Fix checksum calculation bug when the payload is a CompositeByteBuf w…

…ith readerIndex > 0 (apache#4196)

* Add a test that reproduces a bug in checksum calculation

* Revert "Fixed unnecessary copy to heap (apache#2701)" changes to ByteBufList

This partially reverts commit 3c9c710.

* Remove CompositeBuffer unwrapping in DigestManager

* Rename update -> internalUpdate so that unwrapping logic could be added to update

* Remove unnecessary unwrapping logic in Java9IntHash

* Add safe way to handle CompositeByteBuf

* Add license header

* Fix checkstyle

* Refactor ByteBuf visitor solution

* Fix checkstyle

* Reformat

* Refactor recursive visiting

* Revisit equals, hashCode and toString

* Refactor test case

* Add support for UnpooledHeapByteBuf.getBytes which passes an array

* Add support for visiting buffers backed by byte[] arrays

- getBytes calls setBytes with a byte[] argument for
  heap ByteBufs

* Move ByteBufVisitor to org.apache.bookkeeper.util package

* Update javadoc

* Refactor to use stateless visitor so that instance can be shared

* Improve test so that a single scenario can be used for debugging

* Fix bug in Java9IntHash calculation that assumed crc32c_update(x) == ~crc32c_update(~x)

- Java9IntHash uses private methods from java.util.zip.CRC32C class,
  updateBytes and updateDirectByteBuffer.
  When inspecting the use and interface contract, it doesn't match
  how it is used in Java9IntHash. This PR addresses that by introducing
  a separate initial value for initializing the accumulated value
  so that the initial value could match the logic in
  java.util.zip.CRC32C.reset method. There's also a separate
  method for finalizing the accumulated value into a final
  checksum value. This is to match the java.util.zip.CRC32C.getValue
  method's logic (uses bitwise complement operator ~).

- With a quick glance, it might appear that the previous logic is similar.
  However it isn't since I have a failing test which gets fixed with this
  change. I haven't yet added the Java9IntHash level unit test case to prove how
  it differs. It must be related to integer value overflow. For the CRC32C function,
  I believe it means that it cannot be assumed in all cases that
  func(x) == ~func(~x). That's the assumption that the previous code was making.
  It probably applies for many inputs, but not all. It would break in overflow
  cases.

* Fix checkstyle

* Fix checkstyle

* Fix missing depth increment that prevents StackOverflowException

* Properly handle the depth increase and decrease

* Remove unnecessary condition

* Use more efficient way to read bytes to the target array

* Don't use ByteBufVisitor if it's not necessary

* Revert "Fix bug in Java9IntHash calculation that assumed crc32c_update(x) == ~crc32c_update(~x)"

This reverts commit 272e962.

* Fix issue in resume byte[] version that was added

- input and output should be complemented. explanation has been added to the
  resume ByteBuf method

* Polish ByteBufVisitor

- reuse GetBytesCallbackByteBuf instance for handling the root ByteBuf instance

* Use extracted method

* Fix bug with array handling

* Polish ByteBufVisitor

* Optimize the buffer copying in the case where array or memory address cannot be accessed

- read-only buffers will need to be copied before reading
  - use ByteBuf.copy for direct buffers with pooled allocator when the algorithm can accept
    a memory address buffer
- use the 64kB threadlocal byte[] buffer for copying all other inputs

* Check if memory address is accepted

* Improve comments about complement (current = ~current) in resume

* Print thread dump when build is cancelled

* Filter empty buffers and arrays in ByteBufVisitor

.github/workflows/bk-ci.yml

@@ -200,6 +200,10 @@ jobs:
           path: surefire-reports
           retention-days: 7
 
+      - name: print JVM thread dumps when cancelled
+        if: cancelled()
+        run: ./dev/ci-tool print_thread_dumps
+
   integration-tests:
     name: Integration Tests
     runs-on: ubuntu-latest

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/CRC32CDigestManager.java

@@ -46,7 +46,17 @@ void populateValueAndReset(int digest, ByteBuf buf) {
     }
 
     @Override
-    int update(int digest, ByteBuf data, int offset, int len) {
+    int internalUpdate(int digest, ByteBuf data, int offset, int len) {
         return Crc32cIntChecksum.resumeChecksum(digest, data, offset, len);
     }
+
+    @Override
+    int internalUpdate(int digest, byte[] buffer, int offset, int len) {
+        return Crc32cIntChecksum.resumeChecksum(digest, buffer, offset, len);
+    }
+
+    @Override
+    boolean acceptsMemoryAddressBuffer() {
+        return Crc32cIntChecksum.acceptsMemoryAddressBuffer();
+    }
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/CRC32DigestManager.java

