From 3482754f3b4309209f59e6ed8af36e8c5b847567 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 22 Sep 2015 12:03:42 +0200
Subject: [PATCH] Made codeMemory readable from outside
---
.../sasc/biopet/core/BiopetCommandLineFunction.scala | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index 44a7e780f..9ff69d88e 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
@@ -44,7 +44,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
var residentFactor: Double = config("resident_factor", default = 1.2)
- private var coreMemory: Double = _
+ private var _coreMemory: Double = 2.0
+ def coreMemeory = _coreMemory
var executable: String = _
@@ -66,15 +67,15 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
- coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
+ _coreMemory = config("core_memory", default = defaultCoreMemory).asDouble + (0.5 * retry)
if (config.contains("memory_limit")) memoryLimit = config("memory_limit")
- else memoryLimit = Some(coreMemory * threads)
+ else memoryLimit = Some(_coreMemory * threads)
if (config.contains("resident_limit")) residentLimit = config("resident_limit")
- else residentLimit = Some((coreMemory + (0.5 * retry)) * residentFactor)
+ else residentLimit = Some((_coreMemory + (0.5 * retry)) * residentFactor)
- if (!config.contains("vmem")) vmem = Some((coreMemory * (vmemFactor + (0.5 * retry))) + "G")
+ 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)
--
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