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"""mpsd-software: tool for installation of software as on MPSD HPC."""
import argparse
import datetime
import logging
from typing import List, Tuple, Union
__version__ = importlib.metadata.version(__package__ or __name__)
command_name = Path(sys.argv[0]).name
This tool builds software package sets (including toolchains for Octopus).
It follows recipes as used on the MPSD HPC system and the (spack-based)
Octopus buildbot. Compiled software is organised into MPSD software release
versions (such as `dev-23a`) and CPU microarchitecture (such as `sandybridge`).
Compiled packages and toolchains can be activated and used via `module load` as
on the HPC system.
Further documentation is available in the README.rst file, online at
https://gitlab.gwdg.de/mpsd-cs/mpsd-software-manager/-/blob/main/README.rst
$> {command_name}
"""
about_epilog = f"""
Examples:
1. Query what releases are available for installation
$> {command_name} available
2. Query what package sets and toolchains are available for installation in
$> {command_name} available dev-23a
3. Install foss2022a-serial toolchain from the dev-23a release
$> {command_name} install dev-23a foss2022a-serial
4. Check what package sets and toolchains are installed from release dev-23a
$> {command_name} status dev-23a
The `status` command also displays the `module use` command needed to load
the created modules.
call_date_iso = (
datetime.datetime.now().replace(microsecond=0).isoformat().replace(":", "-")
)
"cmd_log_file": "mpsd-software.log",
"metadata_tag_open": "!<meta>",
"metadata_tag_close": "</meta>!",
"spack_environments_repo": "https://gitlab.gwdg.de/mpsd-cs/spack-environments.git",
"init_file": ".mpsd-software-root",
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def log_metadata(key: str, value: str) -> None:
"""Log metadata to the log file.
This function logs metadata to the log file. The metadata is
enclosed in a tag, so that it can be easily found in the log file.
logging module is used to write the metadata to the log file.
Parameters
----------
key : str
key of the metadata
value : str
value of the metadata
returns : None
"""
logging.info(
f"{config_vars['metadata_tag_open']}{key}:{value}{config_vars['metadata_tag_close']}"
)
def read_metadata_from_logfile(logfile: Union[str, Path]) -> dict:
"""Read metadata from the log file.
This function reads metadata from the log file. The metadata is
enclosed in a tag, so that it can be easily found in the log file.
Parameters
----------
logfile : str or Path
log file name
returns : dict
dictionary containing the metadata
"""
with open(logfile, "r") as f:
log_text = f.read()
# check for all data that matches the regex
# metadata_tag_open {key}:{value} metadata_tag_close
# and return a dictionary with all the matches
return {
match.group(1): match.group(2)
for match in re.finditer(
rf"{config_vars['metadata_tag_open']}(\w+):(\w+){config_vars['metadata_tag_close']}",
log_text,
)
}
def create_log_file_name(
mpsd_release: str,
action: str,
date: str = call_date_iso,
package_set: Union[str, None] = None,
) -> Union[str, None]:
"""Create log file names.
This function creates the log file names for either the installer or
If a package_set is given, then the build log file name is created.
if no package_set is given, then the installer log file name is created.
The installer log file hosts the logs of the installer script, while
the build log file hosts the logs of the build process as generated by the
spack_setup.sh script.
Parameters
----------
mpsd_release : str
MPSD software stack version
date : str
date of the call ins iso format
action : str
action performed (install,remove,reinstall,prepare,status)
only install and remove are valid for build log file.
package_set : str or None
package_set name (only for build log file)
log file name
installer_log_file_name or build_log_file_name depending on the
parameters given.
If the action is not one that changes the files on disk (info only actions)
then None is returned.
