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:sc24
and then set Spack up like this:
git clone --depth=100 --branch=releases/v0.23 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@12.3.0.
$ spack install gcc@12.3.0
You can get this in your environment using spack load gcc@12.3.0:
$ spack load gcc@12
$ which gcc
/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/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@12.3.0
==> 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@12.3.0 gcc@11.4.0 gcc@10.5.0
Finally, when you confirmed gcc@12.3.0 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:
$ module show gcc
------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/gcc/12.3.0-gcc-11.4.0-chmemdi:
------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
depends_on("gmp/6.2.1-gcc-11.4.0-2fyiqrp")
depends_on("mpc/1.3.1-gcc-11.4.0-jueol5k")
depends_on("mpfr/4.2.0-gcc-11.4.0-qpadvjw")
depends_on("zlib-ng/2.1.4-gcc-11.4.0-5xcetrv")
depends_on("zstd/1.5.5-gcc-11.4.0-jkznmrm")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/.")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gfortran")
append_path("MANPATH","")
help([[Name : gcc
Version: 12.3.0
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.
]])
module load will execute all of the changes shown above:
$ which gcc
/usr/bin/gcc
$ module load gcc
$ which gcc
/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gcc
and to undo the modifications, you can use module unload:
$ module unload gcc
$ which gcc
/usr/bin/gcc
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@11.4.0 ---------------------
gcc@12.3.0
==> 1 loaded package
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-archive/2023.02.20-gcc-11.4.0-4wbogd6
autoconf/2.69-gcc-11.4.0-mnfnoa5
automake/1.16.5-gcc-11.4.0-d3cncgl
bc/1.07.1-gcc-11.4.0-ra6efl5
berkeley-db/18.1.40-gcc-11.4.0-ku7makq
bzip2/1.0.8-gcc-11.4.0-4oz3kpf
ca-certificates-mozilla/2023-05-30-gcc-11.4.0-ct4al4u
curl/8.4.0-gcc-11.4.0-ijsmc3j
diffutils/3.9-gcc-11.4.0-ueheij3
ed/1.4-gcc-11.4.0-3kggq53
gawk/5.2.2-gcc-11.4.0-t4xydm4
gcc/12.3.0-gcc-11.4.0-chmemdi
gdbm/1.23-gcc-11.4.0-m626hzw
gettext/0.22.3-gcc-11.4.0-y26lmlo
gmake/4.4.1-gcc-11.4.0-znvoani
gmp/6.2.1-gcc-11.4.0-2fyiqrp
libiconv/1.17-gcc-11.4.0-ivn4eq4
libsigsegv/2.14-gcc-11.4.0-zuopqri
libtool/2.4.7-gcc-11.4.0-rgag55h
libxml2/2.10.3-gcc-11.4.0-67qoxbv
lmod/8.7.18-gcc-11.4.0-y47nb2g
lua-luafilesystem/1.8.0-gcc-11.4.0-jw4gyrw
lua-luaposix/36.1-gcc-11.4.0-6rkzyvr
lua/5.4.4-gcc-11.4.0-paqrr2m
m4/1.4.19-gcc-11.4.0-jnv5nut
mpc/1.3.1-gcc-11.4.0-jueol5k
mpfr/4.2.0-gcc-11.4.0-qpadvjw
ncurses/6.4-gcc-11.4.0-qqlh6as
nghttp2/1.57.0-gcc-11.4.0-my64owh
openssl/3.1.3-gcc-11.4.0-35j7wvr
perl/5.38.0-gcc-11.4.0-dg34i2a
pigz/2.7-gcc-11.4.0-catlxmo
pkgconf/1.9.5-gcc-11.4.0-zjgtpdo
readline/8.2-gcc-11.4.0-xxgqlmj
tar/1.34-gcc-11.4.0-vdb3ozo
tcl/8.6.12-gcc-11.4.0-tt2hv6r
texinfo/7.0.3-gcc-11.4.0-km6pqxp
unzip/6.0-gcc-11.4.0-uy5dhue
xz/5.4.1-gcc-11.4.0-axxqoeq
zlib-ng/2.1.4-gcc-11.4.0-5xcetrv
zstd/1.5.5-gcc-11.4.0-jkznmrm
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 --------------
amdblis/4.1-gcc-12.3.0-ywpdccr
autoconf-archive/2023.02.20-gcc-11.4.0-4wbogd6
autoconf/2.69-gcc-11.4.0-mnfnoa5
autoconf/2.69-gcc-12.3.0-kroqjku (D)
automake/1.16.5-gcc-11.4.0-d3cncgl
automake/1.16.5-gcc-12.3.0-dajnwux (D)
bc/1.07.1-gcc-11.4.0-ra6efl5
berkeley-db/18.1.40-gcc-11.4.0-ku7makq
berkeley-db/18.1.40-gcc-12.3.0-krlqpve (D)
bison/3.8.2-gcc-12.3.0-tr45sog
bzip2/1.0.8-gcc-11.4.0-4oz3kpf
bzip2/1.0.8-gcc-12.3.0-bbwtdnr (D)
ca-certificates-mozilla/2023-05-30-gcc-11.4.0-ct4al4u
