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biopet.biopet
Commits
e0a73b48
Commit
e0a73b48
authored
Mar 24, 2015
by
Peter van 't Hof
Browse files
Tweaking setting after testing
parent
81999541
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
View file @
e0a73b48
...
...
@@ -37,13 +37,11 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
var
vmem
:
Option
[
String
]
=
config
(
"vmem"
)
protected
val
defaultCoreMemory
:
Double
=
1.0
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
this
match
{
case
_:
BiopetJavaCommandLineFunction
=>
2.5
case
_
=>
1.5
})
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
1.5
)
var
ressFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
1.2
)
private
var
coreMemory
:
Double
=
config
(
"core_memory"
,
default
=
defaultCoreMemory
)
private
var
coreMemory
:
Double
=
_
var
executable
:
String
=
_
...
...
@@ -65,25 +63,29 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
if
(
threads
==
0
)
threads
=
getThreads
(
defaultThreads
)
if
(
threads
>
1
)
nCoresRequest
=
Option
(
threads
)
if
(
memoryLimit
.
isEmpty
)
memoryLimit
=
Some
(
coreMemory
*
threads
)
coreMemory
=
config
(
"core_memory"
,
default
=
defaultCoreMemory
).
asDouble
+
(
0.5
*
retry
)
if
(
config
.
contains
(
"memory_limit"
))
memoryLimit
=
config
(
"memory_limit"
)
else
memoryLimit
=
Some
(
coreMemory
*
threads
)
if
(
vmem
.
isEmpty
)
vmem
=
Some
((
defaultCoreMemory
*
vmemFactor
)
+
"G"
)
if
(
config
.
contains
(
"resident_limit"
))
memoryLimit
=
config
(
"resident_limit"
)
else
residentLimit
=
Some
((
coreMemory
+
(
0.5
*
retry
))
*
ressFactor
)
if
(!
config
.
contains
(
"vmem"
))
vmem
=
Some
((
coreMemory
*
(
vmemFactor
+
(
0.5
*
retry
)))
+
"G"
)
if
(
vmem
.
isDefined
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
.
get
jobName
=
configName
+
":"
+
(
if
(
firstOutput
!=
null
)
firstOutput
.
getName
else
jobOutputFile
)
super
.
freezeFieldValues
()
}
var
retry
=
0
override
def
setupRetry
()
:
Unit
=
{
super
.
setupRetry
()
if
(
vmem
.
isDefined
)
jobResourceRequests
=
jobResourceRequests
.
filterNot
(
_
.
contains
(
"h_vmem="
))
logger
.
info
(
"Auto raise memory on retry"
)
coreMemory
+=
1.0
vmemFactor
+=
0.5
memoryLimit
=
Some
(
coreMemory
*
threads
)
if
(
vmem
.
isDefined
)
jobResourceRequests
=
jobResourceRequests
.
filter
(
_
!=
"h_vmem="
+
vmem
.
get
)
vmem
=
Some
((
defaultCoreMemory
*
vmemFactor
)
+
"G"
)
jobResourceRequests
:+=
"h_vmem="
+
vmem
.
get
retry
+=
1
this
.
freeze
()
}
/** can override this value is executable may not be converted to CanonicalPath */
...
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