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Added vectorized PairHMM implementation by Mohammad and Mustafa into the Maven build of GATK. 

C++ code has PAPI calls for reading hardware counters

Followed Khalid's suggestion for packing libVectorLoglessCaching into
the jar file with Maven

Native library part of git repo

1. Renamed directory structure from public/c++/VectorPairHMM to
public/VectorPairHMM/src/main/c++ as per Khalid's suggestion
2. Use java.home in public/VectorPairHMM/pom.xml to pass environment
variable JRE_HOME to the make process. This is needed because the
Makefile needs to compile JNI code with the flag -I<JRE_HOME>/../include (among
others). Assuming that the Maven build process uses a JDK (and not just
a JRE), the variable java.home points to the JRE inside maven.
3. Dropped all pretense at cross-platform compatibility. Removed Mac
profile from pom.xml for VectorPairHMM

Moved JNI_README

1. Added the catch UnsatisfiedLinkError exception in
PairHMMLikelihoodCalculationEngine.java to fall back to LOGLESS_CACHING
in case the native library could not be loaded. Made
VECTOR_LOGLESS_CACHING as the default implementation.
2. Updated the README with Mauricio's comments
3. baseline.cc is used within the library - if the machine supports
neither AVX nor SSE4.1, the native library falls back to un-vectorized
C++ in baseline.cc.
4. pairhmm-1-base.cc: This is not part of the library, but is being
heavily used for debugging/profiling. Can I request that we keep it
there for now? In the next release, we can delete it from the
repository.
5. I agree with Mauricio about the ifdefs. I am sure you already know,
but just to reassure you the debug code is not compiled into the library
(because of the ifdefs) and will not affect performance.

1. Changed logger.info to logger.warn in PairHMMLikelihoodCalculationEngine.java
2. Committing the right set of files after rebase

Added public license text to all C++ files

Added license to Makefile

Add package info to Sandbox.java
This commit is contained in:
Karthik Gururaj 2014-02-25 21:44:20 -08:00 committed by Intel Repocontact
parent 6aa67a2585
commit 2648b41398
52 changed files with 1686 additions and 538 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
.gitignore vendored
View File

@ -24,19 +24,5 @@ dump/
lib/
out/
/atlassian-ide-plugin.xml
kg_tmp/
maven-ant-tasks-2.1.3.jar
null-sequenceGraph.25.0.0.raw_readthreading_graph.dot
null-sequenceGraph.25.0.1.cleaned_readthreading_graph.dot
null-sequenceGraph.25.0.1.initial_seqgraph.dot
null-sequenceGraph.3.0.0.raw_readthreading_graph.dot
null-sequenceGraph.3.0.1.cleaned_readthreading_graph.dot
null-sequenceGraph.3.0.1.initial_seqgraph.dot
org/
package-list
resources/
velocity.log
perf
verify
maven-metadata-local.xml
dependency-reduced-pom.xml

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
View File

@ -155,4 +155,8 @@ public class GraphBasedLikelihoodCalculationEngine implements LikelihoodCalculat
}
}
}
@Override
public void close() {
}
}

4
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -433,7 +433,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
*/
@Hidden
@Argument(fullName = "pair_hmm_implementation", shortName = "pairHMM", doc = "The PairHMM implementation to use for genotype likelihood calculations", required = false)
public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.LOGLESS_CACHING;
public PairHMM.HMM_IMPLEMENTATION pairHMM = PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING;
@Hidden
@Argument(fullName="keepRG", shortName="keepRG", doc="Only use read from this read group when making calls (but use all reads to build the assembly)", required = false)
@ -1051,7 +1051,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
referenceConfidenceModel.close();
//TODO remove the need to call close here for debugging, the likelihood output stream should be managed
//TODO (open & close) at the walker, not the engine.
likelihoodCalculationEngine.close();
likelihoodCalculationEngine.close();
logger.info("Ran local assembly on " + result + " active regions");
}

65
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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@ -80,29 +80,37 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
private final boolean noFpga;
private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
@Override
protected PairHMM initialValue() {
switch (hmmType) {
case EXACT: return new Log10PairHMM(true);
case ORIGINAL: return new Log10PairHMM(false);
case LOGLESS_CACHING:
if (noFpga || !CnyPairHMM.isAvailable())
return new LoglessPairHMM();
else
return new CnyPairHMM();
case VECTOR_LOGLESS_CACHING:
return new VectorLoglessPairHMM();
case DEBUG_VECTOR_LOGLESS_CACHING:
return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING);
case ARRAY_LOGLESS:
if (noFpga || !CnyPairHMM.isAvailable())
return new ArrayLoglessPairHMM();
else
return new CnyPairHMM();
default:
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
}
}
@Override
protected PairHMM initialValue() {
switch (hmmType) {
case EXACT: return new Log10PairHMM(true);
case ORIGINAL: return new Log10PairHMM(false);
case LOGLESS_CACHING:
if (noFpga || !CnyPairHMM.isAvailable())
return new LoglessPairHMM();
else
return new CnyPairHMM();
case VECTOR_LOGLESS_CACHING:
try
{
return new VectorLoglessPairHMM();
}
catch(UnsatisfiedLinkError ule)
{
logger.warn("Failed to load native library for VectorLoglessPairHMM - using Java implementation of LOGLESS_CACHING");
return new LoglessPairHMM();
}
case DEBUG_VECTOR_LOGLESS_CACHING:
return new DebugJNILoglessPairHMM(PairHMM.HMM_IMPLEMENTATION.VECTOR_LOGLESS_CACHING);
case ARRAY_LOGLESS:
if (noFpga || !CnyPairHMM.isAvailable())
return new ArrayLoglessPairHMM();
else
return new CnyPairHMM();
default:
throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
}
}
};
// Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
// private final PairHMM pairHMM = pairHMMThreadLocal.get();
@ -169,9 +177,10 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
@Override
public void close() {
if ( likelihoodsStream != null ) likelihoodsStream.close();
pairHMMThreadLocal.get().close();
pairHMMThreadLocal.get().close();
}
private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
if ( WRITE_LIKELIHOODS_TO_FILE ) {
likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
@ -338,7 +347,7 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
private void finalizePairHMM()
{
pairHMMThreadLocal.get().finalizeRegion();
pairHMMThreadLocal.get().finalizeRegion();
}
@ -358,9 +367,9 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
map.filterPoorlyModelledReads(EXPECTED_ERROR_RATE_PER_BASE);
stratifiedReadMap.put(sampleEntry.getKey(), map);
}
//Used mostly by the JNI implementation(s) to free arrays
finalizePairHMM();
//Used mostly by the JNI implementation(s) to free arrays
finalizePairHMM();
return stratifiedReadMap;
}

5
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
View File

@ -79,4 +79,9 @@ public class RandomLikelihoodCalculationEngine implements LikelihoodCalculationE
return result;
}
@Override
public void close() {
}
}

141
protected/java/src/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/DebugJNILoglessPairHMM.java
View File