ca-certificates-mozilla/2023-05-30-gcc-12.3.0-l7zpjxt (D)
cmake/3.27.7-gcc-12.3.0-dukasmm
curl/8.4.0-gcc-11.4.0-ijsmc3j
curl/8.4.0-gcc-12.3.0-u2ni6an (D)
diffutils/3.9-gcc-11.4.0-ueheij3
diffutils/3.9-gcc-12.3.0-sbfcnap (D)
ed/1.4-gcc-11.4.0-3kggq53
expat/2.5.0-gcc-12.3.0-grrt7ig
findutils/4.9.0-gcc-12.3.0-pdopgfr
gawk/5.2.2-gcc-11.4.0-t4xydm4
gcc/12.3.0-gcc-11.4.0-chmemdi
gdbm/1.23-gcc-11.4.0-m626hzw
gdbm/1.23-gcc-12.3.0-w66nich (D)
gettext/0.22.3-gcc-11.4.0-y26lmlo
gettext/0.22.3-gcc-12.3.0-y7ty4lo (D)
gmake/4.4.1-gcc-11.4.0-znvoani
gmake/4.4.1-gcc-12.3.0-6qiak7n (D)
gmp/6.2.1-gcc-11.4.0-2fyiqrp
hwloc/2.9.1-gcc-12.3.0-rvotk5a
krb5/1.20.1-gcc-12.3.0-5d6b7ng
libbsd/0.11.7-gcc-12.3.0-sygavnw
libedit/3.1-20210216-gcc-12.3.0-fm2rgwy
libevent/2.1.12-gcc-12.3.0-3rudtaf
libfabric/1.19.0-gcc-12.3.0-46fsov7
libffi/3.4.4-gcc-12.3.0-ecpriyn
libiconv/1.17-gcc-11.4.0-ivn4eq4
libiconv/1.17-gcc-12.3.0-a34xpad (D)
libmd/1.0.4-gcc-12.3.0-ivvykht
libpciaccess/0.17-gcc-12.3.0-el7pkf4
libsigsegv/2.14-gcc-11.4.0-zuopqri
libsigsegv/2.14-gcc-12.3.0-46vv5f3 (D)
libtool/2.4.7-gcc-11.4.0-rgag55h
libtool/2.4.7-gcc-12.3.0-hvedpuf (D)
libxcrypt/4.4.35-gcc-12.3.0-guszc5m
libxml2/2.10.3-gcc-11.4.0-67qoxbv
libxml2/2.10.3-gcc-12.3.0-damyeos (D)
lmod/8.7.18-gcc-11.4.0-y47nb2g
lua-luafilesystem/1.8.0-gcc-11.4.0-jw4gyrw
lua-luaposix/36.1-gcc-11.4.0-6rkzyvr
lua/5.4.4-gcc-11.4.0-paqrr2m
m4/1.4.19-gcc-11.4.0-jnv5nut
m4/1.4.19-gcc-12.3.0-oebiztm (D)
meson/1.2.2-gcc-12.3.0-htbkkj2
mpc/1.3.1-gcc-11.4.0-jueol5k
mpfr/4.2.0-gcc-11.4.0-qpadvjw
mpich/4.1.2-gcc-12.3.0-cxezwh7
ncurses/6.4-gcc-11.4.0-qqlh6as
ncurses/6.4-gcc-12.3.0-glwymee (D)
netlib-lapack/3.11.0-gcc-12.3.0-4uab534
netlib-scalapack/2.2.0-gcc-12.3.0-f4bc72j
netlib-scalapack/2.2.0-gcc-12.3.0-klad7nj
netlib-scalapack/2.2.0-gcc-12.3.0-ve3uhz5
netlib-scalapack/2.2.0-gcc-12.3.0-3mwyatr (D)
nghttp2/1.57.0-gcc-11.4.0-my64owh
nghttp2/1.57.0-gcc-12.3.0-dvtfejq (D)
ninja/1.11.1-gcc-12.3.0-qf3fwcn
numactl/2.0.14-gcc-12.3.0-iiok6h4
openblas/0.3.24-gcc-12.3.0-qoggfi2
openmpi/4.1.6-gcc-12.3.0-cndwedm
openssh/9.5p1-gcc-12.3.0-6ksmdje
openssl/3.1.3-gcc-11.4.0-35j7wvr
openssl/3.1.3-gcc-12.3.0-v7jc5lq (D)
perl/5.38.0-gcc-11.4.0-dg34i2a
perl/5.38.0-gcc-12.3.0-hh6v2va (D)
pigz/2.7-gcc-11.4.0-catlxmo
pigz/2.7-gcc-12.3.0-m7r2rmw (D)
pkgconf/1.9.5-gcc-11.4.0-zjgtpdo
pkgconf/1.9.5-gcc-12.3.0-ccpwoda (D)
pmix/5.0.1-gcc-12.3.0-tmm3jjd
py-beniget/0.4.1-gcc-12.3.0-fizom4w
py-cython/0.29.36-gcc-12.3.0-ylumqbe
py-flit-core/3.9.0-gcc-12.3.0-nzh222k
py-gast/0.5.3-gcc-12.3.0-h7hu6wn
py-meson-python/0.13.1-gcc-12.3.0-6zbxyin
py-numpy/1.26.1-gcc-12.3.0-4rqb2wc
py-packaging/23.1-gcc-12.3.0-7rj6npn
py-pip/23.1.2-gcc-12.3.0-lvdwpa6
py-ply/3.11-gcc-12.3.0-x3c55tr
py-pybind11/2.11.0-gcc-12.3.0-bo5zrbu
py-pyproject-metadata/0.7.1-gcc-12.3.0-bw34ifa
py-pythran/0.12.2-gcc-12.3.0-7fwfpfj
py-scipy/1.11.3-gcc-12.3.0-b6ldv5o
py-setuptools/68.0.0-gcc-12.3.0-crc6iaj
py-wheel/0.41.2-gcc-12.3.0-zwngepq
python/3.11.6-gcc-12.3.0-oa7j22b
re2c/2.2-gcc-12.3.0-cw5qvcn
readline/8.2-gcc-11.4.0-xxgqlmj
readline/8.2-gcc-12.3.0-cz4lfdu (D)
sqlite/3.43.2-gcc-12.3.0-p3srvwu
tar/1.34-gcc-11.4.0-vdb3ozo
tar/1.34-gcc-12.3.0-waes7yx (D)
tcl/8.6.12-gcc-11.4.0-tt2hv6r
texinfo/7.0.3-gcc-11.4.0-km6pqxp
unzip/6.0-gcc-11.4.0-uy5dhue
util-linux-uuid/2.38.1-gcc-12.3.0-oagevhm
util-macros/1.19.3-gcc-12.3.0-t67cwmg
xz/5.4.1-gcc-11.4.0-axxqoeq
xz/5.4.1-gcc-12.3.0-taa3gkk (D)
yaksa/0.3-gcc-12.3.0-hmywdkq
zlib-ng/2.1.4-gcc-11.4.0-5xcetrv
zlib-ng/2.1.4-gcc-12.3.0-draqwfy (D)
zstd/1.5.5-gcc-11.4.0-jkznmrm
zstd/1.5.5-gcc-12.3.0-ngvd73i (D)
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".