@@ -34,6 +34,7 @@ interface CRC32Digest {
         long getValueAndReset();
 
         void update(ByteBuf buf, int offset,  int len);
+        void update(byte[] buffer, int offset, int len);
     }
 
     private static final FastThreadLocal<CRC32Digest> crc = new FastThreadLocal<CRC32Digest>() {
@@ -62,14 +63,25 @@ void populateValueAndReset(int digest, ByteBuf buf) {
     }
 
     @Override
-    int update(int digest, ByteBuf data, int offset, int len) {
+    int internalUpdate(int digest, ByteBuf data, int offset, int len) {
         crc.get().update(data, offset, len);
         return 0;
     }
 
+    @Override
+    int internalUpdate(int digest, byte[] buffer, int offset, int len) {
+        crc.get().update(buffer, offset, len);
+        return 0;
+    }
+
     @Override
     boolean isInt32Digest() {
         // This is stored as 8 bytes
         return false;
     }
+
+    @Override
+    boolean acceptsMemoryAddressBuffer() {
+        return DirectMemoryCRC32Digest.isSupported();
+    }
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/DigestManager.java

@@ -20,10 +20,8 @@
 import io.netty.buffer.ByteBuf;
 import io.netty.buffer.ByteBufAllocator;
 import io.netty.buffer.ByteBufUtil;
-import io.netty.buffer.CompositeByteBuf;
 import io.netty.buffer.PooledByteBufAllocator;
 import io.netty.buffer.Unpooled;
-import io.netty.util.ReferenceCountUtil;
 import io.netty.util.ReferenceCounted;
 import io.netty.util.concurrent.FastThreadLocal;
 import java.security.GeneralSecurityException;
@@ -34,6 +32,7 @@
 import org.apache.bookkeeper.proto.BookieProtocol;
 import org.apache.bookkeeper.proto.DataFormats.LedgerMetadataFormat.DigestType;
 import org.apache.bookkeeper.util.ByteBufList;
+import org.apache.bookkeeper.util.ByteBufVisitor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -53,10 +52,25 @@ public abstract class DigestManager {
     final long ledgerId;
     final boolean useV2Protocol;
     private final ByteBufAllocator allocator;
+    private final DigestUpdaterByteBufVisitorCallback byteBufVisitorCallback;
 
     abstract int getMacCodeLength();
 
-    abstract int update(int digest, ByteBuf buffer, int offset, int len);
+    abstract int internalUpdate(int digest, ByteBuf buffer, int offset, int len);
+
+    abstract int internalUpdate(int digest, byte[] buffer, int offset, int len);
+
+    final int update(int digest, ByteBuf buffer, int offset, int len) {
+        if (buffer.hasMemoryAddress() && acceptsMemoryAddressBuffer()) {
+            return internalUpdate(digest, buffer, offset, len);
+        } else if (buffer.hasArray()) {
+            return internalUpdate(digest, buffer.array(), buffer.arrayOffset() + offset, len);
+        } else {
+            UpdateContext updateContext = new UpdateContext(digest);
+            ByteBufVisitor.visitBuffers(buffer, offset, len, byteBufVisitorCallback, updateContext);
+            return updateContext.digest;
+        }
+    }
 
     abstract void populateValueAndReset(int digest, ByteBuf buffer);
 
@@ -69,6 +83,7 @@ public DigestManager(long ledgerId, boolean useV2Protocol, ByteBufAllocator allo
         this.useV2Protocol = useV2Protocol;
         this.macCodeLength = getMacCodeLength();
         this.allocator = allocator;
+        this.byteBufVisitorCallback = new DigestUpdaterByteBufVisitorCallback();
     }
 
     public static DigestManager instantiate(long ledgerId, byte[] passwd, DigestType digestType,
@@ -136,34 +151,19 @@ private ReferenceCounted computeDigestAndPackageForSendingV2(long entryId, long
 
         // Compute checksum over the headers
         int digest = update(0, buf, buf.readerIndex(), buf.readableBytes());
-
-        // don't unwrap slices
-        final ByteBuf unwrapped = data.unwrap() != null && data.unwrap() instanceof CompositeByteBuf
-                ? data.unwrap() : data;
-        ReferenceCountUtil.retain(unwrapped);
-        ReferenceCountUtil.safeRelease(data);
-
-        if (unwrapped instanceof CompositeByteBuf) {
-            CompositeByteBuf cbb = (CompositeByteBuf) unwrapped;
-            for (int i = 0; i < cbb.numComponents(); i++) {
-                ByteBuf b = cbb.component(i);
-                digest = update(digest, b, b.readerIndex(), b.readableBytes());
-            }
-        } else {
-            digest = update(digest, unwrapped, unwrapped.readerIndex(), unwrapped.readableBytes());
-        }
+        digest = update(digest, data, data.readerIndex(), data.readableBytes());
 
         populateValueAndReset(digest, buf);
 
