8. Maintainers/Developers Section

8.1. Pre-configuring sites

8.1.1. Preface/general instructions

Preconfigured sites are defined through spack configuration files in the spack-stack directory configs/sites, for example configs/sites/orion. All files in the site-specific subdirectory will be copied into the environment into envs/env-name/site. Site-specific configurations consist of general definitions (config.yaml), packages (packages.yaml), compilers (compilers.yaml), modules (modules.yaml), mirrors (mirrors.yaml) etc. These configurations overwrite the common configurations that are copied from configs/common into envs/env-name/common.

The instructions below are platform-specific tasks that only need to be done once and can be reused for new spack environments. To build new environments on preconfigured platforms, follow the instructions in Section 2.1.1.

8.1.2. MSU Orion

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, and loading the following modules, follow the instructions in Section 5.1.4. Note that the default/system qt@5 can be used on Orion.

module purge
module use /work/noaa/da/jedipara/spack-stack/modulefiles
module load miniconda/3.9.7
module load cmake/3.22.1
module load gcc/10.2.0

8.1.3. NASA Discover

On Discover, miniconda, qt, and ecflow need to be installed as a one-off before spack can be used. When using the GNU compiler, it is also necessary to build your own openmpi or other MPI library, which requires adapting the installation to the network hardware and slurm scheduler.

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

qt (qt@5)

The default qt@5 in /usr is incomplete and thus insufficient for building ecflow. After loading/unloading the modules as shown below, refer to Section 5.1.3 to install qt@5.15.2 in /discover/swdev/jcsda/spack-stack/qt-5.15.2.

ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, qt5, and loading the following modules, follow the instructions in Section 5.1.4.

module purge
module use /discover/swdev/jcsda/spack-stack/modulefiles
module load miniconda/3.9.7
module load cmake/3.21.0
module load qt/5.15.2
module load comp/gcc/10.1.0
openmpi

Installing openmpi requires adapting the installation to the network hardware and slurm scheduler. It is easier to build and test openmpi manually and use it as an external package, instead of building it as part of spack-stack. These instructions were used to build the openmpi@4.1.3 MPI library with gcc@10.1.0 as referenced in the Discover site config. After the installation, create modulefile openmpi/4.1.3-gcc-10.1.0 using the template doc/modulefile_templates/openmpi. Note the site-specific module settings at the end of the template, this will likely be different for other HPCs.

module purge
module use /discover/swdev/jcsda/spack-stack/modulefiles
module load miniconda/3.9.7
module load comp/gcc/10.1.0
CPATH="/usr/include/slurm:$CPATH" ./configure \
    --prefix=/discover/swdev/jcsda/spack-stack/openmpi-4.1.3/gcc-10.1.0/ \
    --with-pmi=/usr/slurm \
    --with-ucx \
    --without-ofi \
    --without-verbs \
    --with-gpfs
CPATH="/usr/include/slurm:$CPATH" make VERBOSE=1 -j4
CPATH="/usr/include/slurm:$CPATH" make check
CPATH="/usr/include/slurm:$CPATH" make install

8.1.5. NCAR-Wyoming Casper

Casper is co-located with Cheyenne and shares the parallel filesystem /glade and more with it. It is, however, a different operating system with a somewhat different software stack. spack-stack was installed on Casper after it was installed on Cheyenne, and prerequisites from Cheyenne were reused where possible (miniconda, qt, ecflow). See below for information on how to install these packages.

8.1.6. NCAR-Wyoming Cheyenne

On Cheyenne, a workaround is needed to avoid the modules provided by CISL take precedence over the spack modules. The default module path for compilers is removed, the module path is set to a different location and that location is then loaded into the module environment. If new compilers or MPI libraries are added to /glade/u/apps/ch/modulefiles/default/compilers by CISL, the spack-stack maintainers need to make the corresponding changes in /glade/work/jedipara/cheyenne/spack-stack/modulefiles/compilers. See Section 3.1.6 for details.

