MemlimitTest_conf.pm

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=pod
 
=head1 NAME
 
    Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::MemlimitTest_conf
 
=head1 SYNOPSIS
 
    init_pipeline.pl Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::MemlimitTest_conf -password <your_password>
 
=head1 DESCRIPTION
 
    This is another example pipeline built around FailureTest.pm RunnableDB. It consists of two analyses:
 
    Analysis_1: JobFactory.pm is used to create an array of jobs -
 
        these jobs are sent down the branch #2 into the second analysis
 
    Analysis_2: FailureTest.pm in "memory grab" mode may overrun the current resource's memory limit and be killed by the LSF
 
=head1 LICENSE
 
    See the NOTICE file distributed with this work for additional information
    regarding copyright ownership.
 
    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
         http://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
 
=head1 CONTACT
 
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
 
=cut
 
 
package Bio::EnsEMBL::Hive::Examples::FailureTest::PipeConfig::MemlimitTest_conf;
 
use strict;
use warnings;
 
use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');  # All Hive databases configuration files should inherit from HiveGeneric, directly or indirectly
 
 
sub resource_classes {
    my ($self) = @_;
    return {
        %{$self->SUPER::resource_classes},  # inherit 'default' from the parent class
 
         'default'      => {'LSF' => '-C0 -M100   -R"select[mem>100]   rusage[mem=100]"' }, # to make sure it fails similarly on both farms
         '200Mb_job'    => {'LSF' => '-C0 -M200   -R"select[mem>200]   rusage[mem=200]"' },
         '400Mb_job'    => {'LSF' => '-C0 -M400   -R"select[mem>400]   rusage[mem=400]"' },
         '1Gb_job'      => {'LSF' => '-C0 -M1000  -R"select[mem>1000]  rusage[mem=1000]"' },
    };
}
 
 
sub pipeline_analyses {
    my ($self) = @_;
    return [
        {   -logic_name => 'generate_jobs',
            -module     => 'Bio::EnsEMBL::Hive::RunnableDB::JobFactory',
            -meadow_type => 'LOCAL',
            -parameters => {
                'column_names' => [ 'grab_mln' ],
            },
            -input_ids => [
                { 'inputlist' => [ 0.6 , 0.8 , 1.0 , 1.2 , 1.4 , 1.6 , 1.8 , 2.0, 2.5, 3.0, 5.0, 7.0, 10 ], },
            ],
 
            -flow_into => {
                2 => [ 'failure_test' ],
            },
        },
 
        {   -logic_name    => 'failure_test',
            -module        => 'Bio::EnsEMBL::Hive::Examples::FailureTest::RunnableDB::FailureTest',
            -parameters => {
                'time_RUN'      => 30,
            },
            -rc_name => 'default',      # pick a valid value from resource_classes() section
        },
    ];
}
 
1;