@ -55,7 +55,7 @@ import org.broadinstitute.sting.utils.haplotype.Haplotype;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.variant.variantcontext.Allele;
import org.broadinstitute.sting.utils.exceptions.UserException;
import static org.broadinstitute.sting.utils.pairhmm.PairHMMModel.*;
import java.util.List;
import java.util.Map;
@ -75,8 +75,9 @@ import java.io.IOException;
*/
public class DebugJNILoglessPairHMM extends LoglessPairHMM {
private static final boolean dumpSandboxOnly = false; //simulates ifdef
private static final boolean debug = false; //simulates ifdef
private static final boolean verify = debug || true; //simulates ifdef
private static final boolean verify = !dumpSandboxOnly && (debug || true); //simulates ifdef
private static final boolean debug0_1 = false; //simulates ifdef
private static final boolean debug1 = false; //simulates ifdef
private static final boolean debug2 = false;
@ -134,9 +135,11 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
public void initialize( final List<Haplotype> haplotypes, final Map<String, List<GATKSAMRecord>> perSampleReadList,
final int readMaxLength, final int haplotypeMaxLength ) {
if(verify)
{
super.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
jniPairHMM.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
haplotypeToHaplotypeListIdxMap = jniPairHMM.getHaplotypeToHaplotypeListIdxMap();
jniPairHMM.initialize(haplotypes, perSampleReadList, readMaxLength, haplotypeMaxLength);
haplotypeToHaplotypeListIdxMap = jniPairHMM.getHaplotypeToHaplotypeListIdxMap();
}
}
/**
@ -145,7 +148,8 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
@Override
public void finalizeRegion()
{
jniPairHMM.finalizeRegion();
if(!dumpSandboxOnly)
jniPairHMM.finalizeRegion();
}
/**
@ -204,46 +208,61 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
++idx;
}
}
jniPairHMM.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
double[] likelihoodArray = jniPairHMM.getLikelihoodArray();
//to compare values
final PerReadAlleleLikelihoodMap likelihoodMap = super.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
double[] likelihoodArray = null;
PerReadAlleleLikelihoodMap likelihoodMap = null;
if(verify)
{
//re-order values in likelihoodArray
double[] tmpArray = new double[numHaplotypes];
idx = 0;
int idxInsideHaplotypeList = 0;
int readIdx = 0;
for(GATKSAMRecord read : reads)
jniPairHMM.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
likelihoodArray = jniPairHMM.getLikelihoodArray();
//to compare values
likelihoodMap = super.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
}
else
{
likelihoodMap = new PerReadAlleleLikelihoodMap();
likelihoodArray = new double[numTestcases];
for(int i=0;i<numTestcases;++i)
likelihoodArray[i] = -0.5;
}
if(verify || dumpSandboxOnly)
{
boolean toDump = dumpSandboxOnly ? true : false;
if(verify)
{
for(int j=0;j<numHaplotypes;++j)
tmpArray[j] = likelihoodArray[readIdx+j];
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet())//order is important - access in same order always
//re-order values in likelihoodArray
double[] tmpArray = new double[numHaplotypes];
idx = 0;
int idxInsideHaplotypeList = 0;
int readIdx = 0;
for(GATKSAMRecord read : reads)
{
idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(currEntry.getValue());
likelihoodArray[idx] = tmpArray[idxInsideHaplotypeList];
++idx;
for(int j=0;j<numHaplotypes;++j)
tmpArray[j] = likelihoodArray[readIdx+j];
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet())//order is important - access in same order always
{
idxInsideHaplotypeList = haplotypeToHaplotypeListIdxMap.get(currEntry.getValue());
likelihoodArray[idx] = tmpArray[idxInsideHaplotypeList];
++idx;
}
readIdx += numHaplotypes;
}
readIdx += numHaplotypes;
}
//for floating point values, no exact equality
//check whether numbers are close in terms of abs_error or relative_error
//For very large values, relative_error is relevant
//For very small values, abs_error is relevant
boolean toDump = false;
for(int i=0;i<likelihoodArray.length;++i)
{
double abs_error = Math.abs(likelihoodArray[i] - mLikelihoodArray[i]);
double relative_error = 0;
if(mLikelihoodArray[i] == 0)
relative_error = 0;
else
relative_error = Math.abs(abs_error/mLikelihoodArray[i]);
if(abs_error > 1e-5 && relative_error > 1e-5)
//for floating point values, no exact equality
//check whether numbers are close in terms of abs_error or relative_error
//For very large values, relative_error is relevant
//For very small values, abs_error is relevant
for(int i=0;i<likelihoodArray.length;++i)
{
toDump = true;
break;
double abs_error = Math.abs(likelihoodArray[i] - mLikelihoodArray[i]);
double relative_error = 0;
if(mLikelihoodArray[i] == 0)
relative_error = 0;
else
relative_error = Math.abs(abs_error/mLikelihoodArray[i]);
if(abs_error > 1e-5 && relative_error > 1e-5)
{
toDump = true;
break;
}
}
}
//if numbers are not close, then dump out the data that produced the inconsistency
@ -251,24 +270,40 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
{
idx = 0;
System.out.println("Dump : Java numReads "+readListSize+" numHaplotypes "+numHaplotypes);
boolean firstLine = true;
for(GATKSAMRecord read : reads)
{
byte [] overallGCP = GCPArrayMap.get(read);
byte[] tmpByteArray = new byte[read.getReadBases().length];
for (Map.Entry<Allele, Haplotype> currEntry : alleleHaplotypeMap.entrySet()) //order is important - access in same order always
{
byte[] haplotypeBases = currEntry.getValue().getBases();
debugDump("debug_dump.txt",new String(haplotypeBases)+" ",true);
debugDump("debug_dump.txt",new String(read.getReadBases())+" ",true);
for(int k=0;k<read.getReadBases().length;++k)
debugDump("debug_dump.txt",String.format("%d",(int)(read.getBaseQualities()[k]))+" ",true);
tmpByteArray[k] = (byte)((int)((read.getBaseQualities())[k]) + 33);
debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
for(int k=0;k<read.getReadBases().length;++k)
debugDump("debug_dump.txt",String.format("%d",(int)(read.getBaseInsertionQualities()[k]))+" ",true);
tmpByteArray[k] = (byte)((int)((read.getBaseInsertionQualities())[k]) + 33);
debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
for(int k=0;k<read.getReadBases().length;++k)
debugDump("debug_dump.txt",String.format("%d",(int)(read.getBaseDeletionQualities()[k]))+" ",true);
tmpByteArray[k] = (byte)((int)((read.getBaseDeletionQualities())[k]) + 33);
debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
for(int k=0;k<read.getReadBases().length;++k)
debugDump("debug_dump.txt",String.format("%d",(int)(overallGCP[k]))+" ",true);
debugDump("debug_dump.txt","\n",true);
debugDump("debug_results.txt",String.format("%e %e\n",mLikelihoodArray[idx],likelihoodArray[idx]),true);
tmpByteArray[k] = (byte)((int)(overallGCP[k]) + 33);
debugDump("debug_dump.txt",new String(tmpByteArray),true);
if(firstLine)
{
debugDump("debug_dump.txt",String.format(" %d %d\n",readListSize, numHaplotypes), true);
firstLine = false;
}
else
debugDump("debug_dump.txt","\n",true);
if(verify)
debugDump("debug_results.txt",String.format("%e %e\n",mLikelihoodArray[idx],likelihoodArray[idx]),true);
else
if(dumpSandboxOnly)
likelihoodMap.add(read, currEntry.getKey(), likelihoodArray[idx]);
++idx;
}
}
@ -414,21 +449,7 @@ public class DebugJNILoglessPairHMM extends LoglessPairHMM {
})
@Ensures("constantsAreInitialized")
protected static void initializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
for (int i = 0; i < insertionGOP.length; i++) {
final int qualIndexGOP = Math.min(insertionGOP[i] + deletionGOP[i], Byte.MAX_VALUE);
transition[i+1][matchToMatch] = QualityUtils.qualToProb((byte) qualIndexGOP);
transition[i+1][indelToMatch] = QualityUtils.qualToProb(overallGCP[i]);
transition[i+1][matchToInsertion] = QualityUtils.qualToErrorProb(insertionGOP[i]);
transition[i+1][insertionToInsertion] = QualityUtils.qualToErrorProb(overallGCP[i]);
transition[i+1][matchToDeletion] = QualityUtils.qualToErrorProb(deletionGOP[i]);
transition[i+1][deletionToDeletion] = QualityUtils.qualToErrorProb(overallGCP[i]);
//TODO it seems that it is not always the case that matchToMatch + matchToDeletion + matchToInsertion == 1.
//TODO We have detected cases of 1.00002 which can cause problems downstream. This are typically masked
//TODO by the fact that we always add a indelToMatch penalty to all PairHMM likelihoods (~ -0.1)
//TODO This is in fact not well justified and although it does not have any effect (since is equally added to all
//TODO haplotypes likelihoods) perhaps we should just remove it eventually and fix this != 1.0 issue here.
}
PairHMMModel.qualToTransProbs(transition,insertionGOP,deletionGOP,overallGCP);
}
/**

0
protected/java/src/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM.java
View File

9
protected/java/src/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
View File

@ -67,8 +67,6 @@ import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
/**
* Created with IntelliJ IDEA.
* User: rpoplin, carneiro
@ -99,8 +97,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
/**
* Return 64-bit mask representing machine capabilities
* Bit 0 is LSB, bit 63 MSB
* Bit 0 represents sse4.2 availability
* Bit 1 represents AVX availability
* Bit 0 represents sse4.1 availability
* Bit 1 represents sse4.2 availability
* Bit 2 represents AVX availability
*/
public native long jniGetMachineType();
@ -127,6 +126,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
//Useful if someone builds his/her own library and wants to override the bundled
//implementation without modifying the Java code
System.loadLibrary("VectorLoglessPairHMM");
logger.info("libVectorLoglessPairHMM found in JVM library path");
}
catch(UnsatisfiedLinkError ule)
{
@ -135,6 +135,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
{
logger.info("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar");
loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so");
logger.info("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar");
}
catch(IOException ioe)
{

