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Loading the spack module available on the cluster

When you connect to a Cineca cluster "preprod" and "prod" spack modules are available. The pre-production module should only be used when any production module of spack is not available.

$ module av spack 
$ module load spack/<version>

By loading the spack module, the setup-env.sh file is sourced. 

Then $SPACK_ROOT is initialised, the spack command is added to your PATH and some nice command line integration tools too.

The folder $USER/spack-<version> is created into your "default" $WORK space ("chprj -l" command to see the default work) and it contains some subfolders created and used by spack during the phase of the packages installation:

  • sources cache: $WORK/$USER/spack-<version>/cache
  • software installation root: $WORK/$USER/spack-<version>/install
  • modulefiles location: $WORK/$USER/spack-<version>/modulefiles
  • user scope:  $WORK/$USER/spack-<version>/user_cache

Remember that $WORK space will be removed at the end of the corresponding project. If you want to define different paths for cache, installation, modules and user scope directories refer to spack manual.

Listing the software packages available to be installed

Check if the software package you want install is available via spack.

$ spack list <pack name> or
$ spack list|grep <pattername>

Providers

Multiple specific packages (e.g. intel-oneapi-mpi, openmpi,...) are able to provide a generic package called “virtual package” (e.g. mpi).  List the available virtual packages

$ spack providers


List the real packages that are able to provide a specific virtual package (e.g. intel-oneapi-mpi and openmpi packages provide “mpi” virtual package , netlib-lapack and openblas provide “lapack” virtual package)

$ spack providers <virtual package>
e.g $ spack providers mpi

Variants an dependencies

If the package of your interest is available to be installed via spack, look at its build “variants” yon can switch in/off or customize and  the  “dependencies” that will be used for the building, linking and running phases and you are able to personalize.

$ spack info <package name>

Listing the software packages installed from Cineca staff with the spack module

Cineca staff has already installed through the spack module that you loaded  a suite of compilers, libraries, tools and applications and you can use them to install additional software (it is strongly recommended). List the packages already installed

$ spack find


Check if a specific package is already installed or what packages have been already installed to provide a specific virtual package (e.g mpi)

$ spack find <package name>  
$ spack find <virtual package name>  (e.g mpi)


List the packages already installed  and see the used variants (-v) and depedencies (-d), without and with the hash (-l)(*)

$ spack find -v <package>
$ spack find -lv <package>
$ spack find -ld <package>

List the packages already installed with their installation path

$ spack find -lp 

List the packages already installed with a specific variant

$ spack find -l +<variant>
e.g. spack find -l +cuda

List the packages already installed and that depend on a specific package (e.g openmpi) or a generic virtual package (e.g. mpi)

$ spack find -l ^<package name>
e.g. spack find -l ^openmpi
e.g. spack find -l ^mpi

List the compilers already installed and ready to be used and the packages installed with a specific compiler

$ spack compilers
$ spack find %<compiler>

(*) What is the hash is explained in the next paragraph.

Installing a new package

Spec command

In order to install a package with the spack module you have to select for it a version, a compiler, the dependencies and the building variants (we’ll see how to do it in the next paragraphes) .

The combination of all these parameters is the "spec "with which the package will be installed.

If you don’t select any combination a default spec is selected from spack and you can know it  by “spack spec” command to be launched before executing “spack install”.

See the default spec with which a package is installed

$ spack spec <pack name>


Each spec is identified by a unique number (e.g. aouyzha), named “hash” and displayed by “-l” (long) option that distinguishes the several installations of a same package  

See the hash number for all the installation of a specific package

$ spack spec -l <pack name>


# Example: see the different hash for openmpi%intel and openmpi%gcc
$ spack spec -l openmpi %intel
aouyzha  openmpi@4.1.1%intel@2021.4.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake
$ spack spec -l openmpi %gcc
2ovg6ub  openmpi@4.1.1%gcc@10.2.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake



The "spec" command also  shows the installation status of the requested package and its dependencies if you use the " -I" (install) option.

See the hash and install status of the selected packages and its dependencies 

$ spack spec -Il <pack name>


# Example: see hash and installing status of openmpi and its cuda dependency
$ spack spec -Il openmpi
-   aouyzha openmpi@4.1.1%intel@2021.4.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake
  [-]  rdd7huh      ^cuda@11.5.0%intel@2021.4.0~dev arch=linux-centos8-cascadelake


The symbol “-” (not installed) or “+/^” (installed/installed from an other user) displayed by -I  option and that precedes the hash of the spec indicates if that spec is already installed.

