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Full Discussion: Help optimizing sort of large files
Top Forums UNIX for Advanced & Expert Users Help optimizing sort of large files Post 302925271 by kogorman3 on Saturday 15th of November 2014 11:00:00 AM
Old 11-15-2014
Quote:
Originally Posted by Corona688
I know. I am concerned you might be making your buffers too large -- ideal settings for 1 process would be twice what your computer can handle when doubled. Halve the buffer size and number of files every time you double the number of threads. Individually their efficiency could go down a bit, but collectively they can get masses more work done if you have enough cache to keep up with them.

You might look into increasing the writeback time on your temp partition. Spending all your I/O time writing changes that are going to be invalidated 60 seconds later could be a waste, let the disk cache do the thrashing.

Which means leaving some RAM for disk cache of course. Using all available RAM forces it to do more I/O. 50/50 for sort vs cache might be a good split off the cuff.

I wonder if your SSD might be a better temp folder than swap -- like you say, you're not using it, and forcing your system to eat into swap can really interfere with caching. An ssd could support a much larger number of streams, potentially.

My SSD is nowhere near big enough for /tmp, so that is assigned to a dedicated 2TB SATA drive. It would be large enough for these tests on a 14GB file, but my real workload has TB-sized inputs, so I test accordingly.

The tests seem to confirm that my buffers are too large. I was testing with 1 GB and larger, based on what the default settings are. But I'm going to be redoing the tests with smaller buffers and larger batches. So long as I can keep it down to 2 passes through the data, it may be much better that way. I wouldn't be surprised to find the best arrangement is 2,000 512-megabyte temporary files merged in a single pass. It all depends on how smart the merge is. If it bubble-sorts, of course, I'm sunk.

I'll have to research writeback time. However, when my input file is larger than RAM, I would expect all temps to be flushed before they get used.

---------- Post updated at 07:30 AM ---------- Previous update was at 07:19 AM ----------

Quote:
Originally Posted by DGPickett
Well defragged disk helps, as sort is doing sequential passes merging data. As a pattern, sequential is the fastest, if the adjacent file pages are really adjacent disk pages.

If sort has a big RAM footprint, it can move out of place items farther on each pass, as each pass reads from all sorted input streams into RAM and the smallest <= last is written to the newest temp output.

Fast sort space is critical, too, more critical than fast swap, but both are nice.
Defragged? I'm not sure how to do that on Linux, so I am using a fresh 2-TB drive formatted ext4 and directing sort to use it for temporaries. It's otherwise empty.

I've got 32 GB RAM and a 64-bit CPU. That's big enough for the whole test file, but the parameters to sort don't let it work that way.

Sort space vs swap space? Not sure, but I guess you mean disk. They're all SATA-III, 7200-RPM.

---------- Post updated at 08:00 AM ---------- Previous update was at 07:30 AM ----------

Quote:
Originally Posted by drl
Hi.

You may wish to look over the documentation for msort. It has numerous options that standard sort does not. Some might be useful for your task:
Code:
msort - sort records in complex ways
http://billposer.org/Software/msort.html
http://freecode.com/projects/msort

However, for tasks that can be done with both:

Best wishes ... cheers, drl
Thanks for the pointer. I had never seen msort. A quick look at the documentation makes it clear that for the current task, GNU sort will be just fine, but I'll keep msort in mind.
Last edited by kogorman3; 11-15-2014 at 12:16 PM..
 

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