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Merge pull request #626 from broadinstitute/intel_pairhmm 

Removed scary warning messages for VectorPairHMM
This commit is contained in:
MauricioCarneiro 2014-05-06 19:23:35 -04:00
parent 587e81fbd9 d9c489f928
commit bd33c3334e
3 changed files with 2 additions and 5 deletions
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5
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
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@ -118,9 +118,6 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
public VectorLoglessPairHMM() { public VectorLoglessPairHMM() {
super(); super();
logger.warn("WARNING: the VectorLoglessPairHMM is an experimental implementation still under active development. " +
"Use at your own risk!");
synchronized(isVectorLoglessPairHMMLibraryLoaded) { synchronized(isVectorLoglessPairHMMLibraryLoaded) {
//Load the library and initialize the FieldIDs //Load the library and initialize the FieldIDs
if(!isVectorLoglessPairHMMLibraryLoaded) { if(!isVectorLoglessPairHMMLibraryLoaded) {
@ -147,7 +144,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
throw ule; throw ule;
} }
} }
logger.info("Using vectorized implementation of PairHMM");
isVectorLoglessPairHMMLibraryLoaded = true; isVectorLoglessPairHMMLibraryLoaded = true;
jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll); //need to do this only once jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll); //need to do this only once
} }

2
public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc
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@ -53,7 +53,7 @@ LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loa
//Function: enabling FTZ converts denormals to 0 in hardware //Function: enabling FTZ converts denormals to 0 in hardware
//Denormals cause microcode to insert uops into the core causing big slowdown //Denormals cause microcode to insert uops into the core causing big slowdown
_MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON); _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n"; //cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n";
#else #else
cout << "FTZ is not set - may slow down performance if denormal numbers encountered\n"; cout << "FTZ is not set - may slow down performance if denormal numbers encountered\n";
#endif #endif

BIN
public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so
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