add pairhmm fpga support

src/main/java/com/intel/gkl/pairhmm/IntelPairHmm.java

@@ -1,5 +1,8 @@
 package com.intel.gkl.pairhmm;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import com.intel.gkl.IntelGKLUtils;
 import com.intel.gkl.NativeLibraryLoader;
 import org.broadinstitute.gatk.nativebindings.pairhmm.HaplotypeDataHolder;
@@ -13,8 +16,10 @@
  * Provides a native PairHMM implementation accelerated for the Intel Architecture.
  */
 public class IntelPairHmm implements PairHMMNativeBinding {
+    private final static Logger logger = LogManager.getLogger(IntelPairHmm.class);
     private static final String NATIVE_LIBRARY_NAME = "gkl_pairhmm";
     private String nativeLibraryName = "gkl_pairhmm";
+    boolean useFpga = false;
 
     void setNativeLibraryName(String nativeLibraryName) {
         this.nativeLibraryName = nativeLibraryName;
@@ -46,13 +51,15 @@ public synchronized boolean load(File tempDir) {
      * @param args the args used to configure native PairHMM
      */
     public void initialize(PairHMMNativeArguments args) {
-        if(args == null)
-        {
+        if (args == null) {
             args = new PairHMMNativeArguments();
             args.useDoublePrecision = false;
             args.maxNumberOfThreads = 1;
         }
-        initNative(ReadDataHolder.class, HaplotypeDataHolder.class, args.useDoublePrecision, args.maxNumberOfThreads);
+        if (args.useDoublePrecision && useFpga) {
+            logger.warn("FPGA PairHMM does not support double precision floating-point. Using AVX PairHMM");
+        }
+        initNative(ReadDataHolder.class, HaplotypeDataHolder.class, args.useDoublePrecision, args.maxNumberOfThreads, useFpga);
     }
 
     /**
@@ -82,7 +89,8 @@ public void done() {
     private native static void initNative(Class<?> readDataHolderClass,
                                           Class<?> haplotypeDataHolderClass,
                                           boolean doublePrecision,
-                                          int maxThreads);
+                                          int maxThreads,
+                                          boolean useFpga);
 
     private native void computeLikelihoodsNative(Object[] readDataArray,
                                                  Object[] haplotypeDataArray,

src/main/java/com/intel/gkl/pairhmm/IntelPairHmmFpga.java

@@ -0,0 +1,13 @@
+package com.intel.gkl.pairhmm;
+
+/**
+ * Provides a native PairHMM implementation accelerated using Intel FPGAs
+ */
+public final class IntelPairHmmFpga extends IntelPairHmm {
+    private static final String NATIVE_LIBRARY_NAME = "gkl_pairhmm_fpga";
+
+    public IntelPairHmmFpga() {
+        setNativeLibraryName(NATIVE_LIBRARY_NAME);
+        useFpga = true;
+    }
+}

src/main/native/pairhmm/CMakeLists.txt

@@ -1,21 +1,37 @@
+#---------------------------------------------------------------------
+# pairhmm_shacc (stub version)
+#---------------------------------------------------------------------
+set(TARGET gkl_pairhmm_shacc)
+add_library(${TARGET} SHARED shacc_pairhmm_stub.cc)
+install(TARGETS ${TARGET} DESTINATION ${CMAKE_BINARY_DIR})
+
 #---------------------------------------------------------------------
 # pairhmm
 #---------------------------------------------------------------------
 set(TARGET gkl_pairhmm)
-
 add_library(${TARGET} SHARED IntelPairHmm.cc)
+if (APPLE)
+  target_link_libraries(${TARGET} gkl_pairhmm_shacc)
+endif()
 install(TARGETS ${TARGET} DESTINATION ${CMAKE_BINARY_DIR})
 
