Seeking to EOF is too inefficient!

[1134efe2-03f1-4cfc-baa6-68518adc5830]

BPO	21638
Nosy	@pitrou, @vstinner

^{Note: these values reflect the state of the issue at the time it was migrated and might not reflect the current state.}

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GitHub fields: ```python assignee = None closed_at = created_at = labels = ['expert-IO', 'performance'] title = 'Seeking to EOF is too inefficient!' updated_at = user = 'https://bugs.python.org/yanlinlin82' ``` bugs.python.org fields: ```python activity = actor = 'yanlinlin82' assignee = 'none' closed = True closed_date = closer = 'yanlinlin82' components = ['IO'] creation = creator = 'yanlinlin82' dependencies = [] files = [] hgrepos = [] issue_num = 21638 keywords = [] message_count = 6.0 messages = ['219586', '219637', '219654', '219709', '219715', '219716'] nosy_count = 4.0 nosy_names = ['pitrou', 'vstinner', 'neologix', 'yanlinlin82'] pr_nums = [] priority = 'normal' resolution = 'third party' stage = None status = 'closed' superseder = None type = 'performance' url = 'https://