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Top Forums Shell Programming and Scripting Honey, I broke awk! (duplicate line removal in 30M line 3.7GB csv file) Post 302895593 by Michael Stora on Tuesday 1st of April 2014 11:59:59 AM
Old 04-01-2014
Quote:
Originally Posted by DGPickett
You did not say how much RAM you have, which is a definite factor.

The MD5 result is impressive. Is MD5 as cheap as a good hash? Perhaps CPUs have gotten so much faster than disk that it is not a factor!

In perl/C/C++/JAVA you can mmap the input file both for input and so your hash map can hold a 64 bit char* for exact verification, reducing copying and space allocation overhead.

The exact verification seems to expand the vm footprint a lot, but the most likely case is that the md5 or hash is new and so the exact compare is not done, greatly reducing processing and the vm footprint with a small minority of duplicates. If there were a lot of duplicates, that hurts the VM footprint with more exact verifications, but conversely there is less final data in the map.
I have 16 GB of ram but my "disks" are also solid state. It's a fast system. The md5 solution is working well for me.

Mike
 

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md5(3)								      OpenSSL								    md5(3)

NAME
MD2, MD4, MD5, MD2_Init, MD2_Update, MD2_Final, MD4_Init, MD4_Update, MD4_Final, MD5_Init, MD5_Update, MD5_Final - MD2, MD4, and MD5 hash functions SYNOPSIS
#include <openssl/md2.h> unsigned char *MD2(const unsigned char *d, unsigned long n, unsigned char *md); void MD2_Init(MD2_CTX *c); void MD2_Update(MD2_CTX *c, const unsigned char *data, unsigned long len); void MD2_Final(unsigned char *md, MD2_CTX *c); #include <openssl/md4.h> unsigned char *MD4(const unsigned char *d, unsigned long n, unsigned char *md); void MD4_Init(MD4_CTX *c); void MD4_Update(MD4_CTX *c, const void *data, unsigned long len); void MD4_Final(unsigned char *md, MD4_CTX *c); #include <openssl/md5.h> unsigned char *MD5(const unsigned char *d, unsigned long n, unsigned char *md); void MD5_Init(MD5_CTX *c); void MD5_Update(MD5_CTX *c, const void *data, unsigned long len); void MD5_Final(unsigned char *md, MD5_CTX *c); DESCRIPTION
MD2, MD4, and MD5 are cryptographic hash functions with a 128 bit output. MD2(), MD4(), and MD5() compute the MD2, MD4, and MD5 message digest of the n bytes at d and place it in md (which must have space for MD2_DIGEST_LENGTH == MD4_DIGEST_LENGTH == MD5_DIGEST_LENGTH == 16 bytes of output). If md is NULL, the digest is placed in a static array. The following functions may be used if the message is not completely stored in memory: MD2_Init() initializes a MD2_CTX structure. MD2_Update() can be called repeatedly with chunks of the message to be hashed (len bytes at data). MD2_Final() places the message digest in md, which must have space for MD2_DIGEST_LENGTH == 16 bytes of output, and erases the MD2_CTX. MD4_Init(), MD4_Update(), MD4_Final(), MD5_Init(), MD5_Update(), and MD5_Final() are analogous using an MD4_CTX and MD5_CTX structure. Applications should use the higher level functions EVP_DigestInit(3) etc. instead of calling the hash functions directly. NOTE
MD2, MD4, and MD5 are recommended only for compatibility with existing applications. In new applications, SHA-1 or RIPEMD-160 should be preferred. RETURN VALUES
MD2(), MD4(), and MD5() return pointers to the hash value. MD2_Init(), MD2_Update(), MD2_Final(), MD4_Init(), MD4_Update(), MD4_Final(), MD5_Init(), MD5_Update(), and MD5_Final() do not return val- ues. CONFORMING TO
RFC 1319, RFC 1320, RFC 1321 SEE ALSO
sha(3), ripemd(3), EVP_DigestInit(3) HISTORY
MD2(), MD2_Init(), MD2_Update() MD2_Final(), MD5(), MD5_Init(), MD5_Update() and MD5_Final() are available in all versions of SSLeay and OpenSSL. MD4(), MD4_Init(), and MD4_Update() are available in OpenSSL 0.9.6 and above. 0.9.7a 2000-08-14 md5(3)
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