Add support to set and get FTZ

.gitignore

@@ -5,6 +5,7 @@ tmp/
 *.dylib
 *.o
 *.a
+*.lo
 
 #================================================================================
 # from https://github.com/github/gitignore/blob/master/Global/JetBrains.gitignore

src/main/java/com/intel/gkl/ftz/FTZ.java

@@ -0,0 +1,42 @@
+package com.intel.gkl.ftz;
+
+import com.intel.gkl.IntelGKLUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.File;
+
+public class FTZ {
+    private final static Logger logger = LogManager.getLogger(FTZ.class);
+
+    private boolean isGklLoaded;
+
+    public FTZ() {
+        this(null);
+    }
+
+    public FTZ(File tmpDir) {
+        isGklLoaded = IntelGKLUtils.load(tmpDir);
+
+        if (!isGklLoaded) {
+            logger.warn("FTZ control is not supported on this platform.");
+        }
+    }
+
+    public boolean isSupported() {
+        return isGklLoaded;
+    }
+
+    public boolean getFlushToZero() {
+        return isGklLoaded && getFlushToZeroNative();
+    }
+
+    public void setFlushToZero(boolean value) {
+        if (isGklLoaded) {
+            setFlushToZeroNative(value);
+        }
+    }
+
+    private native boolean getFlushToZeroNative();
+    private native void setFlushToZeroNative(boolean value);
+}

src/main/native/build

@@ -6,6 +6,10 @@ ZLIB=$COMPRESSION/otc_zlib
 #ZLIB=$COMPRESSION/zlib-1.2.8
 PAIRHMM=pairhmm
 
+cd ftz
+make
+cd -
+
 cd pairhmm
 make
 cd -
@@ -25,14 +29,16 @@ if [[ $os == "Linux" ]]; then
 g++ -z noexecstack -shared -fPIC -O3 -static-libgcc -static-libstdc++ \
     $COMPRESSION/IntelDeflater.o $IGZIP/lib/libisal.a $ZLIB/libz.a \
     $PAIRHMM/IntelPairHmm.o \
+    ftz/ftz.o \
     -o libIntelGKL.so
 
 
 elif [[ $os == "Darwin" ]]; then
 
 g++ -shared -fPIC -O3 \
-    $COMPRESSION/IntelDeflater.o $IGZIP/igzip/libigzip0c.a $ZLIB/libz.a \
+    $COMPRESSION/IntelDeflater.o $IGZIP/lib/libisal.a $ZLIB/libz.a \
     $PAIRHMM/IntelPairHmm.o \
+    ftz/ftz.o \
     -o libIntelGKL.dylib
 
 else

src/main/native/compression/build

@@ -18,6 +18,7 @@ cd -
 
 elif [[ $os == "Darwin" ]]; then 
 
+cd $IGZIP
 make clean
 ./autogen.sh
 ./configure -target=darwin CFLAGS="-fPIC" --prefix=$(pwd)/usr --libdir=$(pwd)/lib

src/main/native/ftz/Makefile

@@ -0,0 +1,20 @@
+CPPFLAGS=-g -O3 -mavx -fPIC -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux -I$(JAVA_HOME)/include/Darwin
+
+OUTPUT_OPTION=-MMD -MP -o $@
+LDLIBS=
+
+TARGET = ftz.o
+
+SRC = $(wildcard *.cc)
+OBJ = $(SRC:.cc=.o)
+DEP = $(SRC:.cc=.d)
+
+all: javah $(TARGET)
+
+javah:
+	javah -o ftz.h -cp ../../java com.intel.gkl.ftz.FTZ
+
+-include $(DEP)
+
+clean:
+	rm -f $(OBJ) $(DEP) $(TARGET)

src/main/native/ftz/ftz.cc

@@ -0,0 +1,37 @@
+#if defined(_MSC_VER)
+  #include <intrin.h> // SIMD intrinsics for Windows
+#else
+  #include <x86intrin.h> // SIMD intrinsics for GCC
+#endif
+
+#include "ftz.h"
+
+//  _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
+
+/*
+ * Class:     com_intel_gkl_ftz_FTZ
+ * Method:    getFlushToZeroNative
+ * Signature: ()Z
+ */
+JNIEXPORT jboolean JNICALL Java_com_intel_gkl_ftz_FTZ_getFlushToZeroNative
+  (JNIEnv *env, jobject obj)
+{
+  jboolean value = _MM_GET_FLUSH_ZERO_MODE() == _MM_FLUSH_ZERO_ON ? 1 : 0;
+  return value;
+}
+
+/*
+ * Class:     com_intel_gkl_ftz_FTZ
+ * Method:    setFlushToZeroNative
+ * Signature: (Z)V
+ */
+JNIEXPORT void JNICALL Java_com_intel_gkl_ftz_FTZ_setFlushToZeroNative
+  (JNIEnv *env, jobject obj, jboolean value)
+{
+  if (value) {
+    _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
+  }
+  else {
+    _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_OFF);
+  }
+}

src/test/java/com/intel/gkl/ftz/FtzUnitTest.java

@@ -0,0 +1,63 @@
+package com.intel.gkl.ftz;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.testng.annotations.Test;
+
+public class FtzUnitTest {
+    private final static Logger log = LogManager.getLogger(FtzUnitTest.class);
+
+    @Test(enabled = true)
+    public void simpleTest() {
+        FTZ ftz = new FTZ();
+        assert(ftz.isSupported());
+
+        log.info("Test setting FTZ");
+        boolean value = false;
+        ftz.setFlushToZero(true);
+        value = ftz.getFlushToZero();
+        assert(value == true);
+
+        log.info("Test clearing FTZ");
+        value = true;
+        ftz.setFlushToZero(false);
+        value = ftz.getFlushToZero();
+        assert(value == false);
+    }
+
+    class ChildThread extends Thread {
+        boolean ftzValue;
+
+        public void run() {
+            FTZ ftz = new FTZ();
+            assert(ftz.isSupported());
+
+            ftzValue = ftz.getFlushToZero();
+            log.info("Child thread FTZ = " + ftzValue);
+        }
+    }
+
+    @Test(enabled = true)
+    public void childThreadTest() {
+        FTZ ftz = new FTZ();
+        assert (ftz.isSupported());
+
+        log.info("Parent setting FTZ = true");
+
+        boolean value = false;
+        ftz.setFlushToZero(true);
+        value = ftz.getFlushToZero();
+        assert(value == true);
+
+        ChildThread childThread = new ChildThread();
+
+        childThread.start();
+        try {
+            childThread.join();
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        }
+
+        assert(childThread.ftzValue == false);
+    }
+}