Re^4: command line perl reading from STDIN

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Re^5: command line perl reading from STDIN by BrowserUk (Patriarch) on Jan 31, 2013 at 18:24 UTC
What do you get if you let perl do the open rather than have the shell redirect>: `time perl -ne '$s=<>;<>;<>; chomp $s; print "$s\n";' A_1_1.fq \| wc -l` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply] [d/l]
Re^6: command line perl reading from STDIN by perlhappy (Novice) on Jan 31, 2013 at 18:58 UTC
The exact same output using both commands and the exact same number of lines. The results are exactly the same but the time performance is really different. Weird	[reply]
Re^7: command line perl reading from STDIN by BrowserUk (Patriarch) on Feb 01, 2013 at 05:15 UTC
but the time performance is really different. Could I trouble you to post that timing data? With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply]
Re^5: command line perl reading from STDIN (strace) by tye (Sage) on Jan 31, 2013 at 19:11 UTC
That is a dramatic difference and is worth investigating further. Making Perl input processing 60-times faster in some cases might be a result. I'd probably run strace on those cases and see what Perl is doing differently. - tye	[reply]
Re^6: command line perl reading from STDIN (strace) by perlhappy (Novice) on Feb 01, 2013 at 14:54 UTC
Ok, a probable reason for the difference. Its not actually as great a huge difference in time anymore. Let me explain, I'm doing work on a server that lots of other people are working on. Because of this the server sometimes gets more jobs to run than other times. I reviewed some of the jobs submission logs yesterday and it was extremely busy yesterday when I was doing the checks. I ran the two again today and used strace to track whats going on. `cat A_1_1.fq` write(1, "12555:2368#0/1\nffafWgggWgagcggff"..., 1048576) = 1048576 read(3, "0004_FC:1:76:5896:2982#0/1\naQXaa"..., 1048576) = 1048576 write(1, "0004_FC:1:76:5896:2982#0/1\naQXaa"..., 1048576) = 1048576 read(3, "\nhhhhhcghghhhhhhhhfhhhhhgfghhhhh"..., 1048576) = 1048576 write(1, "\nhhhhhcghghhhhhhhhfhhhhhgfghhhhh"..., 1048576) = 1048576 `perl -ne '$s=<>;<>;<>; chomp $s; print "$s\n";'` read(0, "ehhhfhhh]\n@HWI-EAS283_0004_FC:1:"..., 4096) = 4096 read(0, "_0004_FC:1:52:6965:11034#0/1\nggg"..., 4096) = 4096 read(0, "0004_FC:1:52:10518:11036#0/1\nhhg"..., 4096) = 4096 read(0, "1:52:14559:11038#0/1\nffffffdfdf["..., 4096) = 4096 write(1, "GCCCCCAGAGCANCGTCTCTGGGGGCAGCCAG"..., 4096) = 4096 read(0, "fgggfcbfffcffdcdfcfaffffaa^fff"..., 4096) = 4096 `>time perl -ne '$s=<>;<>;<>; chomp $s; print "$s\n";' < A_1_1.fq \| wc -l` read(3, "-EAS283_0004_FC:1:21:15451:12331"..., 4096) = 4096 read(3, ":18706:12324#0/1\ncaYYcaaaVTaaZ"..., 4096) = 4096 read(3, "hhhfgahhhhh\n@HWI-EAS283_0004_FC:"..., 4096) = 4096 read(3, "ATCCTCCAGGCGATTCAACGCCTTGGTTCTCT"..., 4096) = 4096 write(1, "TTTCTGTTCACTCTCAACTTCTCCTTCCAGTT"..., 4096) = 4096 read(3, "8646:12340#0/1\ngegcgaKaaaffff_gg"..., 4096) = 4096 There is still a time difference but nowhere near as large as before (see below). The first is however, consistently faster. `>time cat A_1_1.fq \| perl -ne '$s=<>;<>;<>; chomp $s; print "$s\n";' \| wc -l` 26814958 real 0m41.711s user 0m38.406s sys 0m5.096s `>time perl -ne '$s=<>;<>;<>; chomp $s; print "$s\n";' < A_1_1.fq \| wc -l` 26814958 real 3m39.382s user 0m52.811s sys 0m23.169s	[reply] [d/l] [select]


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