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Because of the workaround for the compilers, the miniconda module should be placed in /glade/work/jedipara/cheyenne/spack-stack/misc. Don’t forget to log off and back on to forget about the conda environment.

qt (qt@5)

The default qt@5 in /usr is incomplete and thus insufficient for building ecflow. After loading/unloading the modules as shown below, refer to Section 5.1.3 to install qt@5.15.2 in /glade/work/jedipara/cheyenne/spack-stack/qt-5.15.2. Because of the workaround for the compilers, the qt module should be placed in /glade/work/jedipara/cheyenne/spack-stack/misc.

module purge
module unuse /glade/u/apps/ch/modulefiles/default/compilers
export MODULEPATH_ROOT=/glade/work/jedipara/cheyenne/spack-stack/modulefiles
module use /glade/work/jedipara/cheyenne/spack-stack/modulefiles/compilers
module load gnu/10.1.0
ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, qt5, and loading the following modules, follow the instructions in Section 5.1.4. Because of the workaround for the compilers, the qt module should be placed in /glade/work/jedipara/cheyenne/spack-stack/misc. Also, because of the dependency on miniconda, that module must be loaded automatically in the ecflow module (similar to qt@5.15.2).

module purge
module unuse /glade/u/apps/ch/modulefiles/default/compilers
export MODULEPATH_ROOT=/glade/work/jedipara/cheyenne/spack-stack/modulefiles
module use /glade/work/jedipara/cheyenne/spack-stack/modulefiles/compilers
module use /glade/work/jedipara/cheyenne/spack-stack/modulefiles/misc
module load gnu/10.1.0
module load miniconda/3.9.12
module load qt/5.15.2
module load cmake/3.18.2

8.1.7. NOAA NCO WCOSS2

WORK IN PROGRESS

8.1.8. NOAA Parallel Works (AWS, Azure, Gcloud)

WORK IN PROGRESS

8.1.9. NOAA RDHPCS Gaea

On Gaea, miniconda, qt, and ecflow need to be installed as a one-off before spack can be used.

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment. Use the following workaround to avoid the terminal being spammed by error messages about missing version information (/bin/bash: /lustre/f2/pdata/esrl/gsd/spack-stack/miniconda-3.9.12/lib/libtinfo.so.6: no version information available (required by /lib64/libreadline.so.7)):

cd /lustre/f2/pdata/esrl/gsd/spack-stack/miniconda-3.9.12/lib
mv libtinfow.so.6.3 libtinfow.so.6.3.conda.original
ln -sf /lib64/libtinfo.so.6 libtinfow.so.6.3
qt (qt@5)

The default qt@5 in /usr is incomplete and thus insufficient for building ecflow. After loading/unloading the modules as shown below, refer to Section 5.1.3 to install qt@5.15.2 in /lustre/f2/pdata/esrl/gsd/spack-stack/qt-5.15.2.

module unload intel cray-mpich cray-python darshan PrgEnv-intel
module load gcc/10.3.0
module load PrgEnv-gnu/6.0.5
ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, qt5, and loading the following modules, follow the instructions in Section 5.1.4. Because of the dependency on miniconda, that module must be loaded automatically in the ecflow module (similar to qt@5.15.2). Ensure to follow the extra instructions in that section for Gaea.

module unload intel cray-mpich cray-python darshan PrgEnv-intel module load gcc/10.3.0 module load PrgEnv-gnu/6.0.5 module load cmake/3.20.1 module use /lustre/f2/pdata/esrl/gsd/spack-stack/modulefiles module load miniconda/3.9.12 module load qt/5.15.2

8.1.10. NOAA RDHPCS Hera

On Hera, miniconda must be installed as a one-off before spack can be used.

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

Hera sits behind the NOAA firewall and doesn’t have access to all packages on the web. It is therefore necessary to create a spack mirror on another platform (e.g. Cheyenne). This can be done as described in section Section 8.2 for air-gapped systems.

8.1.11. NOAA RDHPCS Jet

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

module use /lfs4/HFIP/hfv3gfs/spack-stack/modulefiles
module load miniconda/3.9.12
# Need a newer gcc compiler than the default OS compiler gcc-4.8.5
module load gnu/9.2.0

8.1.12. TACC Frontera

Several packages need to be installed as a one-off before spack can be used.

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation in /work2/06146/USERNAME/frontera/spack-stack/miniconda-3.9.12 and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, and loading the following modules, follow the instructions in Section 5.1.4.

module purge
module use /work2/06146/tg854455/frontera/spack-stack/modulefiles
module load miniconda/3.9.12
module load qt5/5.14.2
module load gcc/9.1.0
module load cmake/3.20.3
git-lfs

The following instructions install git-lfs in /work2/06146/tg854455/frontera/spack-stack/git-lfs-2.10.0. Version 2.10.0 is the Centos7 default version.

module purge
cd /work2/06146/tg854455/frontera/spack-stack/
mkdir -p git-lfs-2.10.0/src
cd git-lfs-2.10.0/src
wget --content-disposition https://packagecloud.io/github/git-lfs/packages/el/7/git-lfs-2.10.0-1.el7.x86_64.rpm/download.rpm
rpm2cpio git-lfs-2.10.0-1.el7.x86_64.rpm | cpio -idmv
mv usr/* ../

Create modulefile /work2/06146/tg854455/frontera/spack-stack/modulefiles/git-lfs/2.10.0 from template doc/modulefile_templates/git-lfs and update GITLFS_PATH in this file.