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
------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/gcc/12.3.0-gcc-11.4.0-chmemdi:
------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
depends_on("gmp/6.2.1-gcc-11.4.0-2fyiqrp")
depends_on("mpc/1.3.1-gcc-11.4.0-jueol5k")
depends_on("mpfr/4.2.0-gcc-11.4.0-qpadvjw")
depends_on("zlib-ng/2.1.4-gcc-11.4.0-5xcetrv")
depends_on("zstd/1.5.5-gcc-11.4.0-jkznmrm")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/.")
setenv("CC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gcc")
setenv("CXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/g++")
setenv("FC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gfortran")
setenv("F77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin/gfortran")
append_path("MANPATH","")
help([[Name : gcc
Version: 12.3.0
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"
This can be done either editing the configuration manually, or directly from the command line:
$ spack config add "modules:default:tcl:all:filter:exclude_env_vars:['CC', 'CXX', 'F77', 'FC']"
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
------------------------------------------------------------------------------------------
/home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3/gcc/12.3.0-gcc-11.4.0-chmemdi:
------------------------------------------------------------------------------------------
whatis("The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.")
depends_on("gmp/6.2.1-gcc-11.4.0-2fyiqrp")
depends_on("mpc/1.3.1-gcc-11.4.0-jueol5k")
depends_on("mpfr/4.2.0-gcc-11.4.0-qpadvjw")
depends_on("zlib-ng/2.1.4-gcc-11.4.0-5xcetrv")
depends_on("zstd/1.5.5-gcc-11.4.0-jkznmrm")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/.")
append_path("MANPATH","")
help([[Name : gcc
Version: 12.3.0
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 (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'
all:
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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 --------------
amdblis/4.1-gcc-12.3.0-ywpdccr
autoconf/2.69-gcc-12.3.0-kroqjku
automake/1.16.5-gcc-12.3.0-dajnwux
berkeley-db/18.1.40-gcc-12.3.0-krlqpve
bison/3.8.2-gcc-12.3.0-tr45sog
bzip2/1.0.8-gcc-12.3.0-bbwtdnr
ca-certificates-mozilla/2023-05-30-gcc-12.3.0-l7zpjxt
cmake/3.27.7-gcc-12.3.0-dukasmm
curl/8.4.0-gcc-12.3.0-u2ni6an
diffutils/3.9-gcc-12.3.0-sbfcnap
expat/2.5.0-gcc-12.3.0-grrt7ig
findutils/4.9.0-gcc-12.3.0-pdopgfr
gdbm/1.23-gcc-12.3.0-w66nich
gettext/0.22.3-gcc-12.3.0-y7ty4lo
gmake/4.4.1-gcc-12.3.0-6qiak7n
hwloc/2.9.1-gcc-12.3.0-rvotk5a
krb5/1.20.1-gcc-12.3.0-5d6b7ng
libbsd/0.11.7-gcc-12.3.0-sygavnw
libedit/3.1-20210216-gcc-12.3.0-fm2rgwy
libevent/2.1.12-gcc-12.3.0-3rudtaf
libfabric/1.19.0-gcc-12.3.0-46fsov7
libffi/3.4.4-gcc-12.3.0-ecpriyn
libiconv/1.17-gcc-12.3.0-a34xpad
libmd/1.0.4-gcc-12.3.0-ivvykht
libpciaccess/0.17-gcc-12.3.0-el7pkf4
libsigsegv/2.14-gcc-12.3.0-46vv5f3
libtool/2.4.7-gcc-12.3.0-hvedpuf
libxcrypt/4.4.35-gcc-12.3.0-guszc5m
libxml2/2.10.3-gcc-12.3.0-damyeos
m4/1.4.19-gcc-12.3.0-oebiztm
meson/1.2.2-gcc-12.3.0-htbkkj2
mpich/4.1.2-gcc-12.3.0-cxezwh7
ncurses/6.4-gcc-12.3.0-glwymee
netlib-lapack/3.11.0-gcc-12.3.0-4uab534
netlib-scalapack/2.2.0-gcc-12.3.0-f4bc72j
netlib-scalapack/2.2.0-gcc-12.3.0-klad7nj
netlib-scalapack/2.2.0-gcc-12.3.0-ve3uhz5
netlib-scalapack/2.2.0-gcc-12.3.0-3mwyatr (D)
nghttp2/1.57.0-gcc-12.3.0-dvtfejq
ninja/1.11.1-gcc-12.3.0-qf3fwcn
numactl/2.0.14-gcc-12.3.0-iiok6h4
openblas/0.3.24-gcc-12.3.0-qoggfi2
openmpi/4.1.6-gcc-12.3.0-cndwedm
openssh/9.5p1-gcc-12.3.0-6ksmdje
openssl/3.1.3-gcc-12.3.0-v7jc5lq
perl/5.38.0-gcc-12.3.0-hh6v2va
pigz/2.7-gcc-12.3.0-m7r2rmw
pkgconf/1.9.5-gcc-12.3.0-ccpwoda
pmix/5.0.1-gcc-12.3.0-tmm3jjd
py-beniget/0.4.1-gcc-12.3.0-fizom4w
py-cython/0.29.36-gcc-12.3.0-ylumqbe
py-flit-core/3.9.0-gcc-12.3.0-nzh222k
py-gast/0.5.3-gcc-12.3.0-h7hu6wn
py-meson-python/0.13.1-gcc-12.3.0-6zbxyin
py-numpy/1.26.1-gcc-12.3.0-4rqb2wc
py-packaging/23.1-gcc-12.3.0-7rj6npn
py-pip/23.1.2-gcc-12.3.0-lvdwpa6
py-ply/3.11-gcc-12.3.0-x3c55tr
py-pybind11/2.11.0-gcc-12.3.0-bo5zrbu
py-pyproject-metadata/0.7.1-gcc-12.3.0-bw34ifa
py-pythran/0.12.2-gcc-12.3.0-7fwfpfj
py-scipy/1.11.3-gcc-12.3.0-b6ldv5o
py-setuptools/68.0.0-gcc-12.3.0-crc6iaj
py-wheel/0.41.2-gcc-12.3.0-zwngepq
python/3.11.6-gcc-12.3.0-oa7j22b
re2c/2.2-gcc-12.3.0-cw5qvcn
readline/8.2-gcc-12.3.0-cz4lfdu
sqlite/3.43.2-gcc-12.3.0-p3srvwu
tar/1.34-gcc-12.3.0-waes7yx
util-linux-uuid/2.38.1-gcc-12.3.0-oagevhm
util-macros/1.19.3-gcc-12.3.0-t67cwmg
xz/5.4.1-gcc-12.3.0-taa3gkk
yaksa/0.3-gcc-12.3.0-hmywdkq
zlib-ng/2.1.4-gcc-12.3.0-draqwfy
zstd/1.5.5-gcc-12.3.0-ngvd73i
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".
