Commit 18dfceb0 authored by Leo Gordon's avatar Leo Gordon
Browse files

removed obsolete -maximise_concurrency and -batch_size options from both scripts

parent 346613a2
......@@ -67,7 +67,6 @@ sub main {
$self->{'sleep_minutes'} = 1;
$self->{'verbose_stats'} = 1;
$self->{'maximise_concurrency'} = undef;
$self->{'retry_throwing_jobs'} = undef;
$self->{'hive_output_dir'} = undef;
......@@ -107,9 +106,6 @@ sub main {
'retry_throwing_jobs=i' => \$self->{'retry_throwing_jobs'},
'debug=i' => \$self->{'debug'},
'batch_size=i' => \$self->{'batch_size'}, # OBSOLETE!
'maximise_concurrency=i' => \$self->{'maximise_concurrency'}, # OBSOLETE!
# other commands/options
'h|help' => \$help,
'sync' => \$sync,
......@@ -132,15 +128,6 @@ sub main {
if ($help) { script_usage(0); }
if( defined($self->{'batch_size'}) ) {
print "\nERROR : -batch_size flag is obsolete, please modify batch_size of the analysis instead\n";
script_usage(1);
}
if( defined($self->{'maximise_concurrency'}) ) {
print "\nERROR : -maximise_concurrency flag is obsolete, please set the -priority of the analysis instead\n";
script_usage(1);
}
parse_conf($self, $conf_file);
if($run or $self->{'run_job_id'}) {
......@@ -170,7 +157,6 @@ sub main {
}
my $queen = $self->{'dba'}->get_Queen;
# $queen->{'maximise_concurrency'} = 1 if ($self->{'maximise_concurrency'});
$queen->{'verbose_stats'} = $self->{'verbose_stats'};
my $pipeline_name = destringify(
......@@ -358,7 +344,7 @@ sub generate_worker_cmd {
if ($self->{'run_job_id'}) {
$worker_cmd .= " -job_id ".$self->{'run_job_id'};
} else {
foreach my $worker_option ('job_limit', 'life_span', 'logic_name', 'maximise_concurrency', 'retry_throwing_jobs', 'hive_output_dir', 'debug') {
foreach my $worker_option ('job_limit', 'life_span', 'logic_name', 'retry_throwing_jobs', 'hive_output_dir', 'debug') {
if(defined(my $value = $self->{$worker_option})) {
$worker_cmd .= " -${worker_option} $value";
}
......@@ -532,9 +518,6 @@ __DATA__
-hive_output_dir <path> : directory where stdout/stderr of the hive is redirected
-debug <debug_level> : set debug level of the workers
-batch_size <num> : [OBSOLETE!] Please modify batch_size of the analysis instead
-maximise_concurrency 1 : [OBSOLETE!] Please set the -priority of the analysis instead
=head2 Other commands/options
-help : print this help
......
......@@ -23,7 +23,6 @@ my ($conf_file, $reg_conf, $reg_alias, $url); # Connection par
my ($rc_id, $logic_name, $analysis_id, $input_id, $job_id); # Task specification parameters
my ($job_limit, $life_span, $no_cleanup, $no_write, $hive_output_dir, $worker_output_dir, $retry_throwing_jobs); # Worker control parameters
my ($help, $debug, $show_analysis_stats);
my ($batch_size, $maximise_concurrency); # OBSOLETE options since December 2011
GetOptions(
......@@ -54,31 +53,17 @@ GetOptions(
'worker_output_dir=s' => \$worker_output_dir, # will take precedence over hive_output_dir if set
'retry_throwing_jobs=i' => \$retry_throwing_jobs,
'batch_size=i' => \$batch_size, # OBSOLETE!
# Other commands
'h|help' => \$help,
'debug=i' => \$debug,
'analysis_stats' => \$show_analysis_stats,
'maximise_concurrency=i' => \$maximise_concurrency, # OBSOLETE!
# loose arguments interpreted as database name (for compatibility with mysql[dump])
'<>', sub { $db_conf->{'-dbname'} = shift @_; },
);
if ($help) { script_usage(0); }
if( defined($batch_size) ) {
print "\nERROR : -batch_size flag is obsolete, please modify batch_size of the analysis instead\n";
script_usage(1);
}
if( defined($maximise_concurrency) ) {
print "\nERROR : -maximise_concurrency flag is obsolete, please set the -priority of the analysis instead\n";
script_usage(1);
}
parse_conf($conf_file);
if($reg_conf) { # if reg_conf is defined, we load it regardless of whether it is used to connect to the Hive database or not:
......@@ -103,7 +88,6 @@ unless($DBA and $DBA->isa("Bio::EnsEMBL::Hive::DBSQL::DBAdaptor")) {
}
my $queen = $DBA->get_Queen();
# $queen->{maximise_concurrency} = 1 if ($maximise_concurrency);
my ($meadow_type, $process_id, $exec_host) = Bio::EnsEMBL::Hive::Meadow->guess_current_type_pid_exechost();
......@@ -134,9 +118,6 @@ eval {
-hive_output_dir => $hive_output_dir,
-retry_throwing_jobs => $retry_throwing_jobs,
## Obsolete:
# -batch_size => $batch_size,
# Other parameters:
-debug => $debug,
);
......@@ -252,16 +233,12 @@ __DATA__
-worker_output_dir <path> : directory where stdout/stderr of this particular worker is redirected
-retry_throwing_jobs <0|1> : if a job dies *knowingly*, should we retry it by default?
-batch_size <num> : [OBSOLETE!] Please modify -batch_size of the analysis instead
=head2 Other options:
-help : print this help
-debug <level> : turn on debug messages at <level>
-analysis_stats : show status of each analysis in hive
-maximise_concurrency <0|1> : [OBSOLETE!] Please set the -priority of the analysis instead
=head1 CONTACT
Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
......
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