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Top Forums Shell Programming and Scripting Please suggest alternative to grep Post 302652569 by drl on Thursday 7th of June 2012 09:56:44 AM
Old 06-07-2012
Hi.

First question is does this absolutely need to be faster? How many times are you going to run it? If it's a single-shot, then perhaps just letting it run to completion is the best solution.

Secondly, the first file looks like it is a sequence. If so, then perhaps a regular expression could be used rather than a volume of 5 GB of memory. If not a regular expression, then possibly a code that determines if a piece of the line matches the base + the sequence -- an arithmetic operation, which might be faster than string comparisons (for example, some mainframes & supercomputers had multiple units for arithmetic).

Thirdly, if you have sufficient IO throughput as well as multiple cores, then one could write a program that internally divides the main file into pieces by keeping track of start-stop line positions, and then uses processes or threads to process one segment each. A less elegant solution along the same lines would be to spilt the files into n sections, each in a file, and then run n instances of grep.

Fourthly, splitting the task up among a network of machines that might share the disk; as well as the easiest (but not cheapest) solution: get a faster box.

Best wishes ... cheers, drl
 

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pnmscalefixed(1)					      General Commands Manual						  pnmscalefixed(1)

NAME
pnmscalefixed - scale a portable anymap quickly, but less accurate DESCRIPTION
pnmscalefixed is the same thing as pnmscale except that it uses fixed point arithmetic internally instead of floating point, which makes it run faster. In turn, it is less accurate and may distort the image. Use the pnmscale man page with pnmscalefixed. This man page only describes the difference. pnmscalefixed uses fixed point 12 bit arithmetic. By contrast, pnmscale uses floating point arithmetic which on most machines is probably 24 bit precision. This makes pnmscalefixed run faster (30% faster in one experiment), but the imprecision can cause distortions at the right and bottom edges. The distortion takes the following form: One pixel from the edge of the input is rendered larger in the output than the scaling factor requires. Consequently, the rest of the image is smaller than the scaling factor requires, because the overall dimensions of the image are always as requested. This distortion will usually be very hard to see. pnmscalefixed with the -verbose option tells you how much distortion there is. The amount of distortion depends on the size of the input image and how close the scaling factor is to an integral 1/4096th. If the scaling factor is an exact multiple of 1/4096, there is no distortion. So, for example doubling or halving an image causes no dis- tortion. But reducing it or enlarging it by a third would cause some distortion. To consider an extreme case, scaling a 100,000 row image down to 50,022 rows would create an output image with all of the input squeezed into the top 50,000 rows, and the last row of the input copied into the bottom 22 rows of output. pnmscalefixed could probably be modified to use 16 bit or better arithmetic without losing anything. The modification would consist of a single constant in the source code. Until there is a demonstrated need for that, though, the Netpbm maintainer wants to keep the safety cushion afforded by the original 12 bit precision. pnmscalefixed does not have pnmscale 's -nomix option. 18 November 2000 pnmscalefixed(1)
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