if you look closely you’ll see though that we went too far in
excluding modules: the module for gcc@12.3.0 disappeared as it was
bootstrapped with gcc@11. To specify exceptions to the exclude
rules you can use include:
modules:
default:
tcl:
include:
- gcc
exclude:
- '%gcc@11'
all:
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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@12.3.0 has reappeared:
$ module avail gcc/
------------- /home/spack/spack/share/spack/modules/linux-ubuntu22.04-x86_64_v3 --------------
gcc/12.3.0-gcc-11.4.0-chmemdi
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'
all:
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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'
all:
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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-12.3.0
spec: netlib-scalapack@=2.2.0%gcc@=12.3.0/3mwyatr ~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@=12.3.0/f4bc72j ~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@=12.3.0/ve3uhz5 ~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@=12.3.0/klad7nj ~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'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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 ^python^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 provider
name 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 --------------
amdblis/4.1-gcc-12.3.0
autoconf/2.69-gcc-12.3.0
automake/1.16.5-gcc-12.3.0
berkeley-db/18.1.40-gcc-12.3.0
bison/3.8.2-gcc-12.3.0
bzip2/1.0.8-gcc-12.3.0
ca-certificates-mozilla/2023-05-30-gcc-12.3.0
cmake/3.27.7-gcc-12.3.0
curl/8.4.0-gcc-12.3.0
diffutils/3.9-gcc-12.3.0
expat/2.5.0-gcc-12.3.0
findutils/4.9.0-gcc-12.3.0
gcc/12.3.0-gcc-11.4.0
gdbm/1.23-gcc-12.3.0
gettext/0.22.3-gcc-12.3.0
gmake/4.4.1-gcc-12.3.0
hwloc/2.9.1-gcc-12.3.0
krb5/1.20.1-gcc-12.3.0
libbsd/0.11.7-gcc-12.3.0
libedit/3.1-20210216-gcc-12.3.0
libevent/2.1.12-gcc-12.3.0
libfabric/1.19.0-gcc-12.3.0
libffi/3.4.4-gcc-12.3.0
libiconv/1.17-gcc-12.3.0
libmd/1.0.4-gcc-12.3.0
libpciaccess/0.17-gcc-12.3.0
libsigsegv/2.14-gcc-12.3.0
libtool/2.4.7-gcc-12.3.0
libxcrypt/4.4.35-gcc-12.3.0
libxml2/2.10.3-gcc-12.3.0
m4/1.4.19-gcc-12.3.0
meson/1.2.2-gcc-12.3.0
mpich/4.1.2-gcc-12.3.0
ncurses/6.4-gcc-12.3.0
netlib-lapack/3.11.0-gcc-12.3.0
netlib-scalapack/2.2.0-gcc-12.3.0-netlib-lapack-mpich
netlib-scalapack/2.2.0-gcc-12.3.0-netlib-lapack-openmpi
netlib-scalapack/2.2.0-gcc-12.3.0-openblas-mpich
netlib-scalapack/2.2.0-gcc-12.3.0-openblas-openmpi (D)
nghttp2/1.57.0-gcc-12.3.0
ninja/1.11.1-gcc-12.3.0
numactl/2.0.14-gcc-12.3.0
openblas/0.3.24-gcc-12.3.0
openmpi/4.1.6-gcc-12.3.0
openssh/9.5p1-gcc-12.3.0
openssl/3.1.3-gcc-12.3.0
perl/5.38.0-gcc-12.3.0
pigz/2.7-gcc-12.3.0
pkgconf/1.9.5-gcc-12.3.0
pmix/5.0.1-gcc-12.3.0
py-beniget/0.4.1-gcc-12.3.0
py-cython/0.29.36-gcc-12.3.0
py-flit-core/3.9.0-gcc-12.3.0
py-gast/0.5.3-gcc-12.3.0
py-meson-python/0.13.1-gcc-12.3.0
py-numpy/1.26.1-gcc-12.3.0-openblas
py-packaging/23.1-gcc-12.3.0
py-pip/23.1.2-gcc-12.3.0
py-ply/3.11-gcc-12.3.0
py-pybind11/2.11.0-gcc-12.3.0
py-pyproject-metadata/0.7.1-gcc-12.3.0
py-pythran/0.12.2-gcc-12.3.0-openblas
py-scipy/1.11.3-gcc-12.3.0-openblas
py-setuptools/68.0.0-gcc-12.3.0
py-wheel/0.41.2-gcc-12.3.0
python/3.11.6-gcc-12.3.0
re2c/2.2-gcc-12.3.0
readline/8.2-gcc-12.3.0
sqlite/3.43.2-gcc-12.3.0
tar/1.34-gcc-12.3.0
util-linux-uuid/2.38.1-gcc-12.3.0
util-macros/1.19.3-gcc-12.3.0
xz/5.4.1-gcc-12.3.0
yaksa/0.3-gcc-12.3.0
zlib-ng/2.1.4-gcc-12.3.0
zstd/1.5.5-gcc-12.3.0
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'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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,architectureAny 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/12.3.0-gcc-11.4.0:
------------------------------------------------------------------------------------------
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-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/share/man")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw/.")
