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ensembl-gh-mirror
ensembl
Commits
c25b660f
Commit
c25b660f
authored
Jul 23, 2010
by
Andreas Kusalananda Kähäri
Browse files
Only submit sequence dumping jobs if there are jobs to submit.
parent
76bfdd44
Changes
1
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1 changed file
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27 additions
and
22 deletions
+27
-22
misc-scripts/id_mapping/dump_cache.pl
misc-scripts/id_mapping/dump_cache.pl
+27
-22
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misc-scripts/id_mapping/dump_cache.pl
View file @
c25b660f
...
...
@@ -278,40 +278,45 @@ sub build_cache_by_seq_region {
# run lsf job array
$logger
->
info
("
\n
Submitting
$num_jobs
jobs to lsf.
\n
");
$logger
->
debug
("
$cmd
\n\n
");
$logger
->
debug
("
$pipe
\n\n
");
local
*BSUB
;
open
BSUB
,
$pipe
or
$logger
->
error
("
Could not open open pipe to bsub: $!
\n
");
if
(
$num_jobs
>
0
)
{
$logger
->
debug
("
$cmd
\n\n
");
$logger
->
debug
("
$pipe
\n
\n
");
print
BSUB
$cmd
;
$logger
->
error
("
Error submitting jobs: $!
\n
")
unless
(
$?
==
0
);
close
BSUB
;
local
*BSUB
;
open
BSUB
,
$pipe
or
$logger
->
error
("
Could not open open pipe to bsub: $!
\n
");
# submit dependent job to monitor finishing of jobs
$logger
->
info
(
"
Waiting for jobs to finish...
\n
",
0
,
'
stamped
'
);
print
BSUB
$cmd
;
$logger
->
error
("
Error submitting jobs: $!
\n
")
unless
(
$?
==
0
);
close
BSUB
;
my
$dependent_job
=
qq{bsub -K -w "ended($lsf_name)" }
.
$conf
->
param
('
lsf_opt_run_small
')
.
qq{ -o $logpath/dump_cache.$dbtype.depend.out /bin/true}
;
# submit dependent job to monitor finishing of jobs
$logger
->
info
(
"
Waiting for jobs to finish...
\n
",
0
,
'
stamped
'
);
system
(
$dependent_job
)
==
0
or
$logger
->
error
("
Error submitting dependent job: $!
\n
");
my
$dependent_job
=
qq{bsub -K -w "ended($lsf_name)" }
.
$conf
->
param
('
lsf_opt_run_small
')
.
qq{ -o $logpath/dump_cache.$dbtype.depend.out /bin/true}
;
$logger
->
info
(
"
All jobs finished.
\n
",
0
,
'
stamped
'
);
system
(
$dependent_job
)
==
0
or
$logger
->
error
("
Error submitting dependent job: $!
\n
");
$logger
->
info
(
"
All jobs finished.
\n
",
0
,
'
stamped
'
);
sleep
(
5
);
}
## end if ( $num_jobs > 0 )
# check for lsf errors
sleep
(
5
);
my
$err
;
foreach
my
$i
(
1
..
$num_jobs
)
{
$err
++
unless
(
-
e
"
$logpath
/dump_by_seq_region.
$dbtype
.
$i
.success
"
);
if
(
!-
e
"
$logpath
/dump_by_seq_region.
$dbtype
.
$i
.success
"
)
{
$err
++
;
}
}
if
(
$err
)
{
if
(
$err
>
0
)
{
$logger
->
error
(
"
At least one of your jobs failed.
\n
"
.
"
Please check the logfiles at
$logpath
for errors.
\n
"
);
return
1
;
...
...
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