3. Pre-configured sites¶
Directory configs/sites contains site configurations for several HPC systems, as well as minimal configurations for macOS and Linux. The macOS and Linux configurations are not meant to be used as is, as user setups and package versions vary considerably. Instructions for adding this information can be found in Section 6.
Pre-configured sites are split into two categories: Tier 1 with officially supported spack-stack installations (see Section 3.2), and Tier 2 (sites with configuration files that were tested or contributed by others in the past, but that are not officially supported by the spack-stack team; see Section %s).
3.1. Officially supported spack-stack 1.5.1 installations (tier 1)¶
Ready-to-use spack-stack 1.5.1 installations are available on the following, fully supported platforms. This version supports the JEDI Skylab release 5 of June 2023, and the UFS Weather Model of July 2023. It can also be used for testing spack-stack with other UFS applications (e.g. the UFS Short Range Weather Application, and the EMC Global Workflow). Amazon Web Services AMI are available in the US East 1 or 2 regions.
Organization |
System |
Compilers |
Location |
Maintainers |
|---|---|---|---|---|
HPC platforms |
||||
MSU |
Hercules^* |
GCC, Intel |
|
Cam Book / Dom Heinzeller |
Orion |
GCC, Intel |
|
Cam Book / Dom Heinzeller |
|
NASA |
Discover^** |
GCC, Intel |
|
Dom Heinzeller / ??? |
NCAR-Wyoming |
Casper |
GCC |
|
Dom Heinzeller / ??? |
Derecho |
GCC, Intel |
|
Dom Heinzeller / Mark Potts |
|
NOAA (NCEP) |
Acorn |
Intel |
|
Hang Lei / Alex Richert |
NOAA (RDHPCS) |
Gaea C5 |
Intel |
|
Alex Richert / Dom Heinzeller |
Hera |
GCC, Intel |
|
Mark Potts / Dom Heinzeller |
|
Jet |
GCC, Intel |
|
Cam Book / Dom Heinzeller |
|
U.S. Navy (HPCMP) |
Narwhal |
Intel |
|
Dom Heinzeller / Sarah King |
Narwhal |
GCC |
|
Dom Heinzeller / Sarah King |
|
Nautilus |
Intel^* |
|
Dom Heinzeller / Sarah King |
|
Nautilus |
AOCC |
currently not supported |
Dom Heinzeller / Sarah King |
|
Univ. of Wisconsin |
S4 |
Intel |
|
Dom Heinzeller / Mark Potts |
S4 |
GCC |
currently not supported |
Dom Heinzeller / Mark Potts |
|
Cloud platforms |
||||
Amazon Web Services |
AMI Red Hat 8 |
GCC |
|
Dom Heinzeller / ??? |
Parallelcluster JCSDA R&D |
Intel |
|
Dom Heinzeller / ??? |
|
NOAA (RDHPCS) |
RDHPCS Cloud (Parallel Works) |
Intel |
|
Mark Potts / Cam Book / Dom H |
^* Uses a different wgrib2 version 3.1.1 than the default 2.0.8.
^** Uses a slightly newer version than the spack-stack 1.5.1 release, so that gmao-swell-env is available in the environment.
For questions or problems, please consult the known issues in Section 11, the currently open GitHub issues and discussions first.
3.2. Pre-configured sites (tier 1)¶
3.2.1. MSU Orion¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /work/noaa/epic/role-epic/spack-stack/orion/modulefiles
module load python/3.9.2
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2022.0.2
module load stack-intel-oneapi-mpi/2021.5.1
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading miniconda and ecflow:
module use /work/noaa/epic/role-epic/spack-stack/orion/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/10.2.0
module load stack-openmpi/4.0.4
module load stack-python/3.10.8
module available
3.2.2. MSU Hercules¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /work/noaa/epic/role-epic/spack-stack/hercules/modulefiles
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading mysql and ecflow:
module use /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.9.0
module load stack-intel-oneapi-mpi/2021.9.0
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading mysql and ecflow:
module use /work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/12.2.0
module load stack-mvapich2/2.3.7
module load stack-python/3.10.8
module available
3.2.3. NASA Discover¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /discover/swdev/jcsda/spack-stack/modulefiles
module load miniconda/3.9.7
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /gpfsm/dswdev/jcsda/spack-stack/spack-stack-dev-20231114/envs/unified-env/install/modulefiles/Core
module load stack-intel/2022.0.1
module load stack-intel-oneapi-mpi/2021.5.0
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading miniconda and ecflow:
module use /gpfsm/dswdev/jcsda/spack-stack/spack-stack-dev-20231114/envs/unified-env/install/modulefiles/Core
module load stack-gcc/10.1.0
module load stack-openmpi/4.1.3
module load stack-python/3.10.8
module available
3.2.6. NCAR-Wyoming Casper¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
# ignore that the sticky module ncarenv/... is not unloaded
export LMOD_TMOD_FIND_FIRST=yes
module load ncarenv/23.10
module use /glade/work/epicufsrt/contrib/spack-stack/casper/modulefiles
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with GNU, load the following modules after loading the above modules.