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Examples
--------
# installer log file name for `mpsd-software install dev-23a foss2021a-mpi`
>>> create_log_file_name(
... "dev-23a",
... "install",
... "2023-07-03T12-27-52",
... )
'dev-23a_sandybridge_2023-07-03T12-27-52_APEX_install.log'
# build log file name for `mpsd-software install dev-23a foss2021a-mpi`
>>> create_log_file_name(
... "dev-23a",
... "install",
... "2023-07-03T12-27-52",
... "foss2021a-mpi",
... )
'dev-23a_sandybridge_2023-07-03T12-27-52_BUILD_foss2021a-mpi_install.log'
# installer log file name for `mpsd-software status dev-23a`
>>> create_log_file_name(
... "dev-23a",
... "status",
... "2023-07-03T12-27-52",
... )
'dev-23a_sandybridge_2023-07-03T12-27-52_APEX_status.log'
# build log file name for `mpsd-software status dev-23a` (no log file is created)
>>> create_log_file_name(
... "dev-23a",
... "status",
... "2023-07-03T12-27-52",
... "foss2021a-mpi",
... )
(None)
microarch = get_native_microarchitecture()
if package_set:
# if package_set is given, then we build the build_log_file_name
if action in ["install", "remove"]:
f"{mpsd_release}_{microarch}_{date}_BUILD_{package_set}_{action}.log"
# if package_set is not given, then we build the installer_log_file_name
log_file_name = f"{mpsd_release}_{microarch}_{date}_APEX_{action}.log"
return log_file_name
mpsd_release: str, cmd: str, root_dir: Path, package_set: Union[str, None] = None
"""Get log file path.
This function creates the log file paths for either the installer or
the build log files.
If a package_set is given, then the build log file path is returned.
if no package_set is given, then the installer log file path is returned.
If the logs folder does not exist, then it is created.
Parameters
----------
mpsd_release : str
MPSD software stack version
cmd : str
command to be executed
root_dir : str
root directory of the mpsd software stack
package_set : str
package_set name (only for build log file)
Returns
-------
Path or None
log file path
installer_log_file_path or build_log_file_path depending on the
parameters given.
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Examples
--------
# installer log file path for `mpsd-software install dev-23a foss2021a-mpi`
>>> get_log_file_path(
... "dev-23a",
... "install",
... Path(
... "/tmp/root_dir"
... ),
... )
PosixPath('/tmp/root_dir/dev-23a/logs/dev-23a_zen3_2023-07-03T12-28-55_APEX_install.log')
# build log file path for `mpsd-software install dev-23a foss2021a-mpi`
>>> get_log_file_path(
... "dev-23a",
... "install",
... Path(
... "/tmp/root_dir"
... ),
... "foss2021a-mpi",
... )
PosixPath('/tmp/root_dir/dev-23a/logs/dev-23a_zen3_2023-07-03T12-28-55_BUILD_foss2021a-mpi_install.log')
# installer log file path for `mpsd-software status dev-23a`
>>> get_log_file_path(
... "dev-23a",
... "status",
... Path(
... "/tmp/root_dir"
... ),
... )
PosixPath('/tmp/root_dir/dev-23a/logs/dev-23a_zen3_2023-07-03T12-28-55_APEX_status.log')
# build log file path for `mpsd-software status dev-23a` (no log file is created)
>>> get_log_file_path(
... "dev-23a",
... "status",
... Path(
... "/tmp/root_dir"
... ),
... "foss2021a-mpi",
... )
(None)
log_file_name = create_log_file_name(
mpsd_release=mpsd_release,
action=cmd,
package_set=package_set,

Ashwin Kumar Karnad
committed
)
log_folder = root_dir / mpsd_release / "logs"
if log_file_name:
# if the log_folder dosent exist, create it
if not log_folder.exists():
log_folder.mkdir(parents=True)
return log_folder / log_file_name

Ashwin Kumar Karnad
committed
else:

Ashwin Kumar Karnad
committed
def set_up_logging(loglevel="warning", file_path=None):
"""Set up logging.
This function sets up the logging configuration for the script.
Parameters
----------
loglevel : str or int
Loglevels are:
- warning (default): only print statements if something is unexpected
- info (show more detailed progress)
- debug (show very detailed output)
- filename to save logging messages into
If loglevel is 'debug', save line numbers in log messages.
Returns
-------
None.
Logger instances are generally not passed around, but retrieved from the
logging module as shown below (they are singletons).
We provide two loggers:
1. log = logging.getLogger('')
Typical use:
log.debug("...")
log.info("...")
log.warn("...")
Equivalent to
logging.debug("...")
logging.info("...")
2. print_log = logging.getlogger('print')
This uses the logging module to issue the message, but prints without
any further markup (i.e. no date, loglevel, line number, etc). Think
PRINT via the LOGging module.
