Merge pull request #114 from Kmannth/master

2 Memory related defensive patches for GKL.
IntelLabs · Aug 26, 2020 · 97f3889 · 97f3889
2 parents 26fa84f + 990510c
commit 97f3889
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Showing 3 changed files with 32 additions and 13 deletions.
diff --git a/src/main/native/compression/IntelDeflater.cc b/src/main/native/compression/IntelDeflater.cc
@@ -164,17 +164,25 @@ JNIEXPORT void JNICALL Java_com_intel_gkl_compression_IntelDeflater_generateHuff
 
       jbyte* input = (jbyte*)env->GetPrimitiveArrayCritical(inputBuffer, 0);
 
-      struct isal_huff_histogram *histogram;
+      struct isal_huff_histogram *histogram = (struct isal_huff_histogram *) malloc(sizeof(*histogram)); 
       struct isal_hufftables *hufftables_custom;
 
+      if (histogram == NULL) {
+           DBG ("Malloc failed out of memory");
+           return; 
+      } 
+
       memset(histogram, 0, sizeof(isal_huff_histogram));
       isal_update_histogram((unsigned char*)input, 64*1024, histogram);
       isal_create_hufftables(hufftables_custom, histogram);
       lz_stream->hufftables = hufftables_custom;
 
       env->SetLongField(obj, FID_lz_stream, (jlong)lz_stream);
       env->ReleasePrimitiveArrayCritical(inputBuffer, input, 0);
+
+      free(histogram);
       }
+
 }
 
 /**

diff --git a/src/main/native/smithwaterman/IntelSmithWaterman.cc b/src/main/native/smithwaterman/IntelSmithWaterman.cc
@@ -56,6 +56,11 @@ JNIEXPORT jint JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_align
     jbyte* alternate = (jbyte*)env->GetPrimitiveArrayCritical(alt, 0);
     jbyte* cigarArray = (jbyte*)env->GetPrimitiveArrayCritical(cigar, 0);
 
+    if (reference == NULL | alternate == NULL | cigarArray == NULL) {
+         DBG("GetPrimitiveArrayCritical failed from JAVA unable to contiune"); 
+         return -1;
+    }
+
     jint count = 0;
     jint offset = 0;
 

diff --git a/src/main/native/smithwaterman/PairWiseSW.h b/src/main/native/smithwaterman/PairWiseSW.h
@@ -419,15 +419,21 @@ int32_t CONCAT(runSWOnePairBT_,SIMD_ENGINE)(int32_t match, int32_t mismatch, int
 
 
 
-   int32_t  w_match = match;
-     int32_t   w_mismatch = mismatch;
-     int32_t   w_open = open;
-     int32_t   w_extend = extend;
-
-     int32_t   *E_  = (int32_t *)_mm_malloc((6 * (MAX_SEQ_LEN+ AVX_LENGTH)) * sizeof(int32_t), 64);
-      int16_t  *backTrack_ = (int16_t *)_mm_malloc((2 * MAX_SEQ_LEN * MAX_SEQ_LEN + 2 * AVX_LENGTH) * sizeof(int16_t), 64);
-      int16_t  *cigarBuf_  = (int16_t *)_mm_malloc(4 * MAX_SEQ_LEN * sizeof(int16_t), 64);
-
+    int32_t  w_match = match;
+    int32_t  w_mismatch = mismatch;
+    int32_t  w_open = open;
+    int32_t  w_extend = extend;
+
+    int32_t  *E_  = (int32_t *)_mm_malloc((6 * (MAX_SEQ_LEN+ AVX_LENGTH)) * sizeof(int32_t), 64);
+    int16_t  *backTrack_ = (int16_t *)_mm_malloc((2 * MAX_SEQ_LEN * MAX_SEQ_LEN + 2 * AVX_LENGTH) * sizeof(int16_t), 64);
+    int16_t  *cigarBuf_  = (int16_t *)_mm_malloc(4 * MAX_SEQ_LEN * sizeof(int16_t), 64);
+
+    if (E_ == NULL  | backTrack_  == NULL | cigarBuf_ == NULL) {
+         _mm_free(E_);
+         _mm_free(backTrack_);
+         _mm_free(cigarBuf_);
+	 return -1; 
+    } 
 
     SeqPair p;
     p.seq1 = seq1;
@@ -442,8 +448,8 @@ int32_t CONCAT(runSWOnePairBT_,SIMD_ENGINE)(int32_t match, int32_t mismatch, int
 
     (*cigarCount) = p.cigarCount;
 
-    free(E_);
-    free(backTrack_);
-    free(cigarBuf_);
+    _mm_free(E_);
+    _mm_free(backTrack_);
+    _mm_free(cigarBuf_);
     return p.alignmentOffset;
     }