 #---------------------------------------------------------------------
 # pairhmm_omp
 #---------------------------------------------------------------------
-set(TARGET gkl_pairhmm_omp)
-
 find_package(OpenMP)
 
 if(OPENMP_FOUND)
+  set(TARGET gkl_pairhmm_omp)
   add_library(${TARGET} SHARED IntelPairHmm.cc)
   set_target_properties(${TARGET} PROPERTIES COMPILE_OPTIONS ${OpenMP_CXX_FLAGS})
-  set_target_properties(${TARGET} PROPERTIES LINK_FLAGS ${OpenMP_CXX_FLAGS})
+  target_link_libraries(${TARGET} ${OpenMP_CXX_FLAGS})
   install(TARGETS ${TARGET} DESTINATION ${CMAKE_BINARY_DIR})
 endif()
+
+#---------------------------------------------------------------------
+# pairhmm_fpga
+#---------------------------------------------------------------------
+set(TARGET gkl_pairhmm_fpga)
+add_library(${TARGET} SHARED IntelPairHmm.cc)
+target_link_libraries(${TARGET} gkl_pairhmm_shacc)
+install(TARGETS ${TARGET} DESTINATION ${CMAKE_BINARY_DIR})

src/main/native/pairhmm/IntelPairHmm.cc

@@ -6,13 +6,16 @@
 #include "IntelPairHmm.h"
 #include "pairhmm_common.h"
 #include "avx-pairhmm.h"
+#include "shacc_pairhmm.h"
 #include "JavaData.h"
+#include "debug.h"
 
 bool g_use_double;
 int g_max_threads;
+bool g_use_fpga;
 
-Context<float> ctxf;
-Context<double> ctxd;
+Context<float> g_ctxf;
+Context<double> g_ctxd;
 
 float (*g_compute_full_prob_float)(testcase *tc);
 double (*g_compute_full_prob_double)(testcase *tc);
@@ -24,7 +27,7 @@ double (*g_compute_full_prob_double)(testcase *tc);
  */
 JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_initNative
 (JNIEnv* env, jclass cls, jclass readDataHolder, jclass haplotypeDataHolder,
- jboolean use_double, jint max_threads)
+ jboolean use_double, jint max_threads, jboolean use_fpga)
 {
   DBG("Enter");
 
@@ -37,6 +40,8 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_initNative
   g_max_threads = std::min((int)max_threads, omp_get_max_threads());
 #endif
 
+  g_use_fpga = use_fpga;
+
   // enable FTZ
   _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
 
@@ -49,7 +54,6 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_initNative
   DBG("Exit");
 }
 
-
 /*
  * Class:     com_intel_gkl_pairhmm_IntelPairHmm
  * Method:    computeLikelihoodsNative
@@ -69,18 +73,28 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_computeLikelihood
 
   //==================================================================
   // calcutate pairHMM
+  shacc_pairhmm::Batch batch;
+  bool batch_valid = false;
+  if (g_use_fpga && !g_use_double) {
+    batch = javaData.getBatch();
+    batch_valid = shacc_pairhmm::calculate(batch);
+  }
+
+#ifdef _OPENMP
   #pragma omp parallel for schedule(dynamic, 1) num_threads(g_max_threads)
+#endif
   for (int i = 0; i < testcases.size(); i++) {
     double result_final = 0;
 
-    float result_float = g_use_double ? 0.0f : g_compute_full_prob_float(&testcases[i]);
+    float result_float = g_use_double ? 0.0f : 
+      batch_valid ? batch.results[i] : g_compute_full_prob_float(&testcases[i]);
 
     if (result_float < MIN_ACCEPTED) {
       double result_double = g_compute_full_prob_double(&testcases[i]);
-      result_final = log10(result_double) - ctxd.LOG10_INITIAL_CONSTANT;
+      result_final = log10(result_double) - g_ctxd.LOG10_INITIAL_CONSTANT;
     }
     else {
-      result_final = (double)(log10f(result_float) - ctxf.LOG10_INITIAL_CONSTANT);
+      result_final = (double)(log10f(result_float) - g_ctxf.LOG10_INITIAL_CONSTANT);
     }
 
     javaResults[i] = result_final;

src/main/native/pairhmm/JavaData.h

@@ -3,9 +3,13 @@
 
 #include <vector>
 #include "pairhmm_common.h"
+#include "shacc_pairhmm.h"
+#include "debug.h"
 
 class JavaData {
  public:
+
+  // cache field ids
   static void init(JNIEnv *env, jclass readDataHolder, jclass haplotypeDataHolder) {
     m_readBasesFid = getFieldId(env, readDataHolder, "readBases", "[B");
     m_readQualsFid = getFieldId(env, readDataHolder, "readQuals", "[B");
@@ -15,24 +19,29 @@ class JavaData {
     m_haplotypeBasesFid = getFieldId(env, haplotypeDataHolder, "haplotypeBases", "[B");
   }
 