         // Reset the reader index to the beginning
         buf.readerIndex(0);
 
         if (isSmallEntry) {
-            buf.writeBytes(unwrapped, unwrapped.readerIndex(), unwrapped.readableBytes());
-            unwrapped.release();
+            buf.writeBytes(data, data.readerIndex(), data.readableBytes());
+            data.release();
             return buf;
         } else {
-            return ByteBufList.get(buf, unwrapped);
+            return ByteBufList.get(buf, data);
         }
     }
 
@@ -176,25 +176,9 @@ private ByteBufList computeDigestAndPackageForSendingV3(long entryId, long lastA
         headersBuffer.writeLong(length);
 
         int digest = update(0, headersBuffer, 0, METADATA_LENGTH);
-
-        // don't unwrap slices
-        final ByteBuf unwrapped = data.unwrap() != null && data.unwrap() instanceof CompositeByteBuf
-                ? data.unwrap() : data;
-        ReferenceCountUtil.retain(unwrapped);
-        ReferenceCountUtil.release(data);
-
-        if (unwrapped instanceof CompositeByteBuf) {
-            CompositeByteBuf cbb = ((CompositeByteBuf) unwrapped);
-            for (int i = 0; i < cbb.numComponents(); i++) {
-                ByteBuf b = cbb.component(i);
-                digest = update(digest, b, b.readerIndex(), b.readableBytes());
-            }
-        } else {
-            digest = update(digest, unwrapped, unwrapped.readerIndex(), unwrapped.readableBytes());
-        }
+        digest = update(digest, data, data.readerIndex(), data.readableBytes());
         populateValueAndReset(digest, headersBuffer);
-
-        return ByteBufList.get(headersBuffer, unwrapped);
+        return ByteBufList.get(headersBuffer, data);
     }
 
     /**
@@ -373,4 +357,34 @@ public RecoveryData verifyDigestAndReturnLastConfirmed(ByteBuf dataReceived) thr
         long length = dataReceived.readLong();
         return new RecoveryData(lastAddConfirmed, length);
     }
+
+    private static class UpdateContext {
+        int digest;
+
+        UpdateContext(int digest) {
+            this.digest = digest;
+        }
+    }
+
+    private class DigestUpdaterByteBufVisitorCallback implements ByteBufVisitor.ByteBufVisitorCallback<UpdateContext> {
+
+        @Override
+        public void visitBuffer(UpdateContext context, ByteBuf visitBuffer, int visitIndex, int visitLength) {
+            // recursively visit the sub buffer and update the digest
+            context.digest = internalUpdate(context.digest, visitBuffer, visitIndex, visitLength);
+        }
+
+        @Override
+        public void visitArray(UpdateContext context, byte[] visitArray, int visitIndex, int visitLength) {
+            // update the digest with the array
+            context.digest = internalUpdate(context.digest, visitArray, visitIndex, visitLength);
+        }
+
+        @Override
+        public boolean acceptsMemoryAddress(UpdateContext context) {
+            return DigestManager.this.acceptsMemoryAddressBuffer();
+        }
+    }
+
+    abstract boolean acceptsMemoryAddressBuffer();
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/DirectMemoryCRC32Digest.java

@@ -50,18 +50,32 @@ public void update(ByteBuf buf, int index, int length) {
                 crcValue = (int) updateByteBuffer.invoke(null, crcValue, buf.memoryAddress(), index, length);
             } else if (buf.hasArray()) {
                 // Use the internal method to update from array based
-                crcValue = (int) updateBytes.invoke(null, crcValue, buf.array(), buf.arrayOffset() + index, length);
+                crcValue = updateArray(crcValue, buf.array(), buf.arrayOffset() + index, length);
             } else {
                 // Fallback to data copy if buffer is not contiguous
                 byte[] b = new byte[length];
                 buf.getBytes(index, b, 0, length);
-                crcValue = (int) updateBytes.invoke(null, crcValue, b, 0, b.length);
+                crcValue = updateArray(crcValue, b, 0, length);
             }
         } catch (IllegalAccessException | InvocationTargetException e) {
             throw new RuntimeException(e);
         }
     }
 
+    private static int updateArray(int crcValue, byte[] buf, int offset, int length)
+            throws IllegalAccessException, InvocationTargetException {
+        return (int) updateBytes.invoke(null, crcValue, buf, offset, length);
+    }
+
+    @Override
+    public void update(byte[] buffer, int offset, int len) {
+        try {
+            crcValue = updateArray(crcValue, buffer, offset, len);
+        } catch (IllegalAccessException | InvocationTargetException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
     private static final Method updateByteBuffer;
     private static final Method updateBytes;
 

