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ensembl-gh-mirror
ensembl-hive
Commits
7da8c4b2
Commit
7da8c4b2
authored
Aug 13, 2021
by
Brandon Walts
Browse files
Merge branch 'version/2.6'
* version/2.6: update bacct command line for codon compatibility
parents
fd0117b2
5f83ef26
Changes
2
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8 additions
and
8 deletions
+8
-8
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
+4
-4
t/04.meadow/lsf.t
t/04.meadow/lsf.t
+4
-4
No files found.
modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm
View file @
7da8c4b2
...
...
@@ -25,9 +25,9 @@ return something like undef to tell the caller that no operation was done.
GarbageCollector: [LSF/EBI Meadow:] LOST:20
GarbageCollector: Discovered 20 lost LSF Workers
LSF::parse_report_source_line( "bacct -l '4126850[15]' '4126850[6]' '4126835[24]' '4126850[33]' '4126835[10]' '4126835[39]' '4126850[23]' '4126835[3]' '4126835[19]' '4126835[31]' '4126835[40]' '4126835[41]' '4126850[5]' '4126850[41]' '4126850[2]' '4126850[3]' '4126835[5]' '4126835[33]' '4126850[7]' '4126850[42]'" )
LSF::parse_report_source_line( "bacct
-f -
-l '4126850[15]' '4126850[6]' '4126835[24]' '4126850[33]' '4126835[10]' '4126835[39]' '4126850[23]' '4126835[3]' '4126835[19]' '4126835[31]' '4126835[40]' '4126835[41]' '4126850[5]' '4126850[41]' '4126850[2]' '4126850[3]' '4126835[5]' '4126835[33]' '4126850[7]' '4126850[42]'" )
ls_getclustername(): Slave LIM configuration is not ready yet. Please give file name.
Could not read from 'bacct -l '4126850[15]' '4126850[6]' '4126835[24]' '4126850[33]' '4126835[10]' '4126835[39]' '4126850[23]' '4126835[3]' '4126835[19]' '4126835[31]' '4126835[40]' '4126835[41]' '4126850[5]' '4126850[41]' '4126850[2]' '4126850[3]' '4126835[5]' '4126835[33]' '4126850[7]' '4126850[42]''. Received the error 255
Could not read from 'bacct
-f -
-l '4126850[15]' '4126850[6]' '4126835[24]' '4126850[33]' '4126835[10]' '4126835[39]' '4126850[23]' '4126835[3]' '4126835[19]' '4126835[31]' '4126835[40]' '4126835[41]' '4126850[5]' '4126850[41]' '4126850[2]' '4126850[3]' '4126835[5]' '4126835[33]' '4126850[7]' '4126850[42]''. Received the error 255
=back
...
...
@@ -322,7 +322,7 @@ sub get_report_entries_for_process_ids {
unless
(
$self
->
config_get
('
AccountingDisabled
'))
{
while
(
my
$pid_batch
=
join
('
',
map
{
"
'
$_
'
"
}
splice
(
@
_
,
0
,
20
)))
{
# can't fit too many pids on one shell cmdline
my
$cmd
=
"
bacct -l
$pid_batch
";
my
$cmd
=
"
bacct
-f -
-l
$pid_batch
";
# warn "LSF::get_report_entries_for_process_ids() running cmd:\n\t$cmd\n";
...
...
@@ -348,7 +348,7 @@ sub get_report_entries_for_time_interval {
my
$to_timepiece
=
Time::
Piece
->
strptime
(
$to_time
,
'
%Y-%m-%d %H:%M:%S
')
+
2
*ONE_MINUTE
;
$to_time
=
$to_timepiece
->
strftime
('
%Y/%m/%d/%H:%M
');
my
$cmd
=
"
bacct -l -C
$from_time
,
$to_time
"
.
(
$username
?
"
-u
$username
"
:
'');
my
$cmd
=
"
bacct
-f -
-l -C
$from_time
,
$to_time
"
.
(
$username
?
"
-u
$username
"
:
'');
# warn "LSF::get_report_entries_for_time_interval() running cmd:\n\t$cmd\n";
...
...
t/04.meadow/lsf.t
View file @
7da8c4b2
...
...
@@ -208,13 +208,13 @@ my $expected_bacct = {
$lsf_meadow
->
config_set
("
AccountingDisabled
",
0
);
lives_and
(
sub
{
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-l 34 56[7]
';
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-f -
-l 34 56[7]
';
my
$h
=
$lsf_meadow
->
get_report_entries_for_process_ids
(
34
,
'
56[7]
');
is_deeply
(
$h
,
$expected_bacct
,
'
Got bacct output
');
},
'
Can call bacct on process_ids
');
lives_and
(
sub
{
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-l -C 2020/10/11/12:23,2020/12/12/23:58 -u kb3
';
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-f -
-l -C 2020/10/11/12:23,2020/12/12/23:58 -u kb3
';
my
$h
=
$lsf_meadow
->
get_report_entries_for_time_interval
('
2020-10-11 12:23:45
',
'
2020-12-12 23:56:59
',
'
kb3
');
is_deeply
(
$h
,
$expected_bacct
,
'
Got bacct output
');
},
'
Can call bacct on a date range
');
...
...
@@ -222,13 +222,13 @@ lives_and( sub {
$lsf_meadow
->
config_set
("
AccountingDisabled
",
1
);
lives_and
(
sub
{
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-l 34 56[7]
';
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-f -
-l 34 56[7]
';
my
$h
=
$lsf_meadow
->
get_report_entries_for_process_ids
(
34
,
'
56[7]
');
is_deeply
(
$h
,
{},
'
No bacct output when accounting disabled
');
},
'
Suppressed bacct when AccountingDisabled when checking process_ids
');
lives_and
(
sub
{
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-l -C 2015/10/11/12:23,2015/12/12/23:58 -u kb3
';
local
$ENV
{
EHIVE_EXPECTED_BACCT
}
=
'
-f -
-l -C 2015/10/11/12:23,2015/12/12/23:58 -u kb3
';
my
$h
=
$lsf_meadow
->
get_report_entries_for_time_interval
('
2015-10-11 12:23:45
',
'
2015-12-12 23:56:59
',
'
kb3
');
is_deeply
(
$h
,
{},
'
No bacct output when accounting disabled
');
},
'
Suppressed bacct when AccountingDisabled when checking a date range
');
...
...
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