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ensembl-gh-mirror
ensembl-hive
Commits
02e0979e
Commit
02e0979e
authored
May 20, 2014
by
Leo Gordon
Browse files
api_change: do not assume all Meadows treat job arrays in the same way as LSF (thanks, Lel!)
parent
df91e74f
Changes
2
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2 changed files
with
6 additions
and
7 deletions
+6
-7
modules/Bio/EnsEMBL/Hive/Meadow.pm
modules/Bio/EnsEMBL/Hive/Meadow.pm
+3
-5
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
+3
-2
No files found.
modules/Bio/EnsEMBL/Hive/Meadow.pm
View file @
02e0979e
...
...
@@ -99,12 +99,10 @@ sub job_name_prefix {
}
sub
generate_job
_name
{
my
(
$self
,
$
worker_count
,
$iteration
,
$rc_name
)
=
@_
;
sub
job_array_common
_name
{
my
(
$self
,
$
rc_name
,
$iteration
)
=
@_
;
return
$self
->
job_name_prefix
()
.
"
${rc_name}
-
${iteration}
"
.
((
$worker_count
>
1
)
?
"
[1-
${worker_count}
]
"
:
'');
return
$self
->
job_name_prefix
()
.
"
${rc_name}
-
${iteration}
";
}
...
...
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
View file @
02e0979e
...
...
@@ -289,7 +289,8 @@ sub get_report_entries_for_time_interval {
sub
submit_workers
{
my
(
$self
,
$worker_cmd
,
$required_worker_count
,
$iteration
,
$rc_name
,
$rc_specific_submission_cmd_args
,
$submit_stdout_file
,
$submit_stderr_file
)
=
@_
;
my
$job_name
=
$self
->
generate_job_name
(
$required_worker_count
,
$iteration
,
$rc_name
);
my
$job_array_common_name
=
$self
->
job_array_common_name
(
$rc_name
,
$iteration
);
my
$job_array_name_with_indices
=
$job_array_common_name
.
((
$required_worker_count
>
1
)
?
"
[1-
${required_worker_count}
]
"
:
'');
my
$meadow_specific_submission_cmd_args
=
$self
->
config_get
('
SubmissionOptions
');
$submit_stdout_file
||=
'
/dev/null
';
# a value is required
...
...
@@ -297,7 +298,7 @@ sub submit_workers {
$ENV
{'
LSB_STDOUT_DIRECT
'}
=
'
y
';
# unbuffer the output of the bsub command
my
$cmd
=
qq{bsub -o $submit_stdout_file -e $submit_stderr_file -J "${job_
name
}" $rc_specific_submission_cmd_args $meadow_specific_submission_cmd_args $worker_cmd}
;
my
$cmd
=
qq{bsub -o $submit_stdout_file -e $submit_stderr_file -J "${job_
array_name_with_indices
}" $rc_specific_submission_cmd_args $meadow_specific_submission_cmd_args $worker_cmd}
;
warn
"
LSF::submit_workers() running cmd:
\n\t
$cmd
\n
";
...
...
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