From 0c63d6264f499feadc2beefb46045dfdde5f12d3 Mon Sep 17 00:00:00 2001
From: Karthik Gururaj <karthik.gururaj@intel.com>
Date: Mon, 27 Jan 2014 15:34:58 -0800
Subject: [PATCH] 1. Added synchronization block around loadLibrary in
 VectorLoglessPairHMM 2. Edited Makefile to use static libraries where
 possible

---
 .../sting/utils/pairhmm/VectorLoglessPairHMM.java  | 14 ++++++++------
 public/c++/VectorPairHMM/Makefile                  |  2 +-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
index 192ebacc1..ef11600f0 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
@@ -104,15 +104,17 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
      * */
     private native void jniInitializeClassFieldsAndMachineMask(Class<?> readDataHolderClass, Class<?> haplotypeDataHolderClass, long mask);
 
-    private static boolean isVectorLoglessPairHMMLibraryLoaded = false;
+    private static Boolean isVectorLoglessPairHMMLibraryLoaded = false;
     //The constructor is called only once inside PairHMMLikelihoodCalculationEngine
     public VectorLoglessPairHMM() {
         super();
-        //Load the library and initialize the FieldIDs
-        if(!isVectorLoglessPairHMMLibraryLoaded) {
-            System.loadLibrary("VectorLoglessPairHMM");
-            isVectorLoglessPairHMMLibraryLoaded = true;
-            jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll);        //need to do this only once
+        synchronized(isVectorLoglessPairHMMLibraryLoaded) {
+            //Load the library and initialize the FieldIDs
+            if(!isVectorLoglessPairHMMLibraryLoaded) {
+                System.loadLibrary("VectorLoglessPairHMM");
+                isVectorLoglessPairHMMLibraryLoaded = true;
+                jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll);        //need to do this only once
+            }
         }
     }
 
diff --git a/public/c++/VectorPairHMM/Makefile b/public/c++/VectorPairHMM/Makefile
index e207dd4cc..6eefc3393 100644
--- a/public/c++/VectorPairHMM/Makefile
+++ b/public/c++/VectorPairHMM/Makefile
@@ -54,7 +54,7 @@ pairhmm-template-main:	pairhmm-template-main.o $(COMMON_OBJECTS)
 	$(CXX) $(OMPLFLAGS) -o $@ $^ $(LDFLAGS)
 
 libVectorLoglessPairHMM.so: $(LIBOBJECTS) 
-	$(CXX) $(OMPLFLAGS) -shared -o $@ $(LIBOBJECTS) ${LDFLAGS}
+	$(CXX) $(OMPLFLAGS) -shared -o $@ $(LIBOBJECTS) ${LDFLAGS} -Wl,-Bstatic -limf -lsvml -lirng -Wl,-Bdynamic #-lintlc
 
 
 $(OBJECTS): %.o: %.cc