We use this as a replacement for the print function (i.e. for messages
that should not be affected by logging levels, and which should always
be printed).
Typical and intended use:
print_log.info("Available package_sets are ...")
The major difference from the normal print command is that the output
will be send to the stdout (as for print) AND the file with name
filename, so that these messages appear in the log file together with
normal log output.
# convert loglevel string into loglevel as number
log_level_numeric = getattr(logging, loglevel.upper(), logging.WARNING)
if not isinstance(log_level_numeric, int):
# set up the main logger ("root" logger)
logger = logging.getLogger("")
# - "logger" logs everything
# - we use loglevel at handler level to write everything to file
# - and filter using log_level_numeric (as the user provides) to
# send logging messages to the console
logger.setLevel(0)
# the handler determines where the logs go: stdout/file
# We use 'rich' to provide a Handler:
# https://rich.readthedocs.io/en/stable/logging.html
shell_handler = rich.logging.RichHandler()
# rich handler provides metadata automatically:
logging_format = "%(message)s"
# for shell output, only show time (not date and time)
shell_formatter = logging.Formatter(logging_format, datefmt="[%X]")
# here we hook everything together
shell_handler.setFormatter(shell_formatter)
# use the log_level_numeric to decide how much logging is sent to shell
shell_handler.setLevel(log_level_numeric)
# Here we set the handlers of the RootLogger to be just the one we want.
# The reason is that the logging module will add a <StreamHandler <stderr>
# (NOTSET)> handler if logging.info/logging.debug/... is used before we
# come across this line. And we do not want that additional handler.
logger.handlers = [shell_handler]
# if filename provided, write log messages to that file, too.
if file_path:
file_handler = logging.FileHandler(file_path)
# if we have a file, we write all information in there.
# We could change the level, for example restrict to only DEBUG and above with
# file_handler.setLevel(logging.DEBUG)
file_logging_format = "%(asctime)s %(levelname)7s %(lineno)4d | %(message)s"
file_formatter = logging.Formatter(file_logging_format, datefmt="[%X]")
file_handler.setFormatter(file_formatter)
logger.addHandler(file_handler)
#
# new logger for printing
#
print_log = logging.getLogger("print")
print_log.setLevel(logging.INFO)
print_log.propagate = False
# create formatter 'empty' formatter
formatter = logging.Formatter("%(message)s")
# create, format and set handler for shell output
ch = logging.StreamHandler()
ch.setFormatter(formatter)
# if filename provided, write output of print_log to that file, too
# create, format and add file handler
fh = logging.FileHandler(file_path)
fh.setFormatter(formatter)
print_log.addHandler(fh)
#
# short message
#
f"Logging has been setup, loglevel={loglevel.upper()} " + f"{file_path=}"
def get_available_package_sets(mpsd_release: str) -> List[str]:
"""Given a release, return the available package_sets.
This is based on the spack-environment's repository [1]. For this function
to succeed, we need to have Internet access etc.
We use a temporary directory to clone the repository locally, which is
deleted upon successful completion of the function.
[1] https://gitlab.gwdg.de/mpsd-cs/spack-environments.git
['foss2021a-cuda-mpi',
'foss2021a-mpi',
'foss2021a-serial',
'foss2022a-cuda-mpi',
'foss2022a-mpi',
'foss2022a-serial',
'global',
'global_generic']
logging.debug(f"get_available_package_sets({mpsd_release=})")
print_log = logging.getLogger("print")
logging.info(f"Retrieving available package_sets for release {mpsd_release}")
# create temporary directory
tmp_dir = tempfile.TemporaryDirectory(prefix="mpsd-software-available-")
tmp_dir_path = Path(tmp_dir.name)
# find package_sets by cloning repository and checking out right branch
tmp_dir_path,
config_vars["spack_environments_repo"],
branch=f"releases/{mpsd_release}",
# look for directories defining the package_sets
package_sets = os.listdir(tmp_dir_path / "toolchains")
msg = f"Found package_sets {sorted(package_sets)}"
# the 'package_sets' split into toolchains (such as foss2022a-mpi) and sets
# of packages. Here we split them into the two categories for a more useful
# output:
toolchain_list = [
x.parents[0].name
for x in list((tmp_dir_path / "toolchains").glob("*/spack.yaml"))
]
x.parents[0].name for x in list((tmp_dir_path / "toolchains").glob("*/*.list"))
]
# summarise toolchains found for use, and show packages provided for each
# package_set:
print_log.info(
f"MPSD software release {mpsd_release}, AVAILABLE for installation are"
)
print_log.info("Toolchains: \n " + "\n ".join(sorted(toolchain_list)))
print_log.info("Package sets:")
# that have the regex pattern \w+@\w+
packages = [
line.split()[0].split("%")[0]
for line in open(
tmp_dir_path / "toolchains" / package_set / "global_packages.list"
).readlines()
if re.match(r"^\w+@\w+", line)
]
print_log.info(f" {package_set} ({', '.join(packages)}) ")
# remove temporary directory
tmp_dir.cleanup()
# Helper class to change directory via context manager
class os_chdir:
"""The os_chdir class is a context manager.
