Inheritance diagram for Bio::EnsEMBL::Hive::Meadow::DockerSwarm:

Public Member Functions
public	construct_base_url ()

public	new ()

public	name ()

protected	_get_our_task_attribs ()

public	get_current_hostname ()

public	get_current_worker_process_id ()

public	deregister_local_process ()

public	status_of_all_our_workers ()

public	type_resources_as_numeric ()

public	submit_workers_return_meadow_pids ()

public	run_on_host ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Meadow
public	get_meadow_major_version ()

public	get_meadow_version ()

public	check_version_compatibility ()

public	new ()

protected	_init_meadow ()

public	cached_name ()

public	type ()

public	get_current_hostname ()

public	signature ()

public	pipeline_name ()

public	runWorker_path ()

public	job_name_prefix ()

public	job_array_common_name ()

public	name ()

public	get_current_worker_process_id ()

public	status_of_all_our_workers ()

public	check_worker_is_alive_and_mine ()

public	kill_worker ()

public	parse_report_source_line ()

public	get_report_entries_for_process_ids ()

public	get_report_entries_for_time_interval ()

public	submit_workers_return_meadow_pids ()

public	run_on_host ()

public	cleanup_temp_directory ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Configurable
public	config ()

public	context ()

public	config_get ()

public	config_set ()

Public Member Functions inherited from Bio::EnsEMBL::Hive::Utils::RESTclient
public	new ()

public	base_url ()

public	run_curl_capture_and_parse_result ()

public	GET ()

public	POST ()

Detailed Description

Description

    This is the implementation of Meadow for a Swarm or Docker Engines

Definition at line 12 of file DockerSwarm.pm.

Member Function Documentation

◆ _get_our_task_attribs()

protected Bio::EnsEMBL::Hive::Meadow::DockerSwarm::_get_our_task_attribs ( )

Undocumented method

Code:

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sub _get_our_task_attribs {
    my ($self) = @_;
 
    return $self->{_task_attribs} if $self->{_task_attribs};
 
    # Get the container ID. Although in simple cases, the hostname is the same as
    # the container ID, it is not always true. So we need to dig into cgroup stuff
 
# # docker node ls
# ID                            HOSTNAME            STATUS              AVAILABILITY        MANAGER STATUS      ENGINE VERSION
# lcprncbmd0z1523t0ft8ej9uy *   head-node           Ready               Active              Leader              18.09.0
# ksactwapa4nxaaokcj1xw62pr     worker-1            Ready               Active                                  18.09.0
# wcms6zxgq0hocoutznggs9r0u     worker-2            Ready               Active                                  18.09.0
# ior43tdjz9x7n4bzzmr5njvcr     worker-3            Ready               Active                                  18.09.0
# l6khe63f71z3ntv4abii3n9o1     worker-4            Ready               Active                                  18.09.0
# nvmy341e4a3sqtt9k3cfdmc7w     worker-5            Ready               Active                                  18.09.0
# w42pyk5wvoa0qrzbnjhn1yyt7     worker-6            Ready               Active                                  18.09.0
# 28h1sk9zwkw53bkv4bi95q2f1     worker-7            Ready               Active                                  18.09.0
# rldg2wm4h19oo9cxxrdbpx5n4     worker-8            Ready               Active                                  18.09.0
# 72cv6frnei4gjdv3p3l8bmd3c     worker-9            Ready               Active                                  18.09.0
# u21fny9eapmh09sflk45zzscz     worker-10           Ready               Active                                  18.09.0
 
# # cat /proc/self/cgroup
#13:name=systemd:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#12:pids:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#11:hugetlb:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#10:net_prio:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#9:perf_event:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#8:net_cls:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#7:freezer:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#6:devices:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#5:memory:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#4:blkio:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#3:cpuacct:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#2:cpu:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
#1:cpuset:/docker/c8ecf8b2f3f2a26543971b57fd37205164a19908871d7bd43405914fcd054bfd
 
    open(my $fh, '<', '/proc/self/cgroup');
    my $container_prefix;
    while (<$fh>) {
        if (m{:/docker/(.*)$}) {
            $container_prefix = $1;
            last;
        }
    }
    # Not running in a container
    return unless $container_prefix;
 
    my $tasks_list          = $self->GET( '/tasks' );
    my ($our_task_attribs)  = grep { ($_->{'Status'}{'ContainerStatus'}{'ContainerID'} || '') =~ /^${container_prefix}/ } @$tasks_list;
    $self->{_task_attribs}  = $our_task_attribs;
 
    return $self->{_task_attribs};
}

◆ construct_base_url()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::construct_base_url ( )

Undocumented method

Code:

