Big Data Engineering, Practices and Research: HFile: A Block-Indexed File Format to Store Sorted Key-Value Pairs

Saturday, September 12, 2009

HFile: A Block-Indexed File Format to Store Sorted Key-Value Pairs

1. Intruduction

HFile is a mimic of Google’s SSTable. Now, it is available in Hadoop HBase-0.20.0. And the previous releases of HBase temporarily use an alternate file format – MapFile[4], which is a common file format in Hadoop IO package. I think HFile should also become a common file format when it becomes mature, and should be moved into the common IO package of Hadoop in the future.

Following words of SSTable are from section 4 of Google’s Bigtable paper.

The Google SSTable file format is used internally to store Bigtable data. An SSTable provides a persistent, ordered immutable map from keys to values, where both keys and values are arbitrary byte strings. Operations are provided to look up the value associated with a specified key, and to iterate over all key/value pairs in a specified key range. Internally, each SSTable contains a sequence of blocks (typically each block is 64KB in size, but this is configurable). A block index (stored at the end of the SSTable) is used to locate blocks; the index is loaded into memory when the SSTable is opened. A lookup can be performed with a single disk seek: we first find the appropriate block by performing a binary search in the in-memory index, and then reading the appropriate block from disk. Optionally, an SSTable can be completely mapped into memory, which allows us to perform lookups and scans without touching disk.[1]

The HFile implements the same features as SSTable, but may provide more or less.

2. File Format

Data Block Size

Whenever we say Block Size, it means the uncompressed size.

The size of each data block is 64KB by default, and is configurable in HFile.Writer. It means the data block will not exceed this size more than one key/value pair. The HFile.Writer starts a new data block to add key/value pairs if the current writing block is equal to or bigger than this size. The 64KB size is same as Google’s [1].

To achieve better performance, we should select different block size. If the average key/value size is very short (e.g. 100 bytes), we should select small blocks (e.g. 16KB) to avoid too many key/value pairs in each block, which will increase the latency of in-block seek, because the seeking operation always finds the key from the first key/value pair in sequence within a block.

Maximum Key Length

The key of each key/value pair is currently up to 64KB in size. Usually, 10-100 bytes is a typical size for most of our applications. Even in the data model of HBase, the key (rowkey+column family:qualifier+timestamp) should not be too long.

Maximum File Size

The trailer, file-info and total data block indexes (optionally, may add meta block indexes) will be in memory when writing and reading of an HFile. So, a larger HFile (with more data blocks) requires more memory. For example, a 1GB uncompressed HFile would have about 15600 (1GB/64KB) data blocks, and correspondingly about 15600 indexes. Suppose the average key size is 64 bytes, then we need about 1.2MB RAM (15600X80) to hold these indexes in memory.

Compression Algorithm

- Compression reduces the number of bytes written to/read from HDFS.

- Compression effectively improves the efficiency of network bandwidth and disk space

- Compression reduces the size of data needed to be read when issuing a read

To be as low friction as necessary, a real-time compression library is preferred. Currently, HFile supports following three algorithms:

(1)NONE (Default, uncompressed, string name=”none”)

(2)GZ (Gzip, string name=”gz”)

Out of the box, HFile ships with only Gzip compression, which is fairly slow.

(3)LZO(Lempel-Ziv-Oberhumer, preferred, string name=”lzo”)

To achieve maximal performance and benefit, you must enable LZO, which is a lossless data compression algorithm that is focused on decompression speed.

Following figures show the format of an HFile.

In above figures, an HFile is separated into multiple segments, from beginning to end, they are:

- Data Block segment

To store key/value pairs, may be compressed.

- Meta Block segment (Optional)

To store user defined large metadata, may be compressed.

- File Info segment

It is a small metadata of the HFile, without compression. User can add user defined small metadata (name/value) here.

- Data Block Index segment

Indexes the data block offset in the HFile. The key of each index is the key of first key/value pair in the block.

- Meta Block Index segment (Optional)

Indexes the meta block offset in the HFile. The key of each index is the user defined unique name of the meta block.

- Trailer

The fix sized metadata. To hold the offset of each segment, etc. To read an HFile, we should always read the Trailer firstly.

The current implementation of HFile does not include Bloom Filter, which should be added in the future.

3. LZO Compression

LZO is now removed from Hadoop or HBase 0.20+ because of GPL restrictions. To enable it, we should install native library firstly as following. [6][7][8][9]

(1) Download LZO: http://www.oberhumer.com/, and build.

# ./configure --build=x86_64-redhat-linux-gnu --enable-shared --disable-asm

# make

# make install

Then the libraries have been installed in: /usr/local/lib

(2) Download the native connector library http://code.google.com/p/hadoop-gpl-compression/, and build.

Copy hadoo-0.20.0-core.jar to ./lib.

# ant compile-native

# ant jar

(3) Copy the native library (build/native/ Linux-amd64-64) and hadoop-gpl-compression-0.1.0-dev.jar to your application’s lib directory. If your application is a MapReduce job, copy them to hadoop’s lib directory. Your application should follow the $HADOOP_HOME/bin/hadoop script to ensure that the native hadoop library is on the library path via the system property -Djava.library.path=. [9]

4. Performance Evaluation

Testbed

− 4 slaves + 1 master

− Machine: 4 CPU cores (2.0G), 2x500GB 7200RPM SATA disks, 8GB RAM.

− Linux: RedHat 5.1 (2.6.18-53.el5), ext3, no RAID, noatime

− 1Gbps network, all nodes under the same switch.

− Hadoop-0.20.0 (1GB heap), lzo-2.0.3

Some MapReduce-based benchmarks are designed to evaluate the performance of operations to HFiles, in parallel.

− Total key/value entries: 30,000,000.

− Key/Value size: 1000 bytes (10 for key, and 990 for value). We have totally 30GB of data.

− Sequential key ranges: 60, i.e. each range have 500,000 entries.

− Use default block size.

− The entry value is a string, each continuous 8 bytes are a filled with a same letter (A~Z). E.g. “BBBBBBBBXXXXXXXXGGGGGGGG……”.

We set mapred.tasktracker.map.tasks.maximum=3 to avoid client side bottleneck.

(1) Write

Each MapTask for each range of key, which writes a separate HFile with 500,000 key/value entries.

(2) Full Scan

Each MapTask scans a separate HFile from beginning to end.

(3) Random Seek a specified key

Each MapTask opens one separate HFile, and selects a random key within that file to seek it. Each MapTask runs 50,000 (1/10 of the entries) random seeks.

(4) Random Short Scan

Each MapTask opens one separate HFile, and selects a random key within that file as a beginning to scan 30 entries. Each MapTask runs 50,000 scans, i.e. scans 50,000*30=1,500,000 entries.

This table shows the average entries which are written/seek/scanned per second, and per node.

In this evaluation case, the compression ratio is about 7:1 for gz(Gzip), and about 4:1 for lzo. Even through the compression ratio is just moderate, the lzo column shows the best performance, especially for writes.

The performance of full scan is much better than SequenceFile, so HFile may provide better performance to MapReduce-based analytical applications.

The random seek in HFiles is slow, especially in none-compressed HFiles. But the above numbers already show 6X~10X better performance than a disk seek (10ms). Following Ganglia charts show us the overhead of load, CPU, and network. The random short scan makes the similar phenomena.