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biopet.biopet
Commits
e5384fc2
Commit
e5384fc2
authored
Aug 22, 2016
by
bow
Browse files
Merge branch 'feature-raise_memory' into 'develop'
Raised default residental memory for java jobs See merge request !447
parents
f26c4004
04038e39
Changes
3
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
e5384fc2
...
...
@@ -24,6 +24,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit
=
config
(
"java_gc_heap_freelimit"
,
default
=
10
)
javaGCTimeLimit
=
config
(
"java_gc_timelimit"
,
default
=
50
)
override
def
defaultResidentFactor
:
Double
=
1.5
override
def
defaultVmemFactor
:
Double
=
2.0
/** Constructs java opts, this adds scala threads */
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
View file @
e5384fc2
...
...
@@ -37,9 +37,10 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
var
vmem
:
Option
[
String
]
=
config
(
"vmem"
)
def
defaultCoreMemory
:
Double
=
2.0
def
defaultVmemFactor
:
Double
=
1.4
def
defaultResidentFactor
:
Double
=
1.2
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
defaultVmemFactor
)
var
residentFactor
:
Double
=
config
(
"resident_factor"
,
default
=
1.2
)
var
residentFactor
:
Double
=
config
(
"resident_factor"
,
default
=
defaultResidentFactor
)
private
var
_coreMemory
:
Double
=
2.0
def
coreMemory
=
_coreMemory
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
e5384fc2
...
...
@@ -60,7 +60,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction with Version {
def
versionRegex
=
"""Version: (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
override
def
defaultCoreMemory
=
3
.0
override
def
defaultCoreMemory
=
4
.0
override
def
getVersion
=
{
if
(
jarFile
==
null
)
Picard
.
getBiopetPicardVersion
...
...
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