71
public/VectorPairHMM/README.md 100644
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@ -0,0 +1,71 @@
Implementation overview:
Created a new Java class called VectorLoglessPairHMM which extends LoglessPairHMM and
overrides functions from both LoglessPairHMM and PairHMM.
1. Constructor: Call base class constructors. Then, load the native library located in this
directory and call an init function (with suffix 'jniInitializeClassFieldsAndMachineMask') in the
library to determine fields ids for the members of classes JNIReadDataHolder and
JNIHaplotypeDataHolders. The native code stores the field ids (struct offsets) for the classes and
re-uses them for subsequent computations. Optionally, the user can disable the vector
implementation, by using the 'mask' argument (see comments for a more detailed explanation).
2. When the library is loaded, it invokes the constructor of the class LoadTimeInitializer (because
a global variable g_load_time_initializer is declared in the library). This constructor
(LoadTimeInitializer.cc) can be used to perform various initializations. Currently, it initializes
two global function pointers to point to the function implementation that is supported on the
machine (AVX/SSE/un-vectorized) on which the program is being run. The two pointers are for float
and double respectively. The global function pointers are declared in utils.cc and are assigned in
the function initialize_function_pointers() defined in utils.cc and invoked from the constructor of
LoadTimeInitializer.
Other initializations in LoadTimeInitializer:
* ConvertChar::init - sets some masks for the vector implementation
* FTZ for performance
* stat counters = 0
* debug structs (which are never used in non-debug mode)
This initialization is done only once for the whole program.
3. initialize(): To initialize the region for PairHMM. Pass haplotype bases to native code through
the JNIHaplotypeDataHolder class. Since the haplotype list is common across multiple samples in
computeReadLikelihoods(), we can pass the haplotype bases to the native code once and re-use across
multiple samples.
4. computeLikelihoods(): Copies array references for readBases/quals etc to array of
JNIReadDataHolder objects. Invokes the JNI function to perform the computation and updates the
likelihoodMap.
The JNI function copies the byte array references into an array of testcase structs and invokes the
compute_full_prob function through the function pointers initialized earlier.
The primary native function called is
Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods. It uses
standard JNI calls to get and return data from/to the Java class VectorLoglessPairHMM. The last
argument to the function is the maximum number of OpenMP threads to use while computing PairHMM in
C++. This option is set when the native function call is made from JNILoglessPairHMM
computeLikelihoods - currently it is set to 12 (no logical reason).
Note: OpenMP has been disabled for now - insufficient #testcases per call to computeLikelihoods() to
justify multi-threading.
5. finalizeRegion(): Releases the haplotype arrays initialized in step 3 - should be called at the
end of every region (line 351 in PairHMMLikelihoodCalculationEngine).
Note: Debug code has been moved to a separate class DebugJNILoglessPairHMM.java.
Compiling:
Make sure you have icc (Intel C compiler) available. Currently, gcc does not seem to support all AVX
intrinsics.
This native library is called libVectorLoglessPairHMM.so
Using Maven:
Type 'mvn install' in this directory - this will build the library (by invoking 'make') and copy the
native library to the directory
${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm
The GATK maven build process (when run) will bundle the library into the StingUtils jar file from
the copied directory.
Simple build:
cd src/main/c++
make
Running:
The default implementation of PairHMM is now VECTOR_LOGLESS_CACHING in HaplotypeCaller.java. To use
the Java version, use the command line argument "--pair_hmm_implementation LOGLESS_CACHING". (see
run.sh in src/main/c++).
The native library is bundled with the StingUtils jar file. When HaplotypeCaller is invoked, then
the library is unpacked from the jar file, copied to the /tmp directory (with a unique id) and
loaded by the Java class VectorLoglessPairHMM in the constructor (if it has not been loaded
already).
The default library can be overridden by using the -Djava.library.path argument (see
src/main/c++/run.sh for an example) for the JVM to pass the path to the library. If the library
libVectorLoglessPairHMM.so can be found in java.library.path, then it is loaded and the 'packed'
library is not used.

119
public/VectorPairHMM/pom.xml 100644
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@ -0,0 +1,119 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.broadinstitute.sting</groupId>
<artifactId>sting-root</artifactId>
<version>2.8-SNAPSHOT</version>
<relativePath>../../public/sting-root</relativePath>
</parent>
<artifactId>VectorPairHMM</artifactId>
<packaging>pom</packaging>
<name>Vectorized PairHMM native libraries</name>
<description>Builds a GNU/Linux x86_64 library of VectorPairHMM using icc (Intel C++ compiler). During install, copies it into sting-utils. Neither tested nor expected to work on any other platform.</description>
<properties>
<sourceEncoding>UTF-8</sourceEncoding>
<project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
<project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
<sting.basedir>${project.basedir}/../..</sting.basedir>
<sting-utils.basedir>${sting.basedir}/public/sting-utils</sting-utils.basedir>
<!-- Where to place the library in sting-utils -->
<pairhmm.resources.directory>${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm</pairhmm.resources.directory>
</properties>
<build>
<plugins>
<!-- Print out the architecture - works only on GNU/Linux x86_64 systems -->
<!-- Neither tested nor expected to work on any other platform. -->
<!-- Requires icc (Intel C++ compiler) to be in your PATH. -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>display-info</goal>
</goals>
<phase>validate</phase>
</execution>
</executions>
</plugin>
<!-- Run make -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>exec-maven-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>exec</goal>
</goals>
<phase>compile</phase>
<configuration>
<executable>make</executable>
<workingDirectory>src/main/c++</workingDirectory>
<environmentVariables>
<JRE_HOME>${java.home}</JRE_HOME>
<OUTPUT_DIR>${project.build.directory}</OUTPUT_DIR>
</environmentVariables>
</configuration>
</execution>
</executions>
</plugin>
<!-- Don't actually install this artifact into the user's repo -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<!-- Copy the built library into sting-utils -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>default-install</id>
<goals>
<goal>copy-resources</goal>
</goals>
<phase>install</phase>
<configuration>
<outputDirectory>${pairhmm.resources.directory}</outputDirectory>
<resources>
<resource>
<directory>${project.build.directory}</directory>
<includes>
<include>**/*</include>
</includes>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
<!-- pom.xml cleanup, always sort according to the definitions in sting-root -->
<plugin>
<groupId>com.google.code.sortpom</groupId>
<artifactId>maven-sortpom-plugin</artifactId>
<configuration>
<createBackupFile>false</createBackupFile>
<predefinedSortOrder>custom_1</predefinedSortOrder>
<lineSeparator>\n</lineSeparator>
<encoding>${sourceEncoding}</encoding>
<keepBlankLines>true</keepBlankLines>
<sortDependencies>scope</sortDependencies>
<nrOfIndentSpace>4</nrOfIndentSpace>
<expandEmptyElements>false</expandEmptyElements>
</configuration>
</plugin>
</plugins>
</build>
</project>

2
public/c++/VectorPairHMM/.gitignore → public/VectorPairHMM/src/main/c++/.gitignore vendored
View File

@ -12,3 +12,5 @@ reformat
subdir_checkout.sh
avx/
sse/
triplicate.sh

36
public/c++/VectorPairHMM/LoadTimeInitializer.cc → public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "LoadTimeInitializer.h"
#include "utils.h"
using namespace std;
@ -14,7 +39,6 @@ char* LoadTimeInitializerStatsNames[] =
"dummy"
};
LoadTimeInitializer g_load_time_initializer;
LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loaded
@ -47,7 +71,17 @@ LoadTimeInitializer::LoadTimeInitializer() //will be called when library is loa
m_filename_to_fptr.clear();
m_written_files_set.clear();
//Common buffer - 8MB
unsigned size = 1024*1024;
m_buffer = new uint64_t[size];
m_buffer_size = size*sizeof(uint64_t);
initialize_function_pointers();
//Initialize static members of class
Context<float>::initializeStaticMembers();
Context<double>::initializeStaticMembers();
cout.flush();
}

33
public/c++/VectorPairHMM/LoadTimeInitializer.h → public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef LOAD_TIME_INITIALIZER_H
#define LOAD_TIME_INITIALIZER_H
#include "headers.h"
@ -22,6 +47,10 @@ class LoadTimeInitializer
{
public:
LoadTimeInitializer(); //will be called when library is loaded
~LoadTimeInitializer()
{
delete m_buffer;
}
void print_profiling();
void debug_dump(std::string filename, std::string s, bool to_append, bool add_newline=true);
void debug_close();
@ -43,6 +72,8 @@ class LoadTimeInitializer
uint64_t m_data_transfer_time;
//bytes copied
uint64_t m_bytes_copied;
unsigned get_buffer_size() { return m_buffer_size; }
char* get_buffer() { return (char*)m_buffer; }
private:
std::map<std::string, std::ofstream*> m_filename_to_fptr;
std::set<std::string> m_written_files_set;
@ -52,6 +83,8 @@ class LoadTimeInitializer
double m_sum_square_stats[TOTAL_NUMBER_STATS];
uint64_t m_min_stats[TOTAL_NUMBER_STATS];
uint64_t m_max_stats[TOTAL_NUMBER_STATS];
unsigned m_buffer_size;
uint64_t* m_buffer;
};
extern LoadTimeInitializer g_load_time_initializer;

37
public/c++/VectorPairHMM/Makefile → public/VectorPairHMM/src/main/c++/Makefile
View File

@ -1,11 +1,36 @@
#Copyright (c) 2012 The Broad Institute
#Permission is hereby granted, free of charge, to any person
#obtaining a copy of this software and associated documentation
#files (the "Software"), to deal in the Software without
#restriction, including without limitation the rights to use,
#copy, modify, merge, publish, distribute, sublicense, and/or sell
#copies of the Software, and to permit persons to whom the
#Software is furnished to do so, subject to the following
#conditions:
#The above copyright notice and this permission notice shall be
#included in all copies or substantial portions of the Software.
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
#EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
#OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
#NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
#WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
#FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
#THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
#OMPCFLAGS=-fopenmp
#OMPLFLAGS=-fopenmp #-openmp-link static
#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
#CFLAGS=-O2 -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
JAVA_ROOT=/opt/jdk1.7.0_25/
JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JAVA_ROOT}/include -I${JAVA_ROOT}/include/linux
JRE_HOME?=/opt/jdk1.7.0_25/jre
JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JRE_HOME}/../include -I${JRE_HOME}/../include/linux
COMMON_COMPILATION_FLAGS=$(JNI_COMPILATION_FLAGS) -O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
CC=icc
@ -58,7 +83,7 @@ $(AVX_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xAVX
$(SSE_OBJECTS): CXXFLAGS=$(COMMON_COMPILATION_FLAGS) -xSSE4.2
OBJECTS=$(NO_VECTOR_OBJECTS) $(AVX_OBJECTS) $(SSE_OBJECTS)
all: $(BIN) Sandbox.class
all: $(BIN) Sandbox.class copied_lib
-include $(addprefix $(DEPDIR)/,$(SOURCES:.cc=.d))
@ -79,5 +104,11 @@ $(OBJECTS): %.o: %.cc
Sandbox.class: Sandbox.java
javac Sandbox.java
copied_lib: libVectorLoglessPairHMM.so
ifdef OUTPUT_DIR
mkdir -p $(OUTPUT_DIR)
rsync -a libVectorLoglessPairHMM.so $(OUTPUT_DIR)/
endif
clean:
rm -rf $(BIN) *.o $(DEPDIR) *.class