+  // create array of testcases
   std::vector<testcase> getData(JNIEnv *env, jobjectArray& readDataArray, jobjectArray& haplotypeDataArray) {
     int numReads = env->GetArrayLength(readDataArray);
     int numHaplotypes = env->GetArrayLength(haplotypeDataArray);
 
-    testcases.resize(numReads * numHaplotypes);
+    m_batch.num_reads = numReads;
+    m_batch.num_haps = numHaplotypes;
+
+    std::vector<char*> haplotypes;
+    std::vector<int> haplotypeLengths;
 
-    std::vector<char*> haplotypes(numHaplotypes);
-    std::vector<int> haplotypeLengths(numHaplotypes);
+    long total_hap_length = 0;
+    long total_read_length = 0;
 
     // get haplotypes
     for (int i = 0; i < numHaplotypes; i++) {
       int length = 0;
-      haplotypes[i] = getCharArray(env, haplotypeDataArray, i, m_haplotypeBasesFid, length);
-      haplotypeLengths[i] = length;
+      haplotypes.push_back(getCharArray(env, haplotypeDataArray, i, m_haplotypeBasesFid, length));
+      haplotypeLengths.push_back(length);
+      total_hap_length += length;
     }
-    
+
     // get reads and create testcases 
-    int i = 0;
     for (int r = 0; r < numReads; r++) {
       int length = 0;
       char* reads = getCharArray(env, readDataArray, r, m_readBasesFid, length);
@@ -41,33 +50,69 @@ class JavaData {
       char* delGops = getCharArray(env, readDataArray, r, m_deletionGopFid, length);
       char* gapConts = getCharArray(env, readDataArray, r, m_overallGcpFid, length);
       char* readQuals = getCharArray(env, readDataArray, r, m_readQualsFid, length);
+      total_read_length += length;
 
       for (int h = 0; h < numHaplotypes; h++) {
-        testcases[i].hap = haplotypes[h];
-        testcases[i].haplen = haplotypeLengths[h];
-        testcases[i].rs = reads;
-        testcases[i].rslen = readLength;
-        testcases[i].i = insGops;
-        testcases[i].d = delGops;
-        testcases[i].c = gapConts;
-        testcases[i].q = readQuals;
-        i++;
+        testcase tc;
+        tc.hap = haplotypes[h];
+        tc.haplen = haplotypeLengths[h];
+        tc.rs = reads;
+        tc.rslen = readLength;
+        tc.i = insGops;
+        tc.d = delGops;
+        tc.c = gapConts;
+        tc.q = readQuals;
+        m_testcases.push_back(tc);
       }
     }
 
-    return testcases;
+    m_total_cells = 3 * total_read_length * total_hap_length;
+
+    return m_testcases;
   }
 
   double* getOutputArray(JNIEnv *env, jdoubleArray array) {
     return getDoubleArray(env, array);
   }
 
