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Building a Package

This guide documents how to extend the set of applications that Jarvis is able to deploy. We refer to these as packages (pkgs for short).

Bootstrap a Pkg​

You can bootstrap a pkg to the primary repo as follows:

jarvis repo create [name] [pkg_class]

pkg_class can be one of:

  • service
  • app
  • interceptor

For example:

jarvis repo create hermes service
jarvis repo create hermes_mpiio interceptor
jarvis repo create gray_scott app

We can then create an example pipeline as follows:

jarvis pipeline create test
jarvis pipeline append hermes
jarvis pipeline append hermes_mpiio
jarvis pipeline append gray_scott

This is an example of a pipeline which will deploy Hermes, the Hermes MPI-IO interceptor, and Gray Scott, which is an application which performs I/O using MPI.

The Pkg Base Class​

This section will go over the variables and methods common across all Pkg types. These variables will be initialized automatically.

class Pkg:
  def __init__(self):
    self.pkg_dir = '...'
    self.shared_dir = '...'
    self.private_dir = '...'
    self.env = {}
    self.config = {}
    self.global_id = '...'
    self.pkg_id = '...'

pkg_id and global_id​

The Global ID (global_id) is the globally unique ID of the a package in all of jarvis. It is a dot-separated string. Typically, the format is:

{pipeline_id}.{pkg_id}

The Package ID (pkg_id) is the unique ID of the package relative to a pipeline. This is a simple string (no dots).

For example, from section 5.1, we appended 3 packages: hermes, hermes_mpiio, and gray_scott. hermes, hermes_mpiio, and gray_scott are also the pkg_ids. The global_ids would be:

test.hermes
test.hermes_mpiio
test.gray_scott

Usage:

self.global_id
self.pkg_id

pkg_dir​

The package directory is the location of the class python file on the filesystem. For example, when calling jarvis repo create hermes, the directory created by this command will be the pkg_dir.

One use case for the pkg_dir is for creating template configuration files. For example, OrangeFS has a complex XML configuration which would be a pain to repeat in Python. One could include an OrangeFS XML config in their package directory and commit as part of their Jarvis repo.

Usage:

self.pkg_dir

shared_dir​

The shared_dir is a directory stored on a filesystem common across all nodes in the hostfile. Each node has the same view of data in the shared_dir. The shared_dir contains data for the specific pkg to avoid conflicts in a pipeline with multiple pkgs.

For example, when deploying Hermes, we assume that each node has the Hermes configuration file. Each node is expected to have the same configuration file. We store the Hermes config in the shared_dir.

Usage:

self.shared_dir

private_dir​

This is a directory which is common across all nodes, but nodes do not have the same view of data.

For example, when deploying OrangeFS, it is required that each node has a file called pvfs2tab. It essentially stores the protocol + address that OrangeFS uses for networking. However, the content of this file is different for each node. Storing it in the shared_dir would be incorrect. This is why we need the private_dir.

Usage:

self.private_dir

env​

Jarvis pipelines store the current environment in a YAML file, which represents a python dictionary. The key is the environment variable name (string) and the value is the intended meaning of the variable. There is a single environment used for the entire pipeline. Each pipeline stores its own environment to avoid conflict.

Usage:

self.env['VAR_NAME']

Environments can be modified using various helper functions:

self.track_env(env_track_dict)
self.prepend_env(env_name, val)
self.setenv(env_name, val)

Viewing the env YAML file for the current pipeline from the CLI

cat `jarvis path`/env.yaml

config​

The Jarvis configuration is stored in {pkg_dir}/{pkg_id}.yaml. Unlike the environment dict, this stores variables that are specific to the package. They are not global to the pipeline.

For example, OrangeFS and Hermes need to know the desired port number and RPC protocol. This information is specific to the program, not the entire pipeline.

Usage:

self.config['VAR_NAME']

jarvis​

The Jarvis CD configuration manager stores various properties global to all of Jarvis. The most important information is the hostfile and resource_graph, discussed in the next sections.

Usage:

self.jarvis

hostfile​

The hostfile contains the set of all hosts that Jarvis has access to. The hostfile format is documented here.

Usage:

self.jarvis.hostfile

resource_graph​

The resource graph can be queried to get storage and networking information for storing large volumes of data.

self.jarvis.resource_graph

Building a Service or Application​

Services and Applications implement the same interface, but are logically slightly different. A service is long-running and would typically require the users to manually stop it. Applications stop automatically when it finishes doing what it's doing. Jarvis can deploy services alongside applications to avoid the manual stop when benchmarking.

_init​

The Jarvis constructor (_init) is used to initialize global variables. Don't assume that self.config is initialized. This is to provide an overview of the parameters of this class. Default values should almost always be None.

def _init(self):
  self.gray_scott_path = None

_configure_menu​

The function defines the set of command line options that the user can set. An example configure menu is below:

def _configure_menu(self):
    """
    Create a CLI menu for the configurator method.
    For thorough documentation of these parameters, view:
    https://github.com/scs-lab/jarvis-util/wiki/3.-Argument-Parsing

    :return: List(dict)
    """
    return [
        {
            'name': 'port',
            'msg': 'The port to listen for data on',
            'type': int,
            'default': 8080
        }
    ]

This function is called whenever configuring a package. For example,

jarvis pkg configure hermes --sleep=10 --port=25

This will configure hermes to sleep for 10 seconds after launching to give enough time to fully start Hermes. Sleep is apart of all configure menus by default.