8.1.13. UW (Univ. of Wisconsin) S4

gnu (module only)

The gnu/9.3.0 module provided by the system administrators is broken (circular dependencies etc.). To create a usable version, copy /data/prod/hpc-stack/modulefiles/core/gnu/9.3.0.lua into directory ``/data/prod/jedi/spack-stack/modulefiles/gnu`.`

miniconda

Follow the instructions in Section 5.1.2 to create a basic miniconda installation and associated modulefile for working with spack. Don’t forget to log off and back on to forget about the conda environment.

ecflow

ecFlow must be built manually using the GNU compilers and linked against a static boost library. After installing miniconda, and loading the following modules, follow the instructions in Section 5.1.4.

module purge
module use /data/prod/jedi/spack-stack/modulefiles
module load miniconda/3.9.12
module load gcc/9.3.0

8.1.14. Amazon Web Services Parallelcluster Ubuntu 20.04

See configs/sites/aws-pcluster/README.md.

8.2. Creating/maintaining spack mirrors

Spack mirrors allow downloading the source code required to build environments once to a local directory (in the following also referred to as source cache), and then use this directory for subsequent installations. If a package cannot be found in the mirror (e.g. because a newer version is required), it will automatically be pulled from the web. It won’t be added to the source cache automatically, this is a step that needs to be done manually.

Spack mirrors also make it possible to download the source code for an air-gapped machine on another system, then transferring the entire mirror to the system without internet access and using it during the installation.

8.2.1. Spack mirrors for local reuse

Since all spack-stack installations are based on environments, we only cover spack mirrors for environments here. For a more general discussion, users are referred to the Spack Documentation.

  1. Create an environment as usual, activate it and run the concretization step (spack concretize), but do not start the installation yet.

  2. Create the spack mirror in /path/to/spack-mirror.

spack mirror create -a -d /path/to/spack-source

  1. If the spack mirror already exists, then existing packages will be ignored and only new packages will be added to the mirror.

  2. If not already included in the environment (e.g. from the spack-stack site config), add the mirror:

  1. Proceed with the installation as usual.

8.2.2. Spack mirrors for air-gapped systems

The procedure is similar to using spack mirrors for local reuse, but a few additional steps are needed in between.

  1. On the air-gapped system: Create an environment as usual, activate it and run the concretization step (spack concretize), but do not start the installation yet.

  2. Copy the file spack.lock (in envs/env-name/) to the machine with full internet access using scp, for example.

  3. On the machine with full internet access: Load the basic external modules, if using a machine that is preconfigured for spack-stack (see Section 3) and make sure that git supports lfs (if necessary, load the external modules that spack-stack also uses).

  4. On the machine with full internet access: check out the same version of spack-stack, run setup.sh, and then the following sequence of commands. The mirror will be created in directory ./spack/var/spack/environments/air_gapped_mirror_env.

spack env create air_gapped_mirror_env spack.lock
spack env activate air_gapped_mirror_env
spack mirror create -a

  1. On the air-gapped system: Copy the directory from the system with internet access to the local destination for the spack mirror. It is recommended to use rsync to avoid deleting existing packages, if updating an existing mirror on the air-gapped system.

6.. On the air-gapped system: Add the mirror to the spack environment’s mirror list, unless already included in the site config.

spack mirror add locals-source  file:///path/to/spack-source
spack mirror list

The newly created local mirror should be listed at the top, which means that spack will search this directory first.

  1. On the air-gapped system: Proceed with the installation as usual.

8.3. Testing new packages

8.3.1. Using spack to test/add packages

The simplest case of adding new packages that are available in spack-stack is described in Section 2.1.3. As mentioned there, it is advised to take a backup of the spack environment (and install directories if outside the spack environment directory tree). It is also possible to chain spack installations, which means creating a test environment that uses installed packages and modulefiles from another (e.g. authoritative) spack environment and build the packages to be tested in isolation.

