbm/1.23 5) libbsd/0.11.7 7) libmd/1.0.4 9) openssl/1.1.1t 11) py-numpy 13) python/3.10.10 15) sqlite/3.40.1 17) util-linux-uuid/2.38.1
2) expat/2.5.0 4) gettext/0.21.1 6) libffi/3.4.4 8) libxcrypt/4.4.33 10) pigz/2.7 12) py-setuptools/63.4.3 14) readline/8.2 16) tar/1.34 18) zstd/1.5.5
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.2.0
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:
{% 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 %}
{% block footer %}
{# In case the module needs to be extended with custom LUA code #}
{% endblock %}
The locations where Spack looks for templates are specified
in config.yaml:
# Locations where templates should be found
template_dirs:
- $spack/share/spack/templates
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@11'
hierarchy:
- mpi
- lapack
hash_length: 0
include:
- gcc
exclude:
- '%gcc@11.3.0'
- readline
all:
filter:
exclude_env_vars:
- "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-12.1.0/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@12.1.0
compiler. Since it is currently the default compiler (our current
default is the most recent version of gcc available), we will remove
it now.
$ spack compiler rm gcc@12.1.0
This will ensure the rest of the tutorial goes smoothly for you.