The format of the output dict is documented in more detail here.

configure​

It takes as input a dictionary. The keys of this dict are determined from _configure_menu function output. It is responsible for updating the self.config variable appropriately and generating the application-specific configuration files.

Below is an example for Hermes. This example takes as input the port option, modifies the hermes_server dict, and then stores the dict in a YAML file in the shared directory.

def configure(self, **kwargs):
    """
    Converts the Jarvis configuration to application-specific configuration.
    E.g., OrangeFS produces an orangefs.xml file.

    :param config: The human-readable jarvis YAML configuration for the
    application.
    :return: None
    """
    self.update_config(kwargs, rebuild=False)
    hermes_server_conf = {
      'port': self.config['port']
    }
    YamlFile(f'{self.shared_dir}/hermes_server_yaml').save(hermes_server_conf)

This function is called whenever configuring a packge. Specifically, this is called immediately after _configure_menu. For example,

jarvis pkg configure hermes --sleep=10 --port=25

will make the kwargs dict be:

{
  'sleep': 10,
  'port': 25
}

start​

The start function is called during jarvis pipeline run and jarvis pipeline start. This function should execute the program itself.

Below is an example for Hermes:

def start(self):
    """
    Launch an application. E.g., OrangeFS will launch the servers, clients,
    and metadata services on all necessary pkgs.

    :return: None
    """
    self.daemon_pkg = Exec('hermes_daemon',
                            PsshExecInfo(hostfile=self.jarvis.hostfile,
                                         env=self.env,
                                         exec_async=True))
    time.sleep(self.config['sleep'])
    print('Done sleeping')

stop​

The stop function is called during jarvis pipeline run and jarvis pipeline stop. This function should terminate the program.

Below is an example for Hermes:

def stop(self):
    """
    Stop a running application. E.g., OrangeFS will terminate the servers,
    clients, and metadata services.

    :return: None
    """
    Exec('finalize_hermes',
         PsshExecInfo(hostfile=self.jarvis.hostfile,
                      env=self.env))
    if self.daemon_pkg is not None:
        self.daemon_pkg.wait()
    Kill('hermes_daemon',
         PsshExecInfo(hostfile=self.jarvis.hostfile,
                      env=self.env))

This is not typically implemented for Applications, but it is for Services.

clean​

The clean function is called during jarvis pipeline clean. It clears all intermediate data produced by a pipeline.

Below is the prototype

def clean(self):
    """
    Destroy all data for an application. E.g., OrangeFS will delete all
    metadata and data directories in addition to the orangefs.xml file.

    :return: None
    """
    pass

status​

The status function is called during jarvis pipeline status It determines whether or not a service is running. This is not typically implemented for Applications, but it is for Services.

Building an Interceptor​

Interceptors are used to modify environment variables to route system and library calls to new functions.

Interceptors have a slightly different interface -- they only have: _init, _configure_menu, configure, and modify_env. The only new function here is modify_env. The others were defined in the previous section and behave the exact same way.

configure​

Configuring an interceptor tends to be a little different. The interceptors are not typically responsible for generating configuration files like the applications and services do. These typically are responsible solely for modifying the environment.

Below, we show an example of configure for the Hermes MPI I/O interceptor:

def configure(self, **kwargs):
    """
    Converts the Jarvis configuration to application-specific configuration.
    E.g., OrangeFS produces an orangefs.xml file.

    :param kwargs: Configuration parameters for this pkg.
    :return: None
    """
    self.update_config(kwargs, rebuild=False)
    self.config['HERMES_MPIIO'] = self.find_library('hermes_mpiio')
    if self.config['HERMES_MPIIO'] is None:
        raise Exception('Could not find hermes_mpiio')
    print(f'Found libhermes_mpiio.so at {self.config["HERMES_MPIIO"]}')

Here we use self.find_library() to check if we can find the shared library hermes_mpiio in the system paths. This function introspects LD_LIBRARY_PATH and determines if hermes_mpiio is in the path. It saves the path in the pkg configuration (self.config).

modify_env​

Below is an example of the MPI I/O interceptor for Hermes:

def modify_env(self):
    """
    Modify the jarvis environment.

    :return: None
    """
    self.prepend_env('LD_PRELOAD', self.config['HERMES_MPIIO'])

A Note on jarvis-util​

jarvis-cd aims to provide structure to storing configuration files for simplifying complex benchmarks.

jarvis-util is primarily responsible for handling program execution. This includes things like executing MPI and PSSH in Python. This is where the Exec and PsshExecInfo data structures come from. More information on jarvis-util can be found here.