29
public/c++/VectorPairHMM/Sandbox.cc → public/VectorPairHMM/src/main/c++/Sandbox.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "Sandbox.h"
#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
#include "utils.h"
@ -73,7 +98,9 @@ JNIEXPORT void JNICALL Java_Sandbox_doEverythingNative
(JNIEnv* env, jobject thisObject, jstring fileNameString)
{
const char* fileName = env->GetStringUTFChars(fileNameString, 0);
do_compute((char*)fileName);
char local_array[800];
strncpy(local_array, fileName, 200);
env->ReleaseStringUTFChars(fileNameString, fileName);
do_compute(local_array, true, 10000, false);
}

25
public/c++/VectorPairHMM/Sandbox.h → public/VectorPairHMM/src/main/c++/Sandbox.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class Sandbox */

27
public/c++/VectorPairHMM/Sandbox.java → public/VectorPairHMM/src/main/c++/Sandbox.java
View File

@ -1,3 +1,30 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.vectorpairhmm;
import java.util.List;
import java.util.LinkedList;
import java.util.Map;

0
public/c++/VectorPairHMM/Sandbox_JNIHaplotypeDataHolderClass.h → public/VectorPairHMM/src/main/c++/Sandbox_JNIHaplotypeDataHolderClass.h
View File

0
public/c++/VectorPairHMM/Sandbox_JNIReadDataHolderClass.h → public/VectorPairHMM/src/main/c++/Sandbox_JNIReadDataHolderClass.h
View File

44
public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc 100644
View File

@ -0,0 +1,44 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "template.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_SSE
#define SIMD_ENGINE avx
#define SIMD_ENGINE_AVX
#include "define-float.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
#include "define-double.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
template double compute_full_prob_avxd<double>(testcase* tc, double* nextlog);
template float compute_full_prob_avxs<float>(testcase* tc, float* nextlog);

56
public/c++/VectorPairHMM/baseline.cc → public/VectorPairHMM/src/main/c++/baseline.cc
View File

@ -1,7 +1,34 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "headers.h"
#include "template.h"
#include "utils.h"
#include "LoadTimeInitializer.h"
using namespace std;
template<class NUMBER>
NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
{
@ -10,12 +37,28 @@ NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
int COLS = tc->haplen + 1;
Context<NUMBER> ctx;
//#define USE_STACK_ALLOCATION 1
#ifdef USE_STACK_ALLOCATION
NUMBER M[ROWS][COLS];
NUMBER X[ROWS][COLS];
NUMBER Y[ROWS][COLS];
NUMBER p[ROWS][6];
#else
//allocate on heap in way that simulates a 2D array. Having a 2D array instead of
//a straightforward array of pointers ensures that all data lies 'close' in memory, increasing
//the chance of being stored together in the cache. Also, prefetchers can learn memory access
//patterns for 2D arrays, not possible for array of pointers
//bool locally_allocated = false;
//NUMBER* common_buffer = 0;
NUMBER* common_buffer = new NUMBER[3*ROWS*COLS + ROWS*6];
//unsigned curr_size = sizeof(NUMBER)*(3*ROWS*COLS + ROWS*6);
//if(true)
//{
//common_buffer = new NUMBER[3*ROWS*COLS + ROWS*6];
//locally_allocated = true;
//}
//else
//common_buffer = (NUMBER*)(g_load_time_initializer.get_buffer());
//pointers to within the allocated buffer
NUMBER** common_pointer_buffer = new NUMBER*[4*ROWS];
NUMBER* ptr = common_buffer;
@ -25,14 +68,11 @@ NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
for(;i<4*ROWS;++i, ptr+=6)
common_pointer_buffer[i] = ptr;
//NUMBER M[ROWS][COLS];
//NUMBER X[ROWS][COLS];
//NUMBER Y[ROWS][COLS];
//NUMBER p[ROWS][6];
NUMBER** M = common_pointer_buffer;
NUMBER** X = M + ROWS;
NUMBER** Y = X + ROWS;
NUMBER** p = Y + ROWS;
#endif
p[0][MM] = ctx._(0.0);
@ -47,7 +87,8 @@ NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
int _i = tc->i[r-1] & 127;
int _d = tc->d[r-1] & 127;
int _c = tc->c[r-1] & 127;
p[r][MM] = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
//p[r][MM] = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
SET_MATCH_TO_MATCH_PROB(p[r][MM], _i, _d);
p[r][GapM] = ctx._(1.0) - ctx.ph2pr[_c];
p[r][MX] = ctx.ph2pr[_i];
p[r][XX] = ctx.ph2pr[_c];
@ -111,8 +152,11 @@ NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
if (before_last_log != NULL)
*before_last_log = result;
#ifndef USE_STACK_ALLOCATION
delete common_pointer_buffer;
//if(locally_allocated)
delete common_buffer;
#endif
return result;
//return ctx.LOG10(result) - ctx.LOG10_INITIAL_CONSTANT;

25
public/c++/VectorPairHMM/define-double.h → public/VectorPairHMM/src/main/c++/define-double.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <iostream>
#ifdef PRECISION

25
public/c++/VectorPairHMM/define-float.h → public/VectorPairHMM/src/main/c++/define-float.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <iostream>
#ifdef PRECISION

25
public/c++/VectorPairHMM/define-sse-double.h → public/VectorPairHMM/src/main/c++/define-sse-double.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifdef PRECISION
#undef PRECISION
#undef MAIN_TYPE

25
public/c++/VectorPairHMM/define-sse-float.h → public/VectorPairHMM/src/main/c++/define-sse-float.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifdef PRECISION
#undef PRECISION
#undef MAIN_TYPE

25
public/c++/VectorPairHMM/headers.h → public/VectorPairHMM/src/main/c++/headers.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef COMMON_HEADERS_H
#define COMMON_HEADERS_H

58
public/VectorPairHMM/src/main/c++/jni_common.h 100644
View File

@ -0,0 +1,58 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef JNI_COMMON_H
#define JNI_COMMON_H
#include <jni.h>
/*#define ENABLE_ASSERTIONS 1*/
#define DO_PROFILING 1
/*#define DEBUG 1*/
/*#define DEBUG0_1 1*/
/*#define DEBUG3 1*/
/*#define DUMP_TO_SANDBOX 1*/
#define DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY 1
#ifdef DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY
//Gets direct access to Java arrays
#define GET_BYTE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
#define JNI_RO_RELEASE_MODE JNI_ABORT
#define GET_DOUBLE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
#else
//Likely makes copy of Java arrays to JNI C++ space
#define GET_BYTE_ARRAY_ELEMENTS env->GetByteArrayElements
#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleaseByteArrayElements
#define JNI_RO_RELEASE_MODE JNI_ABORT
#define GET_DOUBLE_ARRAY_ELEMENTS env->GetDoubleArrayElements
#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleaseDoubleArrayElements
#endif //ifdef DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY
#endif //ifndef JNI_COMMON_H

25
public/c++/VectorPairHMM/jnidebug.h → public/VectorPairHMM/src/main/c++/jnidebug.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef JNI_DEBUG_H
#define JNI_DEBUG_H

25
public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc → public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "headers.h"
#include "jni_common.h"
#include "org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h"

25
public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h → public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM */

