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Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302925515 by kogorman3 on Monday 17th of November 2014 03:33:24 PM
Old 11-17-2014
Quote:
Originally Posted by Corona688
ext4 partitions are relatively easy to defrag, being designed with runtime defragmentation in mind (yes, runtime -- no need to unmount) via the e4defrag utility. There's no point defragging an empty partition, but check that your input and output partitions aren't a mess after all this testing.
Nice to know. I tried e4defrag and it showed a fragmentation score of 0 on all directories.

Quote:
The process of merge-sorting doesn't work that way. No matter how big your buffers are, it has to do the same number of merges on the same number of elements of the same sizes, nearly all of them tiny... Starting with billions of 2-element merges, half the number of 4-element merges, etc, etc, etc. (A little oversimplification, but the merging options don't substantially change this.) That's why pushing buffers to ridiculous sizes is so little help -- they're nearly always dead weight except for the final merge, when it's never going to be big enough to matter anyway.
I'm still a bit new to this, even after peeking at the source code. But it seems to me that there are two distinct phases to GNU sort. Both are merge sorts, but there's a big difference between merging in RAM and merging disk files. The main point of my optimizing effort turned out to be minimizing the number of file merges. Here's how I think of it now:

If all of the data can fit in the specified buffer, no temporary files will be created, and the output of the single in-RAM merge will go to the output file.

Otherwise, buffer-loads of data will be merged in RAM, and output to temporary files. There will be at least 2 of these, and perhaps a great many. These will be merged <batch-size> files at a time, with all the I/O time you'd expect. It's therefore desirable to ensure that no more than <batch-size> temporary files are created. If that's impossible, then limit it to the square, or even the cube of that number. Both buffer-size and batch-size affect the achievement of these goals.

Of course, even this is an oversimplification. It ignores effects of the TLB, of the L1 and L2 caches, and the kernel's buffer cache. Thus my interest in measuring actual times.

This is not going well, and I don't know why. Successive runs report quite different times. It's true the system is used for other things, but not heavily -- it's all my personal use. This is showing up in elapsed time, but not much in either system or user time. Odd. Moreover, the results of the second runs were consistently worse than the first. I'm trying third runs now.
 

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GIT-MERGE-INDEX(1)						    Git Manual							GIT-MERGE-INDEX(1)

NAME
git-merge-index - Run a merge for files needing merging SYNOPSIS
git merge-index [-o] [-q] <merge-program> (-a | [--] <file>*) DESCRIPTION
This looks up the <file>(s) in the index and, if there are any merge entries, passes the SHA-1 hash for those files as arguments 1, 2, 3 (empty argument if no file), and <file> as argument 4. File modes for the three files are passed as arguments 5, 6 and 7. OPTIONS
-- Do not interpret any more arguments as options. -a Run merge against all files in the index that need merging. -o Instead of stopping at the first failed merge, do all of them in one shot - continue with merging even when previous merges returned errors, and only return the error code after all the merges. -q Do not complain about a failed merge program (a merge program failure usually indicates conflicts during the merge). This is for porcelains which might want to emit custom messages. If git merge-index is called with multiple <file>s (or -a) then it processes them in turn only stopping if merge returns a non-zero exit code. Typically this is run with a script calling Git's imitation of the merge command from the RCS package. A sample script called git merge-one-file is included in the distribution. ALERT ALERT ALERT! The Git "merge object order" is different from the RCS merge program merge object order. In the above ordering, the original is first. But the argument order to the 3-way merge program merge is to have the original in the middle. Don't ask me why. Examples: torvalds@ppc970:~/merge-test> git merge-index cat MM This is MM from the original tree. # original This is modified MM in the branch A. # merge1 This is modified MM in the branch B. # merge2 This is modified MM in the branch B. # current contents or torvalds@ppc970:~/merge-test> git merge-index cat AA MM cat: : No such file or directory This is added AA in the branch A. This is added AA in the branch B. This is added AA in the branch B. fatal: merge program failed where the latter example shows how git merge-index will stop trying to merge once anything has returned an error (i.e., cat returned an error for the AA file, because it didn't exist in the original, and thus git merge-index didn't even try to merge the MM thing). GIT
Part of the git(1) suite Git 2.17.1 10/05/2018 GIT-MERGE-INDEX(1)
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