背景:
实验室的数据需要将搭建的UCSC Genome Browser进行备份,gbdb文件夹和mysql数据库文件夹总数据量将近10T,使用普通的tar和gzip进行压缩的话非常耗时。
解决方法:
使用pigz软件进行压缩。
A parallel implementation of gzip for modernmulti-processor, multi-core machines。
pigz就是支持并行的gzip,这样就能充分发挥实验室计算机的计算性能了,多开几个线程以提高速度。
至于软件的性能,具体没做测试,其他人测试的结果如下:
1、pigz默认用法(默认并发线程是逻辑cpu个数)可比gzip快5.3倍,CPU消耗则是gzip的8倍,压缩比则相当; 2、并发8线程对比4线程提升:41.2%,16线程对比8线程提升:27.9%,32线程对比16线程提升:3%; 3、在对压缩效率要求较高、但对短时间内CPU消耗较高不受影响的场景,使用pigz非常合适。
具体的命令如下:
压缩文件
tar -cf - /data/rdata1/gb/gbdb/ | pigz -v -p 32 -c - > gbdb-backup.tar.pigz
解压文件
pigz -dc gbdb-backup.tar.pigz | tar -xvf -
pigz的参数如下:
Usage: pigz [options] [files ...] will compress files in place, adding the suffix '.gz'. If no files are specified, stdin will be compressed to stdout. pigz does what gzip does, but spreads the work over multiple processors and cores when compressing. Options: -0 to -9, -11 Compression level (11 is much slower, a few % better) --fast, --best Compression levels 1 and 9 respectively -b, --blocksize mmm Set compression block size to mmmK (default 128K) -c, --stdout Write all processed output to stdout (won't delete) -d, --decompress Decompress the compressed input -f, --force Force overwrite, compress .gz, links, and to terminal -F --first Do iterations first, before block split for -11 -h, --help Display a help screen and quit -i, --independent Compress blocks independently for damage recovery -I, --iterations n Number of iterations for -11 optimization -k, --keep Do not delete original file after processing -K, --zip Compress to PKWare zip (.zip) single entry format -l, --list List the contents of the compressed input -L, --license Display the pigz license and quit -M, --maxsplits n Maximum number of split blocks for -11 -n, --no-name Do not store or restore file name in/from header -N, --name Store/restore file name and mod time in/from header -O --oneblock Do not split into smaller blocks for -11 -p, --processes n Allow up to n compression threads (default is the number of online processors, or 8 if unknown) -q, --quiet Print no messages, even on error -r, --recursive Process the contents of all subdirectories -R, --rsyncable Input-determined block locations for rsync -S, --suffix .sss Use suffix .sss instead of .gz (for compression) -t, --test Test the integrity of the compressed input -T, --no-time Do not store or restore mod time in/from header -v, --verbose Provide more verbose output -V --version Show the version of pigz -z, --zlib Compress to zlib (.zz) instead of gzip format -- All arguments after "--" are treated as files