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/DummyDigestManager.java

@@ -38,7 +38,12 @@ int getMacCodeLength() {
     }
 
     @Override
-    int update(int digest, ByteBuf buffer, int offset, int len) {
+    int internalUpdate(int digest, ByteBuf buffer, int offset, int len) {
+        return 0;
+    }
+
+    @Override
+    int internalUpdate(int digest, byte[] buffer, int offset, int len) {
         return 0;
     }
 
@@ -49,4 +54,9 @@ void populateValueAndReset(int digest, ByteBuf buffer) {}
     boolean isInt32Digest() {
         return false;
     }
+
+    @Override
+    boolean acceptsMemoryAddressBuffer() {
+        return false;
+    }
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/MacDigestManager.java

@@ -96,13 +96,24 @@ void populateValueAndReset(int digest, ByteBuf buffer) {
     }
 
     @Override
-    int update(int digest, ByteBuf data, int offset, int len) {
+    int internalUpdate(int digest, ByteBuf data, int offset, int len) {
         mac.get().update(data.slice(offset, len).nioBuffer());
         return 0;
     }
 
+    @Override
+    int internalUpdate(int digest, byte[] buffer, int offset, int len) {
+        mac.get().update(buffer, offset, len);
+        return 0;
+    }
+
     @Override
     boolean isInt32Digest() {
         return false;
     }
+
+    @Override
+    boolean acceptsMemoryAddressBuffer() {
+        return false;
+    }
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/proto/checksum/StandardCRC32Digest.java

@@ -39,4 +39,9 @@ public long getValueAndReset() {
     public void update(ByteBuf buf, int offset, int len) {
         crc.update(buf.slice(offset, len).nioBuffer());
     }
+
+    @Override
+    public void update(byte[] buffer, int offset, int len) {
+        crc.update(buffer, offset, len);
+    }
 }

bookkeeper-server/src/main/java/org/apache/bookkeeper/util/ByteBufList.java

@@ -22,7 +22,6 @@
 
 import com.google.common.annotations.VisibleForTesting;
 import io.netty.buffer.ByteBuf;
-import io.netty.buffer.CompositeByteBuf;
 import io.netty.buffer.Unpooled;
 import io.netty.channel.ChannelHandler.Sharable;
 import io.netty.channel.ChannelHandlerContext;
@@ -133,43 +132,14 @@ public static ByteBufList get() {
      * Append a {@link ByteBuf} at the end of this {@link ByteBufList}.
      */
     public void add(ByteBuf buf) {
-        final ByteBuf unwrapped = buf.unwrap() != null && buf.unwrap() instanceof CompositeByteBuf
-                ? buf.unwrap() : buf;
-        ReferenceCountUtil.retain(unwrapped);
-        ReferenceCountUtil.release(buf);
-
-        if (unwrapped instanceof CompositeByteBuf) {
-            ((CompositeByteBuf) unwrapped).forEach(b -> {
-                ReferenceCountUtil.retain(b);
-                buffers.add(b);
-            });
-            ReferenceCountUtil.release(unwrapped);
-        } else {
-            buffers.add(unwrapped);
-        }
+        buffers.add(buf);
     }
 
     /**
      * Prepend a {@link ByteBuf} at the beginning of this {@link ByteBufList}.
      */
     public void prepend(ByteBuf buf) {
-        // don't unwrap slices
-        final ByteBuf unwrapped = buf.unwrap() != null && buf.unwrap() instanceof CompositeByteBuf
-                ? buf.unwrap() : buf;
-        ReferenceCountUtil.retain(unwrapped);
-        ReferenceCountUtil.release(buf);
-
-        if (unwrapped instanceof CompositeByteBuf) {
-            CompositeByteBuf composite = (CompositeByteBuf) unwrapped;
-            for (int i = composite.numComponents() - 1; i >= 0; i--) {
-                ByteBuf b = composite.component(i);
-                ReferenceCountUtil.retain(b);
-                buffers.add(0, b);
-            }
-            ReferenceCountUtil.release(unwrapped);
-        } else {
-            buffers.add(0, unwrapped);
-        }
+        buffers.add(0, buf);
     }
 
     /**
@@ -285,7 +255,7 @@ public ByteBufList retain() {
     @Override
     protected void deallocate() {
         for (int i = 0; i < buffers.size(); i++) {
-            ReferenceCountUtil.release(buffers.get(i));
+            buffers.get(i).release();
         }
 
         buffers.clear();