setenv("GCC_ROOT",""/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-11.4.0/gcc-12.3.0-chmemdiqoycjlxz2myvdxqzt5don54uw"")
append_path("MANPATH","")
help([[Name : gcc
Version: 12.3.0
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'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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/4.1.6-gcc-12.3.0:
------------------------------------------------------------------------------------------
whatis("An open source Message Passing Interface implementation.")
depends_on("hwloc/2.9.1-gcc-12.3.0")
depends_on("numactl/2.0.14-gcc-12.3.0")
depends_on("openssh/9.5p1-gcc-12.3.0")
depends_on("pmix/5.0.1-gcc-12.3.0")
depends_on("zlib-ng/2.1.4-gcc-12.3.0")
conflict("openmpi")
prepend_path("PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/bin")
prepend_path("MANPATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/share/man")
prepend_path("PKG_CONFIG_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/lib/pkgconfig")
prepend_path("CMAKE_PREFIX_PATH","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/.")
setenv("MPICC","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/bin/mpicc")
setenv("MPICXX","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/bin/mpic++")
setenv("MPIF77","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/bin/mpif77")
setenv("MPIF90","/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix/bin/mpif90")
setenv("OPENMPI_ROOT",""/home/spack/spack/opt/spack/linux-ubuntu22.04-x86_64_v3/gcc-12.3.0/openmpi-4.1.6-cndwedmmdi6vycttha5zw7yrvn7cgeix"")
setenv("SLURM_MPI_TYPE","pmi2")
setenv("OMPI_MCA_btl_openib_warn_default_git_prefix","0")
append_path("MANPATH","")
help([[Name : openmpi
Version: 4.1.6
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'
all:
conflict:
- '{name}'
filter:
exclude_env_vars:
- "CC"
- "CXX"
- "FC"
- "F77"
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}'
^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 --------------
amdblis/4.1-gcc-12.3.0
autoconf/2.69-gcc-12.3.0
automake/1.16.5-gcc-12.3.0
berkeley-db/18.1.40-gcc-12.3.0
bison/3.8.2-gcc-12.3.0
bzip2/1.0.8-gcc-12.3.0
ca-certificates-mozilla/2023-05-30-gcc-12.3.0
cmake/3.27.7-gcc-12.3.0
curl/8.4.0-gcc-12.3.0
diffutils/3.9-gcc-12.3.0
expat/2.5.0-gcc-12.3.0
findutils/4.9.0-gcc-12.3.0
gcc/12.3.0-gcc-11.4.0
gdbm/1.23-gcc-12.3.0
gettext/0.22.3-gcc-12.3.0
gmake/4.4.1-gcc-12.3.0
hwloc/2.9.1-gcc-12.3.0
krb5/1.20.1-gcc-12.3.0
libbsd/0.11.7-gcc-12.3.0
libedit/3.1-20210216-gcc-12.3.0
libevent/2.1.12-gcc-12.3.0
libfabric/1.19.0-gcc-12.3.0
libffi/3.4.4-gcc-12.3.0
libiconv/1.17-gcc-12.3.0
libmd/1.0.4-gcc-12.3.0
libpciaccess/0.17-gcc-12.3.0
libsigsegv/2.14-gcc-12.3.0
libtool/2.4.7-gcc-12.3.0
libxcrypt/4.4.35-gcc-12.3.0
libxml2/2.10.3-gcc-12.3.0
m4/1.4.19-gcc-12.3.0
meson/1.2.2-gcc-12.3.0
mpich/4.1.2-gcc-12.3.0
ncurses/6.4-gcc-12.3.0
netlib-lapack/3.11.0-gcc-12.3.0
netlib-scalapack/2.2.0-gcc-12.3.0-netlib-lapack-mpich
netlib-scalapack/2.2.0-gcc-12.3.0-netlib-lapack-openmpi
netlib-scalapack/2.2.0-gcc-12.3.0-openblas-mpich
netlib-scalapack/2.2.0-gcc-12.3.0-openblas-openmpi (D)
nghttp2/1.57.0-gcc-12.3.0
ninja/1.11.1-gcc-12.3.0
numactl/2.0.14-gcc-12.3.0
openblas/0.3.24-gcc-12.3.0
openmpi/4.1.6-gcc-12.3.0
openssh/9.5p1-gcc-12.3.0
openssl/3.1.3-gcc-12.3.0
perl/5.38.0-gcc-12.3.0
pigz/2.7-gcc-12.3.0
pkgconf/1.9.5-gcc-12.3.0
pmix/5.0.1-gcc-12.3.0
py-beniget/0.4.1-gcc-12.3.0
py-cython/0.29.36-gcc-12.3.0
py-flit-core/3.9.0-gcc-12.3.0
py-gast/0.5.3-gcc-12.3.0
py-meson-python/0.13.1-gcc-12.3.0
py-numpy/1.26.1-gcc-12.3.0-openblas
py-packaging/23.1-gcc-12.3.0
py-pip/23.1.2-gcc-12.3.0
py-ply/3.11-gcc-12.3.0
py-pybind11/2.11.0-gcc-12.3.0
py-pyproject-metadata/0.7.1-gcc-12.3.0
py-pythran/0.12.2-gcc-12.3.0-openblas
py-scipy/1.11.3-gcc-12.3.0-openblas
py-setuptools/68.0.0-gcc-12.3.0
py-wheel/0.41.2-gcc-12.3.0
python/3.11.6-gcc-12.3.0
re2c/2.2-gcc-12.3.0
readline/8.2-gcc-12.3.0
sqlite/3.43.2-gcc-12.3.0
tar/1.34-gcc-12.3.0
util-linux-uuid/2.38.1-gcc-12.3.0
util-macros/1.19.3-gcc-12.3.0
xz/5.4.1-gcc-12.3.0
yaksa/0.3-gcc-12.3.0
zlib-ng/2.1.4-gcc-12.3.0
zstd/1.5.5-gcc-12.3.0