83
public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc → public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "headers.h"
#include "jni_common.h"
#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
@ -98,6 +123,8 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
}
}
//Create a vector of testcases for computation - copy the references to bytearrays read/readQuals etc into the appropriate
//testcase struct
inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector
(JNIEnv* env, jint numReads, jint numHaplotypes, jobjectArray& readDataArray,
vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector, vector<testcase>& tc_array)
@ -195,21 +222,26 @@ inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_Vector
inline void compute_testcases(vector<testcase>& tc_array, unsigned numTestCases, double* likelihoodDoubleArray,
unsigned maxNumThreadsToUse)
{
#pragma omp parallel for schedule (dynamic,10000) num_threads(maxNumThreadsToUse)
for(unsigned tc_idx=0;tc_idx<numTestCases;++tc_idx)
{
float result_avxf = g_compute_full_prob_float(&(tc_array[tc_idx]), 0);
double result = 0;
if (result_avxf < MIN_ACCEPTED) {
double result_avxd = g_compute_full_prob_double(&(tc_array[tc_idx]), 0);
result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
#ifdef DO_PROFILING
g_load_time_initializer.update_stat(NUM_DOUBLE_INVOCATIONS_IDX, 1);
#ifdef DO_REPEAT_PROFILING
for(unsigned i=0;i<10;++i)
#endif
{
#pragma omp parallel for schedule (dynamic,10000) num_threads(maxNumThreadsToUse)
for(unsigned tc_idx=0;tc_idx<numTestCases;++tc_idx)
{
float result_avxf = g_compute_full_prob_float(&(tc_array[tc_idx]), 0);
double result = 0;
if (result_avxf < MIN_ACCEPTED) {
double result_avxd = g_compute_full_prob_double(&(tc_array[tc_idx]), 0);
result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
#ifdef DO_PROFILING
g_load_time_initializer.update_stat(NUM_DOUBLE_INVOCATIONS_IDX, 1);
#endif
}
else
result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
likelihoodDoubleArray[tc_idx] = result;
}
else
result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
likelihoodDoubleArray[tc_idx] = result;
}
}
@ -227,6 +259,10 @@ inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_Vector
readBasesArrayVector.clear();
}
#ifdef DO_WARMUP
uint64_t g_sum = 0;
#endif
//JNI function to invoke compute_full_prob_avx
//readDataArray - array of JNIReadDataHolderClass objects which contain the readBases, readQuals etc
//haplotypeDataArray - array of JNIHaplotypeDataHolderClass objects which contain the haplotypeBases
@ -263,16 +299,35 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
g_load_time_initializer.m_data_transfer_time += diff_time(start_time);
#endif
//Get double array where results are stored (to pass back to java)
jdouble* likelihoodDoubleArray = (jdouble*)GET_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, &is_copy);
#ifdef ENABLE_ASSERTIONS
assert(likelihoodDoubleArray && "likelihoodArray is NULL");
assert(env->GetArrayLength(likelihoodArray) == numTestCases);
#endif
#ifdef DO_WARMUP //ignore - only for crazy profiling
vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector = g_haplotypeBasesArrayVector;
for(unsigned i=0;i<haplotypeBasesArrayVector.size();++i)
{
unsigned curr_size = env->GetArrayLength(haplotypeBasesArrayVector[i].first);
for(unsigned j=0;j<curr_size;++j)
g_sum += ((uint64_t)((haplotypeBasesArrayVector[i].second)[j]));
}
for(unsigned i=0;i<readBasesArrayVector.size();++i)
{
for(unsigned j=0;j<readBasesArrayVector[i].size();++j)
{
unsigned curr_size = env->GetArrayLength(readBasesArrayVector[i][j].first);
for(unsigned k=0;k<curr_size;++k)
g_sum += ((uint64_t)((readBasesArrayVector[i][j].second)[k]));
}
}
#endif
#ifdef DO_PROFILING
g_load_time_initializer.m_bytes_copied += (is_copy ? numTestCases*sizeof(double) : 0);
get_time(&start_time);
#endif
compute_testcases(tc_array, numTestCases, likelihoodDoubleArray, maxNumThreadsToUse);
compute_testcases(tc_array, numTestCases, likelihoodDoubleArray, maxNumThreadsToUse); //actual computation
#ifdef DO_PROFILING
g_load_time_initializer.m_compute_time += diff_time(start_time);
#endif

25
public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h → public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM */

70
public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc 100644
View File

@ -0,0 +1,70 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
//#define DEBUG 1
//#define DEBUG0_1 1
//#define DEBUG3 1
#include "headers.h"
#include "utils.h"
#include "LoadTimeInitializer.h"
using namespace std;
int main(int argc, char** argv)
{
#define BATCH_SIZE 10000
if(argc < 2)
{
cerr << "Needs path to input file as argument\n";
exit(0);
}
bool use_old_read_testcase = false;
if(argc >= 3 && string(argv[2]) == "1")
use_old_read_testcase = true;
unsigned chunk_size = 10000;
bool do_check = true;
uint64_t mask = ~(0ull);
for(int i=3;i<argc;++i)
{
if(strncmp(argv[i], "-chunk_size", 15) == 0)
{
++i;
chunk_size = strtol(argv[i],0,10);
}
else
if(strncmp(argv[i], "-mask", 15) == 0)
{
++i;
mask = strtoll(argv[i],0,16);
}
else
if(strncmp(argv[i], "-no-check", 15) == 0)
do_check = false;
}
if(mask != (~0ull))
initialize_function_pointers(mask);
do_compute(argv[1], use_old_read_testcase, chunk_size, do_check);
return 0;
}

28
public/c++/VectorPairHMM/pairhmm-template-kernel.cc → public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifdef PRECISION
#include <stdint.h>
@ -116,7 +141,8 @@ template<class NUMBER> void CONCAT(CONCAT(initializeVectors,SIMD_ENGINE), PRECIS
int _d = tc->d[r-1] & 127;
int _c = tc->c[r-1] & 127;
*(ptr_p_MM+r-1) = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
//*(ptr_p_MM+r-1) = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
SET_MATCH_TO_MATCH_PROB(*(ptr_p_MM+r-1), _i, _d);
*(ptr_p_GAPM+r-1) = ctx._(1.0) - ctx.ph2pr[_c];
*(ptr_p_MX+r-1) = ctx.ph2pr[_i];
*(ptr_p_XX+r-1) = ctx.ph2pr[_c];

25
public/c++/VectorPairHMM/pairhmm-template-main.cc → public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "headers.h"
#include "template.h"
#include "vector_defs.h"

5
public/c++/VectorPairHMM/run.sh → public/VectorPairHMM/src/main/c++/run.sh
View File

@ -7,8 +7,9 @@ then
pair_hmm_implementation=$1;
fi
#-Djava.library.path is needed if you are using JNI_LOGLESS_CACHING, else not needed
java -Djava.library.path=${GSA_ROOT_DIR}/public/c++/VectorPairHMM -jar $GSA_ROOT_DIR/dist/GenomeAnalysisTK.jar -T HaplotypeCaller \
#-Djava.library.path is needed if you wish to override the default 'packed' library
#java -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
java -Djava.library.path=${GSA_ROOT_DIR}/public/VectorPairHMM/src/main/c++ -jar $GSA_ROOT_DIR/target/GenomeAnalysisTK.jar -T HaplotypeCaller \
--dbsnp /data/broad/samples/joint_variant_calling/dbSNP/00-All.vcf \
-R /opt/Genomics/ohsu/dnapipeline/humanrefgenome/human_g1k_v37.fasta \
-I /data/simulated/sim1M_pairs_final.bam \

25
public/c++/VectorPairHMM/shift_template.c → public/VectorPairHMM/src/main/c++/shift_template.c
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifdef PRECISION
#ifdef SIMD_ENGINE_AVX

43
public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc 100644
View File

@ -0,0 +1,43 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "template.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#define SIMD_ENGINE sse
#define SIMD_ENGINE_SSE
#include "define-sse-float.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
#include "define-sse-double.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
template double compute_full_prob_ssed<double>(testcase* tc, double* nextlog);
template float compute_full_prob_sses<float>(testcase* tc, float* nextlog);