module use /glade/work/epicufsrt/contrib/spack-stack/casper/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/12.2.0
module load stack-openmpi/4.1.6
module load stack-python/3.10.8
module available
3.2.7. NCAR-Wyoming Derecho¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
# ignore that the sticky module ncarenv/... is not unloaded
export LMOD_TMOD_FIND_FIRST=yes
module load ncarenv/23.09
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/modulefiles
module load ecflow/5.8.4
module load mysql/8.0.33
For spack-stack-1.5.1 with Intel, load the following modules after loading ecflow and mysql:
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.10.0
module load stack-cray-mpich/8.1.25
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading ecflow and mysql:
module use /glade/work/epicufsrt/contrib/spack-stack/derecho/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/12.2.0
module load stack-cray-mpich/8.1.25
module load stack-python/3.10.8
module available
Note
CISL restricts the amount of memory available for processes on the login nodes. For example, it is impossible to compile JEDI with even one task (make -j1) with the Intel compiles in release mode (-O2). We therefore recommend compiling on compute nodes using interactive jobs, if possible.
3.2.8. NOAA Acorn (WCOSS2 test system)¶
For spack-stack-1.5.1, the meta modules are in /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core.
On WCOSS2 OpenSUSE sets CONFIG_SITE which causes libraries to be installed in lib64, breaking the lib assumption made by some packages. Therefore, CONFIG_SITE should be set to empty in compilers.yaml. Also, don’t use module purge on Acorn!
When installing an official spack-stack on Acorn, be mindful of umask and group ownership, as these can be finicky. The umask value should be 002, otherwise various files can be assigned to the wrong group. In any case, running something to the effect of chgrp nceplibs <spack-stack dir> -R and chmod o+rX <spack-stack dir> -R after the whole installation is done is a good idea.
Due to a combined quirk of Cray and Spack, the PrgEnv-gnu and gcc modules must be loaded when ESMF is being installed with gcc.
As of spring 2023, there is an inconsistency in libstdc++ versions on Acorn between the login and compute nodes. It is advisable to compile on the compute nodes, which requires running spack fetch prior to installing through a batch job.
Note that certain packages, such as recent versions of py-scipy, cannot be compiled on compute nodes because their build systems require internet access.
Note
System-wide spack software installations are maintained by NCO on this platform. The spack-stack official installations use those installations for some dependencies.
3.2.9. NOAA Parallel Works (AWS, Azure, Gcloud)¶
The following is required for building new spack environments and for using spack to build and run software. The default module path needs to be removed, otherwise spack detects the system as Cray.
module purge
module unuse /opt/cray/craype/default/modulefiles
module unuse /opt/cray/modulefiles
module use /contrib/spack-stack/modulefiles
module load cmake/3.27.2
module load ecflow/5.8.4
module load mysql/8.0.31
module load git-lfs/2.4.1
For spack-stack-1.5.1 with Intel, proceed with loading the following modules:
module use /contrib/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.3.0
module load stack-intel-oneapi-mpi/2021.3.0
module load stack-python/3.10.8
module available
3.2.10. NOAA RDHPCS Gaea C5¶
The following is required for building new spack environments and for using spack to build and run software. Make sure to log into a C5 head node, and don’t use module purge on Gaea!