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-12.3.0 2) openblas/0.3.24-gcc-12.3.0
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
lmodfile generatorchange the
tcltag tolmodremove the
tclspecificconflictdirectivedeclare which compilers are considered
core_compilersremove 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'
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 --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 mpc/1.3.1 zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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/12.3.0 -----------
amdblis/4.1 numactl/2.0.14
autoconf/2.69 (D) openblas/0.3.24
automake/1.16.5 (D) openmpi/4.1.6
berkeley-db/18.1.40 (D) openssh/9.5p1
bison/3.8.2 openssl/3.1.3 (D)
bzip2/1.0.8 (D) perl/5.38.0 (D)
ca-certificates-mozilla/2023-05-30 (D) pigz/2.7 (D)
cmake/3.27.7 pkgconf/1.9.5 (D)
curl/8.4.0 (D) pmix/5.0.1
diffutils/3.9 (D) py-beniget/0.4.1
expat/2.5.0 py-cython/0.29.36
findutils/4.9.0 py-flit-core/3.9.0
gdbm/1.23 (D) py-gast/0.5.3
gettext/0.22.3 (D) py-meson-python/0.13.1
gmake/4.4.1 (D) py-numpy/1.26.1-openblas
hwloc/2.9.1 py-packaging/23.1
krb5/1.20.1 py-pip/23.1.2
libbsd/0.11.7 py-ply/3.11
libedit/3.1-20210216 py-pybind11/2.11.0
libevent/2.1.12 py-pyproject-metadata/0.7.1
libfabric/1.19.0 py-pythran/0.12.2-openblas
libffi/3.4.4 py-scipy/1.11.3-openblas
libiconv/1.17 (D) py-setuptools/68.0.0
libmd/1.0.4 py-wheel/0.41.2
libpciaccess/0.17 python/3.11.6
libsigsegv/2.14 (D) re2c/2.2
libtool/2.4.7 (D) readline/8.2 (D)
libxcrypt/4.4.35 sqlite/3.43.2
libxml2/2.10.3 (D) tar/1.34 (D)
m4/1.4.19 (D) util-linux-uuid/2.38.1
meson/1.2.2 util-macros/1.19.3
mpich/4.1.2 xz/5.4.1 (D)
ncurses/6.4 (D) yaksa/0.3
netlib-lapack/3.11.0 zlib-ng/2.1.4 (L,D)
nghttp2/1.57.0 (D) zstd/1.5.5 (L,D)
ninja/1.11.1
-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 (L) openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 (L) mpc/1.3.1 (L) zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 (L) zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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".
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/4.1.2-cxezwh7/gcc/12.3.0 ----
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/12.3.0 -----------
amdblis/4.1 numactl/2.0.14
autoconf/2.69 (D) openblas/0.3.24
automake/1.16.5 (D) openmpi/4.1.6
berkeley-db/18.1.40 (D) openssh/9.5p1
bison/3.8.2 openssl/3.1.3 (D)
bzip2/1.0.8 (D) perl/5.38.0 (D)
ca-certificates-mozilla/2023-05-30 (D) pigz/2.7 (D)
cmake/3.27.7 pkgconf/1.9.5 (D)
curl/8.4.0 (D) pmix/5.0.1
diffutils/3.9 (D) py-beniget/0.4.1
expat/2.5.0 py-cython/0.29.36
findutils/4.9.0 py-flit-core/3.9.0
gdbm/1.23 (D) py-gast/0.5.3
gettext/0.22.3 (D) py-meson-python/0.13.1
gmake/4.4.1 (D) py-numpy/1.26.1-openblas
hwloc/2.9.1 (L) py-packaging/23.1
krb5/1.20.1 py-pip/23.1.2
libbsd/0.11.7 py-ply/3.11
libedit/3.1-20210216 py-pybind11/2.11.0
libevent/2.1.12 py-pyproject-metadata/0.7.1
libfabric/1.19.0 (L) py-pythran/0.12.2-openblas
libffi/3.4.4 py-scipy/1.11.3-openblas
libiconv/1.17 (L,D) py-setuptools/68.0.0
libmd/1.0.4 py-wheel/0.41.2
libpciaccess/0.17 (L) python/3.11.6
libsigsegv/2.14 (D) re2c/2.2
libtool/2.4.7 (D) readline/8.2 (D)
libxcrypt/4.4.35 sqlite/3.43.2
libxml2/2.10.3 (L,D) tar/1.34 (D)
m4/1.4.19 (D) util-linux-uuid/2.38.1
meson/1.2.2 util-macros/1.19.3
mpich/4.1.2 (L) xz/5.4.1 (L,D)
ncurses/6.4 (L,D) yaksa/0.3 (L)
netlib-lapack/3.11.0 zlib-ng/2.1.4 (L,D)
nghttp2/1.57.0 (D) zstd/1.5.5 (L,D)
ninja/1.11.1
-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 (L) openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 (L) mpc/1.3.1 (L) zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 (L) zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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) gmp/6.2.1 7) libpciaccess/0.17 13) libfabric/1.19.0
2) mpfr/4.2.0 8) libiconv/1.17 14) yaksa/0.3
3) mpc/1.3.1 9) xz/5.4.1 15) mpich/4.1.2
4) zlib-ng/2.1.4 10) libxml2/2.10.3 16) openblas/0.3.24
5) zstd/1.5.5 11) ncurses/6.4 17) netlib-scalapack/2.2.0-openblas
6) gcc/12.3.0 12) hwloc/2.9.1
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/4.1.2" with "openmpi/4.1.6".