320
public/VectorPairHMM/src/main/c++/template.h 100644
View File

@ -0,0 +1,320 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef TEMPLATES_H_
#define TEMPLATES_H_
#include "headers.h"
#define MM 0
#define GapM 1
#define MX 2
#define XX 3
#define MY 4
#define YY 5
//#define MROWS 500
//#define MCOLS 1000
#define CAT(X,Y) X####Y
#define CONCAT(X,Y) CAT(X,Y)
#define ALIGNED __attribute__((aligned(32)))
typedef union __attribute__((aligned(32))) {
ALIGNED __m256 ALIGNED d;
ALIGNED __m128i ALIGNED s[2];
ALIGNED float ALIGNED f[8];
ALIGNED __m256i ALIGNED i;
} ALIGNED mix_F ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m128 ALIGNED d;
ALIGNED __m64 ALIGNED s[2];
ALIGNED float ALIGNED f[4];
ALIGNED __m128i ALIGNED i;
} ALIGNED mix_F128 ALIGNED;
typedef union ALIGNED {
__m128i vec ;
__m128 vecf ;
uint32_t masks[4] ;
} MaskVec_F ;
typedef union ALIGNED {
__m64 vec ;
__m64 vecf ;
uint32_t masks[2] ;
} MaskVec_F128 ;
typedef union ALIGNED
{
ALIGNED __m128i ALIGNED i;
ALIGNED __m128 ALIGNED f;
} ALIGNED IF_128f ALIGNED;
typedef union ALIGNED
{
ALIGNED int ALIGNED i;
ALIGNED float ALIGNED f;
} ALIGNED IF_32 ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m256d ALIGNED d;
ALIGNED __m128i ALIGNED s[2];
ALIGNED double ALIGNED f[4];
ALIGNED __m256i ALIGNED i;
} ALIGNED mix_D ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m128d ALIGNED d;
ALIGNED __m64 ALIGNED s[2];
ALIGNED double ALIGNED f[2];
ALIGNED __m128i ALIGNED i;
} ALIGNED mix_D128 ALIGNED;
typedef union ALIGNED {
__m128i vec ;
__m128d vecf ;
uint64_t masks[2] ;
} MaskVec_D ;
typedef union ALIGNED {
__m64 vec ;
__m64 vecf ;
uint64_t masks[1] ;
} MaskVec_D128 ;
typedef union ALIGNED
{
ALIGNED __m128i ALIGNED i;
ALIGNED __m128d ALIGNED f;
} ALIGNED IF_128d ALIGNED;
typedef union ALIGNED
{
ALIGNED int64_t ALIGNED i;
ALIGNED double ALIGNED f;
} ALIGNED IF_64 ALIGNED;
#define MAX_QUAL 254
#define MAX_JACOBIAN_TOLERANCE 8.0
#define JACOBIAN_LOG_TABLE_STEP 0.0001
#define JACOBIAN_LOG_TABLE_INV_STEP (1.0 / JACOBIAN_LOG_TABLE_STEP)
#define MAXN 70000
#define LOG10_CACHE_SIZE (4*MAXN) // we need to be able to go up to 2*(2N) when calculating some of the coefficients
#define JACOBIAN_LOG_TABLE_SIZE ((int) (MAX_JACOBIAN_TOLERANCE / JACOBIAN_LOG_TABLE_STEP) + 1)
template<class NUMBER>
struct ContextBase
{
public:
NUMBER ph2pr[128];
NUMBER INITIAL_CONSTANT;
NUMBER LOG10_INITIAL_CONSTANT;
NUMBER RESULT_THRESHOLD;
static bool staticMembersInitializedFlag;
static NUMBER jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
static NUMBER matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
static void initializeStaticMembers()
{
if(!staticMembersInitializedFlag)
{
//Order of calls important - Jacobian first, then MatchToMatch
initializeJacobianLogTable();
initializeMatchToMatchProb();
staticMembersInitializedFlag = true;
}
}
static void deleteStaticMembers()
{
if(staticMembersInitializedFlag)
{
staticMembersInitializedFlag = false;
}
}
//Called only once during library load - don't bother to optimize with single precision fp
static void initializeJacobianLogTable()
{
for (int k = 0; k < JACOBIAN_LOG_TABLE_SIZE; k++) {
jacobianLogTable[k] = (NUMBER)(log10(1.0 + pow(10.0, -((double) k) * JACOBIAN_LOG_TABLE_STEP)));
}
}
//Called only once per library load - don't bother optimizing with single fp
static void initializeMatchToMatchProb()
{
double LN10 = log(10);
double INV_LN10 = 1.0/LN10;
for (int i = 0, offset = 0; i <= MAX_QUAL; offset += ++i)
for (int j = 0; j <= i; j++) {
double log10Sum = approximateLog10SumLog10(-0.1*i, -0.1*j);
double matchToMatchLog10 =
log1p(-std::min(1.0,pow(10,log10Sum))) * INV_LN10;
matchToMatchProb[offset + j] = (NUMBER)(pow(10,matchToMatchLog10));
}
}
//Called during computation - use single precision where possible
static int fastRound(NUMBER d) {
return (d > ((NUMBER)0.0)) ? (int) (d + ((NUMBER)0.5)) : (int) (d - ((NUMBER)0.5));
}
//Called during computation - use single precision where possible
static NUMBER approximateLog10SumLog10(NUMBER small, NUMBER big) {
// make sure small is really the smaller value
if (small > big) {
NUMBER t = big;
big = small;
small = t;
}
if (isinf(small) == -1 || isinf(big) == -1)
return big;
NUMBER diff = big - small;
if (diff >= ((NUMBER)MAX_JACOBIAN_TOLERANCE))
return big;
// OK, so |y-x| < tol: we use the following identity then:
// we need to compute log10(10^x + 10^y)
// By Jacobian logarithm identity, this is equal to
// max(x,y) + log10(1+10^-abs(x-y))
// we compute the second term as a table lookup with integer quantization
// we have pre-stored correction for 0,0.1,0.2,... 10.0
int ind = fastRound((NUMBER)(diff * ((NUMBER)JACOBIAN_LOG_TABLE_INV_STEP))); // hard rounding
return big + jacobianLogTable[ind];
}
};
template<class NUMBER>
struct Context : public ContextBase<NUMBER>
{};
template<>
struct Context<double> : public ContextBase<double>
{
Context():ContextBase<double>()
{
for (int x = 0; x < 128; x++)
ph2pr[x] = pow(10.0, -((double)x) / 10.0);
INITIAL_CONSTANT = ldexp(1.0, 1020.0);
LOG10_INITIAL_CONSTANT = log10(INITIAL_CONSTANT);
RESULT_THRESHOLD = 0.0;
}
double LOG10(double v){ return log10(v); }
inline double POW(double b, double e) { return pow(b,e); }
static double _(double n){ return n; }
static double _(float n){ return ((double) n); }
};
template<>
struct Context<float> : public ContextBase<float>
{
Context() : ContextBase<float>()
{
for (int x = 0; x < 128; x++)
{
ph2pr[x] = powf(10.f, -((float)x) / 10.f);
}
INITIAL_CONSTANT = ldexpf(1.f, 120.f);
LOG10_INITIAL_CONSTANT = log10f(INITIAL_CONSTANT);
RESULT_THRESHOLD = ldexpf(1.f, -110.f);
}
float LOG10(float v){ return log10f(v); }
inline float POW(float b, float e) { return powf(b,e); }
static float _(double n){ return ((float) n); }
static float _(float n){ return n; }
};
#define SET_MATCH_TO_MATCH_PROB(output, insQual, delQual) \
{ \
int minQual = delQual; \
int maxQual = insQual; \
if (insQual <= delQual) \
{ \
minQual = insQual; \
maxQual = delQual; \
} \
(output) = (MAX_QUAL < maxQual) ? \
((NUMBER)1.0) - ctx.POW(((NUMBER)10), ctx.approximateLog10SumLog10(((NUMBER)-0.1)*minQual, ((NUMBER)-0.1)*maxQual)) \
: ctx.matchToMatchProb[((maxQual * (maxQual + 1)) >> 1) + minQual]; \
}
typedef struct
{
int rslen, haplen;
/*int *q, *i, *d, *c;*/
/*int q[MROWS], i[MROWS], d[MROWS], c[MROWS];*/
char *q, *i, *d, *c;
char *hap, *rs;
int *ihap;
int *irs;
} testcase;
int normalize(char c);
int read_testcase(testcase *tc, FILE* ifp=0);
#define MIN_ACCEPTED 1e-28f
#define NUM_DISTINCT_CHARS 5
#define AMBIG_CHAR 4
class ConvertChar {
static uint8_t conversionTable[255] ;
public:
static void init() {
assert (NUM_DISTINCT_CHARS == 5) ;
assert (AMBIG_CHAR == 4) ;
conversionTable['A'] = 0 ;
conversionTable['C'] = 1 ;
conversionTable['T'] = 2 ;
conversionTable['G'] = 3 ;
conversionTable['N'] = 4 ;
}
static inline uint8_t get(uint8_t input) {
return conversionTable[input] ;
}
};
#endif

123
public/c++/VectorPairHMM/utils.cc → public/VectorPairHMM/src/main/c++/utils.cc
View File