+  // create shacc_pairhmm::batch from array of testcases
+  shacc_pairhmm::Batch getBatch() {
+    int num_testcases = m_batch.num_reads * m_batch.num_haps;
+
+    // get reads
+    for (int i = 0; i < num_testcases; i += m_batch.num_haps) {
+      shacc_pairhmm::Read read;
+      read.bases = m_testcases[i].rs;
+      read.length = m_testcases[i].rslen;
+      read.i = m_testcases[i].i;
+      read.d = m_testcases[i].d;
+      read.c = m_testcases[i].c;
+      read.q = m_testcases[i].q;
+      m_reads.push_back(read);
+    }
+    m_batch.reads = m_reads.data();
+
+    // get haplotypes
+    for (int i = 0; i < m_batch.num_haps; i++) {
+      shacc_pairhmm::Haplotype hap;
+      DBG("hap #%d len = %d", i, m_testcases[i].haplen);
+      hap.bases = m_testcases[i].hap;
+      hap.length = m_testcases[i].haplen;
+      m_haps.push_back(hap);
+    }
+    m_batch.haps = m_haps.data();
+
+    m_batch.num_cells = m_total_cells;
+
+    return m_batch;
+  }
+
   void releaseData(JNIEnv *env) {
-    for (int i = 0; i < byteArrays.size(); i++) {
-      env->ReleaseByteArrayElements(byteArrays[i].first, byteArrays[i].second, 0);
+    for (int i = 0; i < m_byteArrays.size(); i++) {
+      env->ReleaseByteArrayElements(m_byteArrays[i].first, m_byteArrays[i].second, 0);
     }
-    for (int i = 0; i < doubleArrays.size(); i++) {
-      env->ReleaseDoubleArrayElements(doubleArrays[i].first, doubleArrays[i].second, 0);
+    for (int i = 0; i < m_doubleArrays.size(); i++) {
+      env->ReleaseDoubleArrayElements(m_doubleArrays[i].first, m_doubleArrays[i].second, 0);
     }
   }
 
@@ -88,7 +133,7 @@ class JavaData {
       env->ThrowNew(env->FindClass("java/lang/OutOfMemoryError"), "Unable to access jbyteArray");
     }
     length = env->GetArrayLength(byteArray);
-    byteArrays.push_back(std::make_pair(byteArray, primArray));
+    m_byteArrays.push_back(std::make_pair(byteArray, primArray));
     return (char*)primArray;
   }
 
@@ -97,13 +142,17 @@ class JavaData {
     if (primArray == NULL) {
       env->ThrowNew(env->FindClass("java/lang/OutOfMemoryError"), "Unable to access jdoubleArray");
     }
-    doubleArrays.push_back(std::make_pair(array, primArray));
+    m_doubleArrays.push_back(std::make_pair(array, primArray));
     return (double*)primArray;
   }
 
-  std::vector<testcase> testcases;
-  std::vector<std::pair<jbyteArray, jbyte*> > byteArrays;
-  std::vector<std::pair<jdoubleArray, jdouble*> > doubleArrays;
+  shacc_pairhmm::Batch m_batch;
+  std::vector<shacc_pairhmm::Read> m_reads;
+  std::vector<shacc_pairhmm::Haplotype> m_haps;
+  std::vector<testcase> m_testcases;
+  std::vector<std::pair<jbyteArray, jbyte*> > m_byteArrays;
+  std::vector<std::pair<jdoubleArray, jdouble*> > m_doubleArrays;
+  long m_total_cells;
 
   static jfieldID m_readBasesFid;
   static jfieldID m_readQualsFid;

src/main/native/pairhmm/debug.h

@@ -0,0 +1,18 @@
+#ifndef DEBUG_H
+#define DEBUG_H
+
+#include <stdio.h>
+
+#ifdef DEBUG
+#  define DBG(M, ...) fprintf(stderr, "[DEBUG] (%s:%d) : " M "\n", __FUNCTION__, __LINE__, ##__VA_ARGS__)
+#  define INFO(M, ...) fprintf(stderr, "[INFO] (%s:%d) : " M "\n", __FUNCTION__, __LINE__, ##__VA_ARGS__)
+#  define WARN(M, ...) fprintf(stderr, "[WARNING] (%s:%d) : " M "\n", __FUNCTION__, __LINE__, ##__VA_ARGS__)
+#  define ERROR(M, ...) fprintf(stderr, "[ERROR] (%s:%d) :" M "\n", __FUNCTION__, __LINE__, ##__VA_ARGS__)
+#else
+#  define DBG(M, ...)
+#  define INFO(M, ...) fprintf(stderr, "[INFO] " M "\n", ##__VA_ARGS__)
+#  define WARN(M, ...) fprintf(stderr, "[WARNING] " M "\n", ##__VA_ARGS__)
+#  define ERROR(M, ...) fprintf(stderr, "[ERROR] " M "\n", ##__VA_ARGS__)
+#endif
+
+#endif