It changes the current directory to a specified directory
and returns to the original directory after execution.
"""
"""Initialize, save original directory."""
self.new_dir = new_dir
self.saved_dir = os.getcwd()
"""Go to target directory (main action for context)."""
def __exit__(self, exc_type, exc_val, exc_tb):
"""On exist we return to original directory."""
def run(*args, counter=[0], **kwargs):
"""
Convenience function to call `subprocess.run` and provide some metadata
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about the call.
Parameters
----------
args : tuple
passed on to subprocess.run(*args). For example
("ls -l") or (["ls", "-l"])
counter : TYPE, optional
list with one integer, starting from [0].
This is (a Python hack) to count the number of
calls of this function, so the different calls of subprocess.run
are easier to follow in the log files.
kwargs : dict
keyword-value arguments to be passed to subprocess.run. For example,
`shell=True`.
Returns
-------
process : subprocess.CompletedProcess
CompletedProcess object as returned by `subprocess.run` .
Examples
--------
>>> run(['date', '+%Y-%m-%d'])
##-03 Starting subprocess.run(['date', '+%Y-%m-%d']) with options
##-03 getcwd=/Users/fangohr/git/mpsd-software-environments
##-03 COMMAND=date +%Y-%m-%d
2023-05-30
##-03 Completed in 0.0054s.
##-03
CompletedProcess(args=['date', '+%Y-%m-%d'], returncode=0)
>>> run(['date +%Y-%m-%d'], shell=True)
##-04 Starting subprocess.run(['date +%Y-%m-%d']) with options shell=True
##-04 getcwd=/Users/fangohr/git/mpsd-software-environments
##-04 COMMAND=date +%Y-%m-%d
2023-05-30
##-04 Completed in 0.0069s.
##-04
CompletedProcess(args=['date +%Y-%m-%d'], returncode=0)
"""
# token is printed in front of every meta-data line - useful for
# searching the logs. Starts with "##-00", then "##-01", ...
token = f"##-{counter[0]:02d}"
counter[0] += 1 # increase counter
# make command nicely readable: ["ls", "-l"] -> "ls -l"
assert isinstance(args, tuple)
assert len(args) == 1
arg = args[0]
# either args is a tuple containing a string | Example: ('ls -1',)
if isinstance(arg, str):
command = arg
# or we have a tuple containing a list of strings.
# Example: (['ls', '-1'],)
elif isinstance(arg, list):
command = " ".join(arg)
else:
# we do not expect this to happen
raise NotImplementedError(f"{arg=}, {args=}")
# make options (such as `shell=True`) nicely readable
options = ", ".join([f"{key}={value}" for key, value in kwargs.items()])
# provide information about upcoming subprocess.run call
logging.debug(
f"{token} Starting subprocess.run('{command}') with options {options}"
)
logging.debug(f"""{token} getcwd={os.getcwd()}""")
logging.debug(f"""{token} subprocess.run("{arg}")""")
time_start = time.time()
process = subprocess.run(*args, **kwargs)
execution_time = time.time() - time_start
logging.debug(f"{token} Completed in {execution_time:.4f}s.")
logging.debug(f"{token}") # near-empty line to make reading logs easier
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def write_to_file(file_path: Path, content: str) -> None:
"""Write content to file.