@ -1,14 +1,48 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "headers.h"
#include "template.h"
#include "utils.h"
#include "vector_defs.h"
#include "LoadTimeInitializer.h"
using namespace std;
//static members from ConvertChar
uint8_t ConvertChar::conversionTable[255];
//Global function pointers in utils.h
float (*g_compute_full_prob_float)(testcase *tc, float* before_last_log) = 0;
double (*g_compute_full_prob_double)(testcase *tc, double* before_last_log) = 0;
//Static members in ContextBase
bool ContextBase<double>::staticMembersInitializedFlag = false;
double ContextBase<double>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
double ContextBase<double>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
bool ContextBase<float>::staticMembersInitializedFlag = false;
float ContextBase<float>::jacobianLogTable[JACOBIAN_LOG_TABLE_SIZE];
float ContextBase<float>::matchToMatchProb[((MAX_QUAL + 1) * (MAX_QUAL + 2)) >> 1];
using namespace std;
bool is_avx_supported()
{
@ -61,6 +95,7 @@ uint64_t get_machine_capabilities()
void initialize_function_pointers(uint64_t mask)
{
//mask = 0ull;
//mask = (1 << SSE41_CUSTOM_IDX);
if(is_avx_supported() && (mask & (1<< AVX_CUSTOM_IDX)))
{
cout << "Using AVX accelerated implementation of PairHMM\n";
@ -286,6 +321,13 @@ double getCurrClk() {
return (double)tv.tv_sec + (double)tv.tv_usec / 1000000.0;
}
inline unsigned long long rdtsc(void)
{
unsigned hi, lo;
__asm__ __volatile__ ("rdtsc" : "=a"(lo), "=d"(hi));
return ( (unsigned long long)lo)|( ((unsigned long long)hi)<<32 );
}
void get_time(struct timespec* store_struct)
{
clock_gettime(CLOCK_REALTIME, store_struct);
@ -298,9 +340,12 @@ uint64_t diff_time(struct timespec& prev_time)
return (uint64_t)((curr_time.tv_sec-prev_time.tv_sec)*1000000000+(curr_time.tv_nsec-prev_time.tv_nsec));
}
//#define DUMP_COMPUTE_VALUES 1
#define BATCH_SIZE 10000
#define RUN_HYBRID
#ifdef USE_PAPI
#include "papi.h"
#define NUM_PAPI_COUNTERS 4
#endif
void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size, bool do_check)
{
FILE* fptr = 0;
@ -321,7 +366,22 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
uint64_t vector_compute_time = 0;
uint64_t baseline_compute_time = 0;
uint64_t num_double_calls = 0;
unsigned num_testcases = 0;
bool all_ok = do_check ? true : false;
#ifdef USE_PAPI
uint32_t all_mask = (0);
uint32_t no_usr_mask = (1 << 16); //bit 16 user mode, bit 17 kernel mode
uint32_t no_kernel_mask = (1 << 17); //bit 16 user mode, bit 17 kernel mode
PAPI_num_counters();
int events[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
char* eventnames[NUM_PAPI_COUNTERS]= { "cycles", "itlb_walk_cycles", "dtlb_load_walk_cycles", "dtlb_store_walk_cycles" };
assert(PAPI_event_name_to_code("UNHALTED_REFERENCE_CYCLES:u=1:k=1",&(events[0])) == PAPI_OK);
assert(PAPI_event_name_to_code("ITLB_MISSES:WALK_DURATION", &(events[1])) == PAPI_OK);
assert(PAPI_event_name_to_code("DTLB_LOAD_MISSES:WALK_DURATION", &(events[2])) == PAPI_OK);
assert(PAPI_event_name_to_code("DTLB_STORE_MISSES:WALK_DURATION", &(events[3])) == PAPI_OK);
long long values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
long long accum_values[NUM_PAPI_COUNTERS] = { 0, 0, 0, 0 };
#endif
while(1)
{
int break_value = use_old_read_testcase ? read_testcase(&tc, fptr) : read_mod_testcase(ifptr,&tc,true);
@ -336,26 +396,42 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
results_vec.resize(tc_vector.size());
baseline_results_vec.resize(tc_vector.size());
struct timespec start_time;
#ifdef USE_PAPI
assert(PAPI_start_counters(events, NUM_PAPI_COUNTERS) == PAPI_OK);
#endif
get_time(&start_time);
#pragma omp parallel for schedule(dynamic,chunk_size) num_threads(12)
for(unsigned i=0;i<tc_vector.size();++i)
{
testcase& tc = tc_vector[i];
float result_avxf = g_compute_full_prob_float(&tc, 0);
double result = 0;
if (result_avxf < MIN_ACCEPTED) {
double result_avxd = g_compute_full_prob_double(&tc, 0);
result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
++num_double_calls;
}
else
result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
#ifdef DUMP_COMPUTE_VALUES
g_load_time_initializer.debug_dump("return_values_vector.txt",to_string(result),true);
#ifdef DO_REPEAT_PROFILING
for(unsigned z=0;z<10;++z)
#endif
results_vec[i] = result;
{
for(unsigned i=0;i<tc_vector.size();++i)
{
testcase& tc = tc_vector[i];
float result_avxf = g_compute_full_prob_float(&tc, 0);
double result = 0;
if (result_avxf < MIN_ACCEPTED) {
double result_avxd = g_compute_full_prob_double(&tc, 0);
result = log10(result_avxd) - log10(ldexp(1.0, 1020.0));
++num_double_calls;
}
else
result = (double)(log10f(result_avxf) - log10f(ldexpf(1.f, 120.f)));
#ifdef DUMP_COMPUTE_VALUES
g_load_time_initializer.debug_dump("return_values_vector.txt",to_string(result),true);
#endif
results_vec[i] = result;
}
}
#ifdef USE_PAPI
assert(PAPI_stop_counters(values, NUM_PAPI_COUNTERS) == PAPI_OK);
#endif
vector_compute_time += diff_time(start_time);
#ifdef USE_PAPI
for(unsigned k=0;k<NUM_PAPI_COUNTERS;++k)
accum_values[k] += values[k];
#endif
num_testcases += tc_vector.size();
if(do_check)
{
get_time(&start_time);
@ -401,10 +477,15 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
if(all_ok)
{
cout << "All output values within acceptable error\n";
cout << "Baseline compute time "<<baseline_compute_time*1e-9<<"\n";
cout << "Baseline double precision compute time "<<baseline_compute_time*1e-9<<"\n";
}
cout << "Num double invocations "<<num_double_calls<<"\n";
cout << "Num testcase "<<num_testcases<< " num double invocations "<<num_double_calls<<"\n";
cout << "Vector compute time "<< vector_compute_time*1e-9 << "\n";
#ifdef USE_PAPI
for(unsigned i=0;i<NUM_PAPI_COUNTERS;++i)
cout << eventnames[i] << " : "<<accum_values[i]<<"\n";
#endif
if(use_old_read_testcase)
fclose(fptr);
else

32
public/c++/VectorPairHMM/utils.h → public/VectorPairHMM/src/main/c++/utils.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef PAIRHMM_UTIL_H
#define PAIRHMM_UTIL_H
@ -40,4 +65,11 @@ enum ProcessorCapabilitiesEnum
uint64_t get_machine_capabilities();
void initialize_function_pointers(uint64_t mask=ENABLE_ALL_HARDWARE_FEATURES);
void do_compute(char* filename, bool use_old_read_testcase=true, unsigned chunk_size=10000, bool do_check=true);
//#define DO_WARMUP
//#define DO_REPEAT_PROFILING
//#define DUMP_COMPUTE_VALUES 1
#define BATCH_SIZE 10000
#define RUN_HYBRID
#endif

55
public/VectorPairHMM/src/main/c++/vector_defs.h 100644
View File

@ -0,0 +1,55 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#undef SIMD_ENGINE_SSE
#define SIMD_ENGINE avx
#define SIMD_ENGINE_AVX
#include "define-float.h"
#include "vector_function_prototypes.h"
#include "define-double.h"
#include "vector_function_prototypes.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#define SIMD_ENGINE sse
#define SIMD_ENGINE_SSE
#include "define-sse-float.h"
#include "vector_function_prototypes.h"
#include "define-sse-double.h"
#include "vector_function_prototypes.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#undef SIMD_ENGINE_SSE

25
public/c++/VectorPairHMM/vector_function_prototypes.h → public/VectorPairHMM/src/main/c++/vector_function_prototypes.h
View File

@ -1,3 +1,28 @@
/*Copyright (c) 2012 The Broad Institute
*Permission is hereby granted, free of charge, to any person
*obtaining a copy of this software and associated documentation
*files (the "Software"), to deal in the Software without
*restriction, including without limitation the rights to use,
*copy, modify, merge, publish, distribute, sublicense, and/or sell
*copies of the Software, and to permit persons to whom the
*Software is furnished to do so, subject to the following
*conditions:
*The above copyright notice and this permission notice shall be
*included in all copies or substantial portions of the Software.
*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
inline void CONCAT(CONCAT(_vector_shift,SIMD_ENGINE), PRECISION) (UNION_TYPE &x, MAIN_TYPE shiftIn, MAIN_TYPE &shiftOut);
inline void CONCAT(CONCAT(_vector_shift_last,SIMD_ENGINE), PRECISION) (UNION_TYPE &x, MAIN_TYPE shiftIn);
inline void CONCAT(CONCAT(precompute_masks_,SIMD_ENGINE), PRECISION)(const testcase& tc, int COLS, int numMaskVecs, MASK_TYPE (*maskArr)[NUM_DISTINCT_CHARS]);

41
public/c++/VectorPairHMM/JNI_README
View File

@ -1,41 +0,0 @@
Implementation overview:
Created a new Java class called VectorLoglessPairHMM which extends LoglessPairHMM and
overrides functions from both LoglessPairHMM and PairHMM.
1. Constructor: Call base class constructors. Then, load the native library located in this
directory and call a global init function in the library to determine fields ids for the
members of classes JNIReadDataHolder and JNIHaplotypeDataHolders.
2. When the library is loaded, it initializes two global function pointers to point to the
function implementation that is supported on the machine on which the program is being
run. The two pointers are for float and double respectively. This initialization is done
only once for the whole program.
3. initialize(): To initialized the region for PairHMM. Pass haplotype bases to native
code through the JNIHaplotypeDataHolders class. Since the haplotype list is common across
multiple samples in computeReadLikelihoods(), we can store the haplotype bases to the
native code once and re-use across multiple samples.
4. computeLikelihoods(): Copies array references for readBases/quals etc to array of
JNIReadDataHolder objects. Invokes the JNI function to perform the computation and
updates the likelihoodMap.
Note: Debug code has been moved to a separate class DebugJNILoglessPairHMM.java.
On the C++ side, the primary function called is
Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods. It
uses standard JNI calls to get and return data from/to the Java class
VectorLoglessPairHMM. The last argument to the function is the maximum number of OpenMP
threads to use while computing PairHMM in C++. This option is set when the native function
call is made from JNILoglessPairHMM computeLikelihoods - currently it is set to 12 (no
logical reason).
Note: OpenMP has been disabled for now.
Compiling:
Make sure you have icc (Intel C compiler) available. Currently, gcc does not seem to
support all AVX intrinsics.
Type 'make'. This should create a library called libVectorLoglessPairHMM.so
Running:
If libVectorLoglessPairHMM.so is compiled using icc, make sure that the Intel Composer XE
libraries are in your LD_LIBRARY_PATH :
source <COMPOSER_XE_DIR>/bin/compilervars.sh intel64
See run.sh in this directory on how to invoke HaplotypeCaller with the native library. The
argument -Djava.library.path is needed if the native implementation is selected, else
unnecessary.