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) gmp/6.2.1 10) xz/5.4.1 19) openssl/3.1.3
2) mpfr/4.2.0 11) libxml2/2.10.3 20) krb5/1.20.1
3) mpc/1.3.1 12) ncurses/6.4 21) libedit/3.1-20210216
4) zlib-ng/2.1.4 13) hwloc/2.9.1 22) libxcrypt/4.4.35
5) zstd/1.5.5 14) numactl/2.0.14 23) openssh/9.5p1
6) gcc/12.3.0 15) bzip2/1.0.8 24) libevent/2.1.12
7) openblas/0.3.24 16) pigz/2.7 25) pmix/5.0.1
8) libpciaccess/0.17 17) tar/1.34 26) openmpi/4.1.6
9) libiconv/1.17 18) gettext/0.22.3 27) netlib-scalapack/2.2.0-openblas
$ module avail
---- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openmpi/4.1.6-cndwedm/gcc/12.3.0 ----
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/12.3.0 -----------
amdblis/4.1 numactl/2.0.14 (L)
autoconf/2.69 (D) openblas/0.3.24 (L)
automake/1.16.5 (D) openmpi/4.1.6 (L)
berkeley-db/18.1.40 (D) openssh/9.5p1 (L)
bison/3.8.2 openssl/3.1.3 (L,D)
bzip2/1.0.8 (L,D) perl/5.38.0 (D)
ca-certificates-mozilla/2023-05-30 (D) pigz/2.7 (L,D)
cmake/3.27.7 pkgconf/1.9.5 (D)
curl/8.4.0 (D) pmix/5.0.1 (L)
diffutils/3.9 (D) py-beniget/0.4.1
expat/2.5.0 py-cython/0.29.36
findutils/4.9.0 py-flit-core/3.9.0
gdbm/1.23 (D) py-gast/0.5.3
gettext/0.22.3 (L,D) py-meson-python/0.13.1
gmake/4.4.1 (D) py-numpy/1.26.1-openblas
hwloc/2.9.1 (L) py-packaging/23.1
krb5/1.20.1 (L) py-pip/23.1.2
libbsd/0.11.7 py-ply/3.11
libedit/3.1-20210216 (L) py-pybind11/2.11.0
libevent/2.1.12 (L) py-pyproject-metadata/0.7.1
libfabric/1.19.0 py-pythran/0.12.2-openblas
libffi/3.4.4 py-scipy/1.11.3-openblas
libiconv/1.17 (L,D) py-setuptools/68.0.0
libmd/1.0.4 py-wheel/0.41.2
libpciaccess/0.17 (L) python/3.11.6
libsigsegv/2.14 (D) re2c/2.2
libtool/2.4.7 (D) readline/8.2 (D)
libxcrypt/4.4.35 (L) sqlite/3.43.2
libxml2/2.10.3 (L,D) tar/1.34 (L,D)
m4/1.4.19 (D) util-linux-uuid/2.38.1
meson/1.2.2 util-macros/1.19.3
mpich/4.1.2 xz/5.4.1 (L,D)
ncurses/6.4 (L,D) yaksa/0.3
netlib-lapack/3.11.0 zlib-ng/2.1.4 (L,D)
nghttp2/1.57.0 (D) zstd/1.5.5 (L,D)
ninja/1.11.1
-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 (L) openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 (L) mpc/1.3.1 (L) zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 (L) zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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) gmp/6.2.1 14) numactl/2.0.14 27) libmd/1.0.4
2) mpfr/4.2.0 15) bzip2/1.0.8 28) libbsd/0.11.7
3) mpc/1.3.1 16) pigz/2.7 29) expat/2.5.0
4) zlib-ng/2.1.4 17) tar/1.34 30) readline/8.2
5) zstd/1.5.5 18) gettext/0.22.3 31) gdbm/1.23
6) gcc/12.3.0 19) openssl/3.1.3 32) libffi/3.4.4
7) openblas/0.3.24 20) krb5/1.20.1 33) sqlite/3.43.2
8) libpciaccess/0.17 21) libedit/3.1-20210216 34) util-linux-uuid/2.38.1
9) libiconv/1.17 22) libxcrypt/4.4.35 35) python/3.11.6
10) xz/5.4.1 23) openssh/9.5p1 36) amdblis/4.1
11) libxml2/2.10.3 24) libevent/2.1.12 37) netlib-lapack/3.11.0
12) ncurses/6.4 25) pmix/5.0.1 38) netlib-scalapack/2.2.0-netlib-lapack
13) hwloc/2.9.1 26) openmpi/4.1.6
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
MPIorLAPACKSoftware that depends only on
MPISoftware that depends only on
LAPACKSoftware 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'
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/0.3.24" 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/0.3.24".