module load PrgEnv-intel/8.3.3
module load intel-classic/2023.1.0
module load cray-mpich/8.1.25
module load python/3.9.12
module use /lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/modulefiles
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2023.1.0
module load stack-cray-mpich/8.1.25
module load stack-python/3.10.8
module -t available
Note
On Gaea C5, running module available without the option -t leads to an error: /usr/bin/lua5.3: /opt/cray/pe/lmod/lmod/libexec/Spider.lua:568: stack overflow
Note
On Gaea C5, a current limitation is that any executable that is linked against the MPI library (cray-mpich) must be run through srun on a compute node, even if it is run serially (one process). This is in particular a problem when using ctest for unit testing created by the ecbuild add_test macro. A workaround is to use the cmake cross-compiling emulator for this:
cmake -DCMAKE_CROSSCOMPILING_EMULATOR="/usr/bin/srun;-n;1" -DMPIEXEC_EXECUTABLE="/usr/bin/srun" -DMPIEXEC_NUMPROC_FLAG="-n" PATH_TO_SOURCE
3.2.11. NOAA RDHPCS Hera¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /scratch1/NCEPDEV/jcsda/jedipara/spack-stack/modulefiles
module load miniconda/3.9.12
module load ecflow/5.5.3
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.5.0
module load stack-intel-oneapi-mpi/2021.5.1
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading miniconda and ecflow:
module use /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/9.2.0
module load stack-openmpi/4.1.5
module load stack-python/3.10.8
module available
Note that on Hera, a dedicated node exists for ecflow server jobs (hecflow01). Users starting ecflow_server on the regular login nodes will see their servers being killed every few minutes, and may be barred from accessing the system.
3.2.12. NOAA RDHPCS Jet¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /lfs4/HFIP/hfv3gfs/spack-stack/modulefiles
module load miniconda/3.9.12
module load ecflow/5.5.3
module use /lfs4/HFIP/hfv3gfs/role.epic/modulefiles
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.5.0
module load stack-intel-oneapi-mpi/2021.5.1
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU, load the following modules after loading miniconda and ecflow:
module use /mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/9.2.0
module load stack-openmpi/3.1.4
module load stack-python/3.10.8
module available
3.2.13. UW (Univ. of Wisconsin) S4¶
The following is required for building new spack environments and for using spack to build and run software.
module purge
module use /data/prod/jedi/spack-stack/modulefiles
module load miniconda/3.9.12
module load ecflow/5.8.4
module load mysql/8.0.31
For spack-stack-1.5.1 with Intel, load the following modules after loading miniconda and ecflow:
module use /data/prod/jedi/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2021.5.0
module load stack-intel-oneapi-mpi/2021.5.0
module load stack-python/3.10.8
module unuse /opt/apps/modulefiles/Compiler/intel/non-default/22
module unuse /opt/apps/modulefiles/Compiler/intel/22
module available
Note the two module unuse commands, that need to be run after the stack metamodules are loaded. Loading the Intel compiler meta module loads the Intel compiler module provided by the sysadmins, which adds those two directories to the module path. These contain duplicate libraries that are not compatible with our stack, such as hdf4.
Note
There is currently no support for GNU on S4, because recent updates to hdf5 require a newer version of mpich (or other MPI library) than available on the system.
3.2.14. Amazon Web Services Parallelcluster Ubuntu 20.04¶
Access to the JCSDA-managed AWS Parallel Clusters is not available to the public. The following instructions are for JCSDA core staff and in-kind contributors.
For spack-stack-1.5.1 with Intel on the JCSDA R&D cluster (hpc6a.48xlarge instances), run the following commands/load the following modules:
module purge
ulimit -s unlimited
source /opt/intel/oneapi/compiler/2022.1.0/env/vars.sh
module use /mnt/experiments-efs/skylab-v7/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-intel/2022.1.0
module load stack-intel-oneapi-mpi/2021.6.0
module load stack-python/3.10.8
module available
For spack-stack-1.5.1 with GNU on the JCSDA R&D cluster (hpc6a.48xlarge instances), run the following commands/load the following modules:
module purge ulimit -s unlimited module use /mnt/experiments-efs/skylab-v7/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core module load stack-gcc/9.4.0 module load stack-openmpi/4.1.4 module load stack-python/3.10.8 module available
Note
The GNU stack is currently under testing and may not work as expected. We recommend using the well-tested Intel setup.
3.2.15. Amazon Web Services Red Hat 8¶
Use a c6i.4xlarge instance or larger if running out of memory with AMI “skylab-6.1.0-redhat8” (see JEDI documentation at https://jointcenterforsatellitedataassimilation-jedi-docs.readthedocs-hosted.com/en/latest for more information).