19
public/c++/VectorPairHMM/avx_function_instantiations.cc
View File

@ -1,19 +0,0 @@
#include "template.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_SSE
#define SIMD_ENGINE avx
#define SIMD_ENGINE_AVX
#include "define-float.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
#include "define-double.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
template double compute_full_prob_avxd<double>(testcase* tc, double* nextlog);
template float compute_full_prob_avxs<float>(testcase* tc, float* nextlog);

33
public/c++/VectorPairHMM/jni_common.h
View File

@ -1,33 +0,0 @@
#ifndef JNI_COMMON_H
#define JNI_COMMON_H
#include <jni.h>
/*#define ENABLE_ASSERTIONS 1*/
#define DO_PROFILING 1
/*#define DEBUG 1*/
/*#define DEBUG0_1 1*/
/*#define DEBUG3 1*/
/*#define DUMP_TO_SANDBOX 1*/
#define DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY 1
#ifdef DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY
//Gets direct access to Java arrays
#define GET_BYTE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
#define JNI_RO_RELEASE_MODE JNI_ABORT
#define GET_DOUBLE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
#else
//Likely makes copy of Java arrays to JNI C++ space
#define GET_BYTE_ARRAY_ELEMENTS env->GetByteArrayElements
#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleaseByteArrayElements
#define JNI_RO_RELEASE_MODE JNI_ABORT
#define GET_DOUBLE_ARRAY_ELEMENTS env->GetDoubleArrayElements
#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleaseDoubleArrayElements
#endif //ifdef DIRECT_ACCESS_TO_JAVA_HEAP_MEMORY
#endif //ifndef JNI_COMMON_H

45
public/c++/VectorPairHMM/pairhmm-1-base.cc
View File

@ -1,45 +0,0 @@
//#define DEBUG 1
//#define DEBUG0_1 1
//#define DEBUG3 1
#include "headers.h"
#include "utils.h"
#include "LoadTimeInitializer.h"
using namespace std;
int main(int argc, char** argv)
{
#define BATCH_SIZE 10000
if(argc < 2)
{
cerr << "Needs path to input file as argument\n";
exit(0);
}
bool use_old_read_testcase = false;
if(argc >= 3 && string(argv[2]) == "1")
use_old_read_testcase = true;
unsigned chunk_size = 10000;
bool do_check = true;
uint64_t mask = ~(0ull);
for(int i=3;i<argc;++i)
{
if(strncmp(argv[i], "-chunk_size", 15) == 0)
{
++i;
chunk_size = strtol(argv[i],0,10);
}
else
if(strncmp(argv[i], "-mask", 15) == 0)
{
++i;
mask = strtoll(argv[i],0,16);
}
else
if(strncmp(argv[i], "-no-check", 15) == 0)
do_check = false;
}
if(mask != (~0ull))
initialize_function_pointers(mask);
do_compute(argv[1], use_old_read_testcase, chunk_size, do_check);
return 0;
}

18
public/c++/VectorPairHMM/sse_function_instantiations.cc
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@ -1,18 +0,0 @@
#include "template.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#define SIMD_ENGINE sse
#define SIMD_ENGINE_SSE
#include "define-sse-float.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
#include "define-sse-double.h"
#include "shift_template.c"
#include "pairhmm-template-kernel.cc"
template double compute_full_prob_ssed<double>(testcase* tc, double* nextlog);
template float compute_full_prob_sses<float>(testcase* tc, float* nextlog);

194
public/c++/VectorPairHMM/template.h
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@ -1,194 +0,0 @@
#ifndef TEMPLATES_H_
#define TEMPLATES_H_
#include "headers.h"
#define MM 0
#define GapM 1
#define MX 2
#define XX 3
#define MY 4
#define YY 5
//#define MROWS 500
//#define MCOLS 1000
#define CAT(X,Y) X####Y
#define CONCAT(X,Y) CAT(X,Y)
#define ALIGNED __attribute__((aligned(32)))
typedef union __attribute__((aligned(32))) {
ALIGNED __m256 ALIGNED d;
ALIGNED __m128i ALIGNED s[2];
ALIGNED float ALIGNED f[8];
ALIGNED __m256i ALIGNED i;
} ALIGNED mix_F ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m128 ALIGNED d;
ALIGNED __m64 ALIGNED s[2];
ALIGNED float ALIGNED f[4];
ALIGNED __m128i ALIGNED i;
} ALIGNED mix_F128 ALIGNED;
typedef union ALIGNED {
__m128i vec ;
__m128 vecf ;
uint32_t masks[4] ;
} MaskVec_F ;
typedef union ALIGNED {
__m64 vec ;
__m64 vecf ;
uint32_t masks[2] ;
} MaskVec_F128 ;
typedef union ALIGNED
{
ALIGNED __m128i ALIGNED i;
ALIGNED __m128 ALIGNED f;
} ALIGNED IF_128f ALIGNED;
typedef union ALIGNED
{
ALIGNED int ALIGNED i;
ALIGNED float ALIGNED f;
} ALIGNED IF_32 ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m256d ALIGNED d;
ALIGNED __m128i ALIGNED s[2];
ALIGNED double ALIGNED f[4];
ALIGNED __m256i ALIGNED i;
} ALIGNED mix_D ALIGNED;
typedef union __attribute__((aligned(32))) {
ALIGNED __m128d ALIGNED d;
ALIGNED __m64 ALIGNED s[2];
ALIGNED double ALIGNED f[2];
ALIGNED __m128i ALIGNED i;
} ALIGNED mix_D128 ALIGNED;
typedef union ALIGNED {
__m128i vec ;
__m128d vecf ;
uint64_t masks[2] ;
} MaskVec_D ;
typedef union ALIGNED {
__m64 vec ;
__m64 vecf ;
uint64_t masks[1] ;
} MaskVec_D128 ;
typedef union ALIGNED
{
ALIGNED __m128i ALIGNED i;
ALIGNED __m128d ALIGNED f;
} ALIGNED IF_128d ALIGNED;
typedef union ALIGNED
{
ALIGNED int64_t ALIGNED i;
ALIGNED double ALIGNED f;
} ALIGNED IF_64 ALIGNED;
template<class T>
struct Context{};
template<>
struct Context<double>
{
Context()
{
for (int x = 0; x < 128; x++)
ph2pr[x] = pow(10.0, -((double)x) / 10.0);
INITIAL_CONSTANT = ldexp(1.0, 1020.0);
LOG10_INITIAL_CONSTANT = log10(INITIAL_CONSTANT);
RESULT_THRESHOLD = 0.0;
}
double LOG10(double v){ return log10(v); }
static double _(double n){ return n; }
static double _(float n){ return ((double) n); }
double ph2pr[128];
double INITIAL_CONSTANT;
double LOG10_INITIAL_CONSTANT;
double RESULT_THRESHOLD;
};
template<>
struct Context<float>
{
Context()
{
for (int x = 0; x < 128; x++)
{
ph2pr[x] = powf(10.f, -((float)x) / 10.f);
}
INITIAL_CONSTANT = ldexpf(1.f, 120.f);
LOG10_INITIAL_CONSTANT = log10f(INITIAL_CONSTANT);
RESULT_THRESHOLD = ldexpf(1.f, -110.f);
}
float LOG10(float v){ return log10f(v); }
static float _(double n){ return ((float) n); }
static float _(float n){ return n; }
float ph2pr[128];
float INITIAL_CONSTANT;
float LOG10_INITIAL_CONSTANT;
float RESULT_THRESHOLD;
};
typedef struct
{
int rslen, haplen;
/*int *q, *i, *d, *c;*/
/*int q[MROWS], i[MROWS], d[MROWS], c[MROWS];*/
char *q, *i, *d, *c;
char *hap, *rs;
int *ihap;
int *irs;
} testcase;
int normalize(char c);
int read_testcase(testcase *tc, FILE* ifp=0);
#define MIN_ACCEPTED 1e-28f
#define NUM_DISTINCT_CHARS 5
#define AMBIG_CHAR 4
class ConvertChar {
static uint8_t conversionTable[255] ;
public:
static void init() {
assert (NUM_DISTINCT_CHARS == 5) ;
assert (AMBIG_CHAR == 4) ;
conversionTable['A'] = 0 ;
conversionTable['C'] = 1 ;
conversionTable['T'] = 2 ;
conversionTable['G'] = 3 ;
conversionTable['N'] = 4 ;
}
static inline uint8_t get(uint8_t input) {
return conversionTable[input] ;
}
};
#endif

30
public/c++/VectorPairHMM/vector_defs.h
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@ -1,30 +0,0 @@
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#undef SIMD_ENGINE_SSE
#define SIMD_ENGINE avx
#define SIMD_ENGINE_AVX
#include "define-float.h"
#include "vector_function_prototypes.h"
#include "define-double.h"
#include "vector_function_prototypes.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#define SIMD_ENGINE sse
#define SIMD_ENGINE_SSE
#include "define-sse-float.h"
#include "vector_function_prototypes.h"
#include "define-sse-double.h"
#include "vector_function_prototypes.h"
#undef SIMD_ENGINE
#undef SIMD_ENGINE_AVX
#undef SIMD_ENGINE_SSE

6
public/sting-root/pom.xml
View File

@ -335,7 +335,11 @@
<artifactId>maven-assembly-plugin</artifactId>
<version>2.4</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>1.3.1</version>
</plugin>
<!--
surefire/failsafe configurations are global, even across poms
not directly aggregated, for example package-tests/pom.xml

BIN
public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so 100644
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