From 483fe407c65233acdb8e544c2ca6d528a3deeeb5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 30 Jun 2015 15:55:45 +0200
Subject: [PATCH] possible to override defaultVmemFactor now
---
.../lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala | 3 ++-
.../lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala | 2 ++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 614aed759..e732abbfa 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -37,7 +37,8 @@ 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 = 1.5)
+ protected val defaultVmemFactor: Double = 1.4
+ var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
var residentFactor: Double = config("resident_factor", default = 1.2)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index d0d4496e9..6904cdcd0 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
@@ -25,6 +25,8 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
javaGCTimeLimit = config("java_gc_timelimit")
+ override protected val defaultVmemFactor: Double = 2.0
+
/** Constructs java opts, this adds scala threads */
override def javaOpts = super.javaOpts +
optional("-Dscala.concurrent.context.numThreads=", threads, spaceSeparated = false, escape = false)
--
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