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ensembl-gh-mirror
ensembl-hive
Commits
11ebc755
Commit
11ebc755
authored
Sep 16, 2010
by
Leo Gordon
Browse files
more uniform treatment of worker_options
parent
cd2723ef
Changes
2
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2 changed files
with
9 additions
and
11 deletions
+9
-11
scripts/beekeeper.pl
scripts/beekeeper.pl
+7
-9
scripts/runWorker.pl
scripts/runWorker.pl
+2
-2
No files found.
scripts/beekeeper.pl
View file @
11ebc755
...
...
@@ -91,7 +91,7 @@ sub main {
'
meadow_options|lsf_options=s
'
=>
\
$meadow_options
,
# 'lsf_options' is deprecated (please investigate the resource requirements, they may suit your needs way better)
# worker control
'
jlimit=i
'
=>
\
$self
->
{'
job_limit
'},
'
j
ob_limit|j
limit=i
'
=>
\
$self
->
{'
job_limit
'},
'
batch_size=i
'
=>
\
$self
->
{'
batch_size
'},
'
lifespan=i
'
=>
\
$self
->
{'
lifespan
'},
'
logic_name=s
'
=>
\
$self
->
{'
logic_name
'},
...
...
@@ -322,13 +322,11 @@ sub generate_worker_cmd {
if
(
$self
->
{'
run_job_id
'})
{
$worker_cmd
.=
"
-job_id
"
.
$self
->
{'
run_job_id
'};
}
else
{
$worker_cmd
.=
(
defined
(
$self
->
{'
job_limit
'})
?
"
-limit
$self
->{'job_limit'}
"
:
'')
.
(
defined
(
$self
->
{'
batch_size
'})
?
"
-batch_size
$self
->{'batch_size'}
"
:
'')
.
(
defined
(
$self
->
{'
lifespan
'})
?
"
-lifespan
$self
->{'lifespan'}
"
:
'')
.
(
defined
(
$self
->
{'
logic_name
'})
?
"
-logic_name
$self
->{'logic_name'}
"
:
'')
.
(
$self
->
{'
maximise_concurrency
'}
?
'
-maximise_concurrency 1
'
:
'')
.
(
defined
(
$self
->
{'
retry_throwing_jobs
'})
?
"
-retry_throwing_jobs
$self
->{'retry_throwing_jobs'}
"
:
'')
.
(
$self
->
{'
hive_output_dir
'}
?
"
-hive_output_dir
$self
->{'hive_output_dir'}
"
:
'');
foreach
my
$worker_option
('
batch_size
',
'
job_limit
',
'
lifespan
',
'
logic_name
',
'
maximize_concurrency
',
'
retry_throwing_jobs
',
'
hive_output_dir
')
{
if
(
defined
(
my
$value
=
$self
->
{
$worker_option
}))
{
$worker_cmd
.=
"
-
${worker_option}
$value
";
}
}
}
if
(
$self
->
{'
reg_file
'})
{
...
...
@@ -505,7 +503,7 @@ __DATA__
=head2 Worker control
-jlimit <num>
: #jobs to run before worker can die naturally
-j
ob_
limit <num> : #jobs to run before worker can die naturally
-batch_size <num> : #jobs a worker can claim at once
-lifespan <num> : lifespan limit for each worker
-logic_name <string> : restrict the pipeline stat/runs to this analysis logic_name
...
...
scripts/runWorker.pl
View file @
11ebc755
...
...
@@ -66,7 +66,7 @@ GetOptions(
'
rc_id=i
'
=>
\
$self
->
{'
rc_id
'},
'
logic_name=s
'
=>
\
$self
->
{'
logic_name
'},
'
batch_size=i
'
=>
\
$self
->
{'
batch_size
'},
'
limit=i
'
=>
\
$self
->
{'
job_limit
'},
'
job_limit|
limit=i
'
=>
\
$self
->
{'
job_limit
'},
'
lifespan=i
'
=>
\
$self
->
{'
lifespan
'},
'
hive_output_dir|outdir=s
'
=>
\
$self
->
{'
hive_output_dir
'},
# keep compatibility with the old name
'
bk=s
'
=>
\
$self
->
{'
beekeeper
'},
# deprecated and ignored
...
...
@@ -295,7 +295,7 @@ __DATA__
-analysis_id <id> : analysis_id in db
-logic_name <string> : logic_name of analysis to make this worker
-batch_size <num> : #jobs to claim at a time
-limit <num>
: #jobs to run before worker can die naturally
-
job_
limit <num> : #jobs to run before worker can die naturally
-lifespan <num> : number of minutes this worker is allowed to run
-hive_output_dir <path> : directory where stdout/stderr of the hive is redirected
-bk <string> : beekeeper identifier (deprecated and ignored)
...
...
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