Activating Modules:
1) openblas/0.3.24
$ module avail
---- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openmpi/4.1.6-cndwedm/openblas/0.3.24-qoggfi2/gcc/12.3.0 ----
netlib-scalapack/2.2.0
---- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openblas/0.3.24-qoggfi2/gcc/12.3.0 ----
py-numpy/1.26.1 py-pythran/0.12.2 py-scipy/1.11.3
----------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.3.0 -----------
amdblis/4.1 (L) nghttp2/1.57.0 (D)
autoconf/2.69 (D) ninja/1.11.1
automake/1.16.5 (D) numactl/2.0.14 (L)
berkeley-db/18.1.40 (D) openblas/0.3.24 (L)
bison/3.8.2 openmpi/4.1.6 (L)
bzip2/1.0.8 (L,D) openssh/9.5p1 (L)
ca-certificates-mozilla/2023-05-30 (D) openssl/3.1.3 (L,D)
cmake/3.27.7 perl/5.38.0 (D)
curl/8.4.0 (D) pigz/2.7 (L,D)
diffutils/3.9 (D) pkgconf/1.9.5 (D)
expat/2.5.0 (L) pmix/5.0.1 (L)
findutils/4.9.0 py-beniget/0.4.1
gdbm/1.23 (L,D) py-cython/0.29.36
gettext/0.22.3 (L,D) py-flit-core/3.9.0
gmake/4.4.1 (D) py-gast/0.5.3
hwloc/2.9.1 (L) py-meson-python/0.13.1
krb5/1.20.1 (L) py-packaging/23.1
libbsd/0.11.7 (L) py-pip/23.1.2
libedit/3.1-20210216 (L) py-ply/3.11
libevent/2.1.12 (L) py-pybind11/2.11.0
libfabric/1.19.0 py-pyproject-metadata/0.7.1
libffi/3.4.4 (L) py-setuptools/68.0.0
libiconv/1.17 (L,D) py-wheel/0.41.2
libmd/1.0.4 (L) python/3.11.6 (L)
libpciaccess/0.17 (L) re2c/2.2
libsigsegv/2.14 (D) readline/8.2 (L,D)
libtool/2.4.7 (D) sqlite/3.43.2 (L)
libxcrypt/4.4.35 (L) tar/1.34 (L,D)
libxml2/2.10.3 (L,D) util-linux-uuid/2.38.1 (L)
m4/1.4.19 (D) util-macros/1.19.3
meson/1.2.2 xz/5.4.1 (L,D)
mpich/4.1.2 yaksa/0.3
ncurses/6.4 (L,D) zlib-ng/2.1.4 (L,D)
netlib-lapack/3.11.0 zstd/1.5.5 (L,D)
-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 (L) openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 (L) mpc/1.3.1 (L) zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 (L) zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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 openmpi
$ module avail
---- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openmpi/4.1.6-cndwedm/openblas/0.3.24-qoggfi2/gcc/12.3.0 ----
netlib-scalapack/2.2.0
---- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/openblas/0.3.24-qoggfi2/gcc/12.3.0 ----
py-numpy/1.26.1 py-pythran/0.12.2 py-scipy/1.11.3
----------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/gcc/12.3.0 -----------
amdblis/4.1 (L) nghttp2/1.57.0 (D)
autoconf/2.69 (D) ninja/1.11.1
automake/1.16.5 (D) numactl/2.0.14 (L)
berkeley-db/18.1.40 (D) openblas/0.3.24 (L)
bison/3.8.2 openmpi/4.1.6 (L)
bzip2/1.0.8 (L,D) openssh/9.5p1 (L)
ca-certificates-mozilla/2023-05-30 (D) openssl/3.1.3 (L,D)
cmake/3.27.7 perl/5.38.0 (D)
curl/8.4.0 (D) pigz/2.7 (L,D)
diffutils/3.9 (D) pkgconf/1.9.5 (D)
expat/2.5.0 (L) pmix/5.0.1 (L)
findutils/4.9.0 py-beniget/0.4.1
gdbm/1.23 (L,D) py-cython/0.29.36
gettext/0.22.3 (L,D) py-flit-core/3.9.0
gmake/4.4.1 (D) py-gast/0.5.3
hwloc/2.9.1 (L) py-meson-python/0.13.1
krb5/1.20.1 (L) py-packaging/23.1
libbsd/0.11.7 (L) py-pip/23.1.2
libedit/3.1-20210216 (L) py-ply/3.11
libevent/2.1.12 (L) py-pybind11/2.11.0
libfabric/1.19.0 py-pyproject-metadata/0.7.1
libffi/3.4.4 (L) py-setuptools/68.0.0
libiconv/1.17 (L,D) py-wheel/0.41.2
libmd/1.0.4 (L) python/3.11.6 (L)
libpciaccess/0.17 (L) re2c/2.2
libsigsegv/2.14 (D) readline/8.2 (L,D)
libtool/2.4.7 (D) sqlite/3.43.2 (L)
libxcrypt/4.4.35 (L) tar/1.34 (L,D)
libxml2/2.10.3 (L,D) util-linux-uuid/2.38.1 (L)
m4/1.4.19 (D) util-macros/1.19.3
meson/1.2.2 xz/5.4.1 (L,D)
mpich/4.1.2 yaksa/0.3
ncurses/6.4 (L,D) zlib-ng/2.1.4 (L,D)
netlib-lapack/3.11.0 zstd/1.5.5 (L,D)
-------------- /home/spack/spack/share/spack/lmod/linux-ubuntu22.04-x86_64/Core --------------
autoconf-archive/2023.02.20 gmake/4.4.1 nghttp2/1.57.0
autoconf/2.69 gmp/6.2.1 (L) openssl/3.1.3
automake/1.16.5 libiconv/1.17 perl/5.38.0
bc/1.07.1 libsigsegv/2.14 pigz/2.7
berkeley-db/18.1.40 libtool/2.4.7 pkgconf/1.9.5
bzip2/1.0.8 libxml2/2.10.3 readline/8.2
ca-certificates-mozilla/2023-05-30 lmod/8.7.18 tar/1.34
curl/8.4.0 lua-luafilesystem/1.8.0 tcl/8.6.12
diffutils/3.9 lua-luaposix/36.1 texinfo/7.0.3
ed/1.4 lua/5.4.4 unzip/6.0
gawk/5.2.2 m4/1.4.19 xz/5.4.1
gcc/12.3.0 (L) mpc/1.3.1 (L) zlib-ng/2.1.4
gdbm/1.23 mpfr/4.2.0 (L) zstd/1.5.5
gettext/0.22.3 ncurses/6.4
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".
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/4.1.6" with "mpich/4.1.2".
Due to MODULEPATH changes, the following have been reloaded:
1) netlib-scalapack/2.2.0
$ module load netlib-lapack
Lmod is automatically replacing "openblas/0.3.24" with "netlib-lapack/3.11.0".
Inactive Modules:
1) py-numpy
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:
{% block conflict %}
{% for name in conflicts %}
conflict("{{ name }}")
{% endfor %}
{% endblock %}
{% block environment %}
{% for command_name, cmd in environment_modifications %}
{% if command_name == 'PrependPath' %}
prepend_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name in ('AppendPath', 'AppendFlagsEnv') %}
append_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name in ('RemovePath', 'RemoveFlagsEnv') %}
remove_path("{{ cmd.name }}", "{{ cmd.value }}", "{{ cmd.separator }}")
{% elif command_name == 'SetEnv' %}
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'
- 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@12.3.0
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@12.3.0
This will ensure the rest of the tutorial goes smoothly for you.