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◆ deregister_local_process()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::deregister_local_process ( )

Undocumented method

Code:

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◆ get_current_hostname()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::get_current_hostname ( )

Undocumented method

Code:

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◆ get_current_worker_process_id()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::get_current_worker_process_id ( )

Undocumented method

Code:

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◆ name()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::name ( )

Undocumented method

Code:

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◆ new()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::new ( )

Undocumented method

Code:

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◆ run_on_host()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::run_on_host ( )

Undocumented method

Code:

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◆ status_of_all_our_workers()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::status_of_all_our_workers ( )

Undocumented method

Code:

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◆ submit_workers_return_meadow_pids()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::submit_workers_return_meadow_pids ( )

Undocumented method

Code:

click to view

sub submit_workers_return_meadow_pids {
    my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_log_subdir) = @_;
 
    my $worker_cmd_components = [ split_for_bash($worker_cmd) ];
 
    my $job_array_common_name = $self->job_array_common_name($rc_name, $iteration);
 
    # Name collision detection
    my $extra_suffix = 0;
    my $service_name = $job_array_common_name;
    while (scalar(@{ $self->GET( '/tasks?filters={"name":["' . $service_name . '"]}' ) })) {
        $extra_suffix++;
        $service_name = "$job_array_common_name-$extra_suffix";
    }
    if ($extra_suffix) {
        warn "'$job_array_common_name' already used to name a service. Using '$service_name' instead.\n";
        $job_array_common_name = $service_name;
    }
 
    die "The image name for the ".$self->name." DockerSwarm meadow is not configured. Cannot submit jobs !" unless $self->config_get('ImageName');
 
    # If the resource description is missing, use 1 core
    my $default_resources = {
        'Reservations'  => {
            'NanoCPUs'  => 1_000_000_000,
        },
    };
    my $resources = destringify($rc_specific_submission_cmd_args);
 
    my $service_create_data = {
        'Name'          => $job_array_common_name,      # NB: service names in DockerSwarm have to be unique!
        'TaskTemplate'  => {
            'ContainerSpec' => {
                'Image'     => $self->config_get('ImageName'),
                'Args'      => $worker_cmd_components,
                'Mounts'    => $self->config_get('Mounts'),
                'Env'       => [
                                # Propagate these to the workers
                               "DOCKER_MASTER_ADDR=$self->{'_DOCKER_MASTER_ADDR'}",
                               "_EHIVE_HIDDEN_PASS=$ENV{'_EHIVE_HIDDEN_PASS'}",
                ],
            },
            # NOTE: By default, docker alway keeps logs. Should we disable them here
            #       $submit_log_subdir has been set ? There are no options to redirect
            #       the logs, so the option's value would be ignored.
            #'LogDriver' => {
                #'Name'      => 'none',
            #},
            'Resources'     => $resources || $default_resources,
            'RestartPolicy' => {
                'Condition' => 'none',
            },
        },
        'Mode'          => {
            'Replicated'    => {
                'Replicas'  => int($required_worker_count),
            },
        },
    };
    type_resources_as_numeric($service_create_data->{'TaskTemplate'}->{'Resources'});
 
    my $service_created_struct  = $self->POST( '/services/create', $service_create_data );
    unless (exists $service_created_struct->{'ID'}) {
        die "Submission unsuccessful: " . ($service_created_struct->{'message'} // stringify($service_created_struct)) . "\n";
    }
 
    # Give some time to the Docker daemon to process the request
    sleep(5);
 
    my $service_id              = $service_created_struct->{'ID'};
    my $service_tasks_list      = $self->GET( qq{/tasks?filters={"service":["$service_id"]}} );
    if (scalar(@$service_tasks_list) != int($required_worker_count)) {
        die "Submission unsuccessful: found " . scalar(@$service_tasks_list) . " tasks instead of " . int($required_worker_count) . "\n";
    }
 
    my @children_task_ids       = map { $_->{'ID'} } @$service_tasks_list;
 
    return \@children_task_ids;
}

◆ type_resources_as_numeric()

public Bio::EnsEMBL::Hive::Meadow::DockerSwarm::type_resources_as_numeric ( )

Undocumented method

Code:

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The documentation for this class was generated from the following file:

ensembl-hive-docker-swarm/modules/Bio/EnsEMBL/Hive/Meadow/DockerSwarm.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ _get_our_task_attribs()

◆ construct_base_url()

◆ deregister_local_process()

◆ get_current_hostname()

◆ get_current_worker_process_id()

◆ name()

◆ new()

◆ run_on_host()

◆ status_of_all_our_workers()

◆ submit_workers_return_meadow_pids()

◆ type_resources_as_numeric()