 If the dependency spec (e.g. cuda) of the selected package (e.g openmpi) is not installed (-), it will be by default from spack during the installation of the selected package. The dependency spec installed by default from spack to meet  the building requirement of the selected pack is called “implicit” installation, the selected pack “explicit” installation.

On Cineca clusters it’s recommended to execute always “spec” command before installing a package to make sure its dependencies are fullfilled by the cineca installations (^) if they are available. The cineca installations are optimised and tested for the architecture of the specific cluster.

If a dependency is not fullfilled by the cineca installation even if it is available, it shows “-” symbol and it will be installed with a different hash because it's a different spec.

In the following example openmpi dependency is not fullfilled by the cineca installation (-) even if it is already available with a specific hash as the "spack find -l openmpi"  command  shows. This means that Openmpi will be installed again from spack with a different combination of building values and consequently with a different hash (aouyzha). In order to use the cineca openmpi installation you would have to provide its spec to spack, for example through the hash that  “spack find -l openmpi ”command shows

$ spack find -l openmpi
==> 1 installed package
-- linux-centos8-cascadelake / gcc@10.2.0 -----------------------
ov3ei7j openmpi@4.1.1

# Example: parmetis will be installed with a spec of openmpi that has not been installed from Cineca staff (-)
$ spack spec -Il parmetis %gcc@10.2.0 ^openmpi
-   oytpej7  parmetis@4.0.3%gcc@10.2.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d arch=linux-centos8-cascadelake
  [-]      aouyzha   ^openmpi@4.1.1%gcc@10.2.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake


# Example: parmetis will be installed with the spec installed from Cineca staff defined by the hash "ov3ei7j" as the command "spack find -l openmpi" shows
$ spack spec -Il parmetis %gcc@10.2.0 ^/ov3ei7j
-   oefbg6x  parmetis@4.0.3%gcc@10.2.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d arch=linux-centos8-cascadelake
 [^]      ov3ei7j      ^openmpi@4.1.1%gcc@10.2.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake


Prova

# Example: parmetis will be installed with the spec installed from Cineca staff defined by the hash "ov3ei7j" as the command "spack find -l openmpi" shows
spack spec -Il parmetis %gcc@10.2.0 ^/ov3ei7j
-   oefbg6x  parmetis@4.0.3%gcc@10.2.0~gdb~int64~ipo+shared build_type=RelWithDebInfo patches=4f892531eb0a807eb1b82e683a416d3e35154a455274cf9b162fb02054d11a5b,50ed2081bc939269689789942067c58b3e522c269269a430d5d34c00edbc5870,704b84f7c7444d4372cb59cca6e1209df4ef3b033bc4ee3cf50f369bce972a9d arch=linux-centos8-cascadelake
 [^]      ov3ei7j      ^openmpi@4.1.1%gcc@10.2.0~atomics+cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker~pmi+pmix~singularity~sqlite3+static~thread_multiple+vt+wrapper-rpath fabrics=ucx schedulers=slurm arch=linux-centos8-cascadelake

Install command

For a specific package you can install the default spec  or a custom spec by selecting a specific version (through @ symbol), and/or a specific compiler (through % symbol), building variants (through +,-,= symbols) and specific dependencies (through ^ symbol).

# default package installation

$ spack install <package>


# custom package installation

$ spack install <package>@<version> +/-/<variant> <variant>=<value> %<compiler>@<version> ^<dependency name>

or

$ spack install <package>@<version> +/-/<variant> <variant>=<value> %<compiler>@<version> ^/<dependency hash>


The available versions of the package, the building variants and the dependencies that you can customise you can find them by executing the command "spack info <package name>", as described in previous chapters.

The command "spack compilers" shows all the compilers you can use for your installation and "spack find -l" all the dependencies installed from Cineca staff with their hash.

Remember to install the new package after executing “spack spec” command as described previously and use the cineca installations for the dependencies if they are available.

If you installed a new compiler, in order to use it remember to add it to your “compilers.yaml” file in the following way:

$ spack install <compiler_package>
$ spack load <compiler_package>
$ spack compiler add
$ spack compilers

Module command

After installing a package you can use it as module.

# To create the modulefile of your installation

$ spack module tcl refresh --upstream-modules <pack name> or
$ spack module tcl refresh --upstream-modules /<spec hash>


# To use the created modulefile

$ module load spack
$ module av <package module>
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