Parameters
----------
file_path : Path
The path to the file to write to.
content : str
The content to write to the file.
Returns
-------
None
"""
with open(file_path, "a") as f:
f.write(content)
def write_to_cmd_log(root_dir: Path, msg: str) -> None:
"""Write message to command log.
Parameters
----------
root_dir : Path
The path where the script is initialized.
msg : str
The message to write to the command log.
Returns
-------
- None
"""
cmd_log_file_path = root_dir / config_vars["cmd_log_file"]
write_to_file(cmd_log_file_path, msg)
def record_script_execution_summary(
root_dir: Path, apex_log_file: Union[Path, None] = None
) -> None:
"""Log the command used to build the package_set.
A date time header is added to the log file each time the script is called,
following which the commands executed by the user is logged.
The APEX log file is also logged if it is created.
for example:
```
2023-06-28T11:18:10.718020
$ mpsd-software install dev-23a foss2021a-mpi
```
- root_dir : Path
The path where the script is initialized.
Returns
-------
- None
cmd_line = command_name + " " + " ".join(sys.argv[1:])
date_time = datetime.datetime.now().replace(microsecond=0).isoformat()
msg = f"\n {date_time}\n"
msg += f"$ {cmd_line}\n"
if apex_log_file:
# apex_log_file is not known when `init` is called
msg += f"> logging to {apex_log_file}\n"
def clone_repo(
target_path: Path, repo_url: str, branch=None, capture_output=True
) -> None:
"""Clone repo locally. Optionally checkout a branch.
target_path : Path
Where to check the repository out to
repo_url: str
where to clone the git repository from
branch: str (defaults to None)
if provided, checkout this branch after cloning
capture_output: bool (defaults to True)
capture output, i.e. do not send it to stdout.
if not target_path.exists():
target_path.mkdir()
["git", "clone", repo_url, str(target_path)],
capture_output=capture_output,
)
if branch:
with os_chdir(target_path):
# Git fetch and checkout the release branch and git pull
# to be sure that the resulting repo is up to date
run(["git", "fetch", "--all"], check=True, capture_output=capture_output)
checkout_result = run(
["git", "checkout", branch], capture_output=capture_output
)
if checkout_result.returncode != 0:
branches_result = run(
["git", "branch", "-a"], check=True, capture_output=True
branches_list = branches_result.stdout.decode().split("\n")
# strip off 'remotes/origin' (needs Python 3.9):
branches_list = [
b.strip().removeprefix("remotes/origin/") for b in branches_list
]
msg += f"Available branches are {branches_list}"
logging.error(msg)
raise Exception(msg, branches_result)
else:
run(["git", "pull"], check=True, capture_output=capture_output)
def get_available_releases(print_result: bool = False) -> List[str]:
"""
Return available MPSD software release versions.
Example
-------
>>> get_available_releases()
["dev-23a"]
Notes
-----
This needs to be updated when a new version (such as 23b) is released.
"""
releases = ["dev-23a"]
print_log = logging.getLogger("print")
if print_result:
print_log.info("Available MPSD software releases:")
for release in releases:
print_log.info(f" {release}")
return releases
def get_release_info(mpsd_release: str, root_dir: Path) -> Tuple[str, str, List[str]]:
Get information about the specified release.
Get information about the specified release, such as the branch and commit hash
of the Spack environments repository and the available package_sets.
Parameters
----------
The name of the release to get information for.
The base directory where releases are stored.
Returns
-------
The name of the branch for the Spack environments repository.
The commit hash for the Spack environments repository.
available_package_sets : list
A list of strings representing the available package_sets for the release.
Raises
------
If the release directory does not exist.
# TODO - review this function: can we re-use get_available_package_sets?
# Get the info for release
release_base_dir = root_dir / mpsd_release
if not os.path.exists(release_base_dir):
logging.debug(f"get_release_info({mpsd_release=}, {root_dir=})")
raise FileNotFoundError(
with os_chdir(release_base_dir):
with os_chdir("spack-environments"):
# Get the branch and commit hash of the spack-environments repo
spe_commit_hash = (
run(["git", "rev-parse", "HEAD"], stdout=subprocess.PIPE, check=True)
spe_branch = (
["git", "rev-parse", "--abbrev-ref", "HEAD"],
stdout=subprocess.PIPE,
check=True,
available_package_sets = os.listdir("toolchains")
return spe_branch, spe_commit_hash, available_package_sets
def prepare_environment(mpsd_release: str, root_dir: Path) -> List[str]:
Create the directory structure for the given MPSD release.