8.3.1.1. Chaining spack-stack installations

Chaining spack-stack installations is a powerful way to test adding new packages without affecting the existing packages. The idea is to define one or more upstream spack installations that the environment can use as dependencies. One possible way to do this is:

  1. Mirror the environment config of the upstream repository, i.e. copy the entire directory without the install and .spack_env directories and without spack.lock. For example:

rsync -av --exclude='install' --exclude='.spack-env' --exclude='spack.lock' \
    envs/jedi-ufs/ \
    envs/jedi-ufs-chain-test/

  1. Edit envs/jedi-ufs-chain-test/spack.yaml` and add an upstream configuration entry directly under the spack: config so that the contents looks like:

spack:
  upstreams:
    spack-instance-1:
      install_tree: /path/to/spack-stack-1.0.0/envs/jedi-ufs/install
  concretizer:
    unify: when_possible
  ...

  1. Activate the environment

  2. Install the new packages, for example:

spack install -v --reuse esmf@8.3.0b09+debug

  1. Create modulefiles

spack module [lmod|tcl] refresh

  1. When using tcl module files, run the spack stack setup-meta-modules script. This is not needed when using lmod modulefiles, because the meta modules in /path/to/spack-stack-1.0.0/envs/jedi-ufs-chain-test/install/modulefiles/Core will be ignored entirely.

To use the chained spack environment, first load the usual modules from the upstream spack environment. Then add the full path to the newly created modules manually, ignoring the meta modules (.../Core), for example:

module use /path/to/spack-stack-1.0.0/envs/jedi-ufs-chain-test/install/modulefiles/openmpi/4.1.3/apple-clang/13.1.6

  1. Load the newly created modules. When using tcl module files, make sure that conflicting modules are unloaded (lmod takes care of this).

Note

After activating the chained environment, spack find doesn’t show the packages installed in upstream, unfortunately.

Note

More details and a few words of caution can be found in the Spack documentation. Those words of caution need to be taken seriously, especially those referring to not deleting modulefiles and dependencies in the upstream spack environment (if having permissions to do so)!

8.3.2. Testing/adding packages outside of spack

Sometimes, users may want to build new versions of packages frequently without using spack, for example as part of an existing build system (e.g. a cmake submodule or an ecbuild bundle). Also, users may wish to test developmental code that is not available and/or not ready for release in spack-stack. In this case, users need to unload the modules of the packages that are to be replaced, including their dependencies, and build the new version(s) themselves within the existing build system or manually. The loaded modules from the spack environment in this case provide the necessary dependencies, just like for any other build system.

Note

Users are strongly advised to not interfere with the spack install tree. The environment install tree and module files should only be modified using spack.

Users can build multiple packages outside of spack and install them in a separate install tree, for example MY_INSTALL_TREE. In order to find these packages, users must extend their environment as required for the system/the packages to be installed:

export PATH="$MY_INSTALL_TREE/bin:$PATH"
export CPATH="$MY_INSTALL_TREE/include:$PATH"
export LD_LIBRARY_PATH="$MY_INSTALL_TREE/lib64:$MY_INSTALL_TREE/lib:$LD_LIBRARY_PATH"
# macOS
export DYLD_LIBRARY_PATH="$MY_INSTALL_TREE/lib64:$MY_INSTALL_TREE/lib:$DYLD_LIBRARY_PATH"
# Python packages, use correct lib/lib64 and correct python version
export PYTHONPATH="$MY_INSTALL_TREE/lib/pythonX.Y/site-packages:$PYTHONPATH"

Python packages can be added in various ways:

  1. Using python setup.py install --prefix=$MY_INSTALL_TREE ... or python3 -m pip install --no-deps --prefix=$MY_INSTALL_TREE .... The --no-deps options is very important, because pip may otherwise attempt to install dependencies that already exist in spack-stack. These dependencies are not only duplicates, they may also be different versions and/or compiled with different compilers/libraries (because they are wheels). This approach requires adding the appropriate subdirectories of $MY_INSTALL_TREE to the different search paths, as shown above.

  2. Using Python virtual environments. Two important flags need to be passed to the command that creates the environment --system-site-packages and --without-pip. After activating the environment, packages can be installed using python3 -m pip without having to specify --no-deps or --prefix, and without having to manually modify PATH, PYTHONPATH, etc.

python3 -m venv --system-site-packages --without-pip $MY_INSTALL_TREE
source $MY_INSTALL_TREE/bin/activate
python3 -m pip install ...

Note

Users are equally strongly advised to not use conda or miniconda in combination with Python modules provided by spack-stack, as well as not installing packages other than poetry in the basic miniconda installation for spack-stack (if using such a setup).