For spack-stack-1.5.1, run:
ulimit -s unlimited
scl_source enable gcc-toolset-11
module use /home/ec2-user/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core
module load stack-gcc/11.2.1
module load stack-openmpi/4.1.5
module load stack-python/3.10.8
module available
3.3. Create local environment¶
The following instructions install a new spack environment on a pre-configured site. Instructions for creating a new site config on a configurable system (i.e. a generic Linux or macOS system) can be found in Section 6. The options for the spack stack extension are explained in Section 9.
git clone --recurse-submodules https://github.com/jcsda/spack-stack.git
cd spack-stack
# Ensure Python 3.8+ is available and the default before sourcing spack
# Sources Spack from submodule and sets ${SPACK_STACK_DIR}
source setup.sh
# See a list of sites and templates
spack stack create env -h
# Create a pre-configured Spack environment in envs/<template>.<site>
# (copies site-specific, application-specific, and common config files into the environment directory)
spack stack create env --site hera --template unified-dev --name unified-dev.hera
# Activate the newly created environment
# Optional: decorate the command line prompt using -p
# Note: in some cases, this can mess up long lines in bash
# because color codes are not escaped correctly. In this
# case, use export SPACK_COLOR='never' first.
cd envs/unified-dev.hera/
spack env activate [-p] .
# Edit the main config file for the environment and adjust the compiler matrix
# to match the compilers available on your system, or a subset of them (see
# note below for more information). Replace
# definitions:
# - compilers: ['%apple-clang', '%gcc', '%intel']
# with the appropriate list of compilers for your system and desires, e.g.
# definitions:
# - compilers: ['%gcc', '%intel']
emacs envs/unified-dev.hera/spack.yaml
# Optionally edit config files (spack.yaml, packages.yaml compilers.yaml, site.yaml)
emacs envs/unified-dev.hera/common/*.yaml
emacs envs/unified-dev.hera/site/*.yaml
# Process/concretize the specs; optionally check for duplicate packages
spack concretize | ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d [-c] log.concretize
# Optional step for systems with a pre-configured spack mirror, see below.
# Install the environment, recommended to always use --source
# to install the source code with the compiled binary package
spack install --source [--verbose] [--fail-fast]
# Create lua module files
spack module lmod refresh
# Create meta-modules for compiler, mpi, python
spack stack setup-meta-modules
# Check permissions for systems where non-owning users/groups need access
${SPACK_STACK_DIR}/util/check_permissions.sh
Note
You may want to capture the output from spack concretize and spack install comands in log files.
For example:
spack concretize 2>&1 | tee log.concretize
spack install [--verbose] [--fail-fast] 2>&1 | tee log.install
Note
For platforms with multiple compilers in the site config, make sure that the correct compiler and corresponding MPI library are set correctly in envs/jedi-fv3.hera/site/packages.yaml before running spack concretize. Also, check the output of spack concretize to make sure that the correct compiler is used (e.g. %intel-2022.0.1). If not, edit envs/jedi-fv3.hera/site/compilers.yaml and remove the offending compiler. Then, remove envs/jedi-fv3.hera/spack.lock and rerun spack concretize.
3.4. Extending environments¶
Additional packages (and their dependencies) or new versions of packages can be added to existing environments. It is recommended to take a backup of the existing environment directory (e.g. using rsync) or test this first as described in Section 12.4, especially if new versions of packages are added that act themselves as dependencies for other packages. In some cases, adding new versions of packages will require rebuilding large portions of the stack, for example if a new version of hdf5 is needed. In this case, it is recommended to start over with an entirely new environment.
In the simplest case, a new package (and its basic dependencies) or a new version of an existing package that is not a dependency for other packages can be added as described in the following example for a new version of ecmwf-atlas.
Check if the package has any variants defined in the common (
env_dir/common/packages.yaml) or site (env_dir/site/packages.yaml) package config and make sure that these are reflected correctly in thespeccommand:
spack spec ecmwf-atlas@0.29.0
Add package to environment specs:
spack add ecmwf-atlas@0.29.0
Run
concretizestep
spack concretize
Install
spack install [--verbose] [--fail-fast]
Further information on how to define variants for new packages, how to use these non-standard versions correctly as dependencies, …, can be found in the Spack Documentation. Details on the spack stack extension of the spack are provided in Section 9.
Note
Instead of spack add ecmwf-atlas@0.29.0, spack concretize and spack install, one can also just use spack install ecmwf-atlas@0.29.0 after checking in the first step (spack spec) that the package will be installed as desired.