It does the following steps:
Clones the spack-environments repository.
Determines the branch and commit hash of the spack-environments repository
Parameters
----------
mpsd_release : str
The name of the MPSD release to prepare the environment for.
The base directory to create the release folder and
clone the spack-environments repository into.
available_package_sets : list
A list of available package_sets for the given MPSD release.
Example
-------
>>> prepare_environment('dev-23a', Path('.'))
['foss2021a-cuda-mpi',
'foss2021a-mpi',
'foss2021a-serial',
'foss2022a-cuda-mpi',
'foss2022a-mpi',
'foss2022a-serial',
'global',
'global_generic']
# TODO review: - does this function need to return anything? If yes:
# TODO review: - can we re-use get_available_package sets?
# Creates the directory structure for the specified release and clone the
# Spack environments repository if it doesn't exist:
# Create the directory structure for the release
release_base_dir = root_dir / mpsd_release
release_base_dir.mkdir(parents=True, exist_ok=True)
repo_path = release_base_dir / "spack-environments"
if repo_path.exists():
logging.debug(f"directory {repo_path} exists already, will update")
with os_chdir(repo_path):
run(["git", "pull", "-v"], capture_output=True)
else:
repo_url = config_vars["spack_environments_repo"]
logging.info(f"cloning repository {repo_path} from {repo_url}")
clone_repo(repo_path, repo_url, branch=f"releases/{mpsd_release}")
logging.getLogger("print").info(
f"Release {mpsd_release} is prepared in {release_base_dir}"
)
spe_branch, spe_commit_hash, available_package_sets = get_release_info(
write_to_cmd_log(
root_dir=root_dir,
msg=(
f"Spack environments branch: {spe_branch} "
f"(commit hash: {spe_commit_hash})\n"
),
def get_native_microarchitecture():
"""Return native microarchitecture.
On MPSD machines, there should be an environment variable "microarch".
We try to read that. If it fails, we use the 'archspec cpu' command.
If that fails, we ask the user to install it.
Returns
-------
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
Example
-------
>>> get_native_microarchitecture()
'haswell'
"""
# attempt to get MICRO_ARCH from environment variable (should work on
# MPSD_HPC and MPSD linux laptops). If not defined, return
# "UNKNOWN_MICROARCH"
microarch = os.environ.get("MPSD_MICROARCH", "UNKNOWN_MICROARCH")
# if we have not found the microarchitecture environment variable,
# try calling archspec
if microarch == "UNKNOWN_MICROARCH":
logging.debug(
"Couldn't find MPSD_MICROARCH environment variable. Will try archspec."
)
try:
process = run(["archspec", "cpu"], stdout=subprocess.PIPE, text=True)
except FileNotFoundError as e:
logging.debug(f"Call of 'archspec cpu' failed: {e=}")
# Presumably 'archspec' is not installed.
msg = "Please install archspec, for example via 'pipx install archspec'.\n"
msg += "The command we need to execute is 'archspec cpu'.\n"
msg += "Documentation of package: https://archspec.readthedocs.io/"
logging.error(msg)
else: # we have found archspec and executed it
if process.returncode == 0: # sanity check
microarch = process.stdout.strip()
logging.debug(
f"Found microarchitecture from 'archspec cpu' to be '{microarch}'"
)
assert len(microarch) > 0 # sanity check
else:
raise ValueError(
f"Some error occurred when calling 'archspec cpu': {process=}"
)
# at this point, we have determined the microarchitecture
log_metadata("microarchitecture", microarch)
return microarch
def install_environment(
mpsd_release: str,
enable_build_cache: bool = False,
) -> None:
Install the specified MPSD release and package_sets.
The function installs the package_set to the specified directory, using Spack.
Parameters
----------
mpsd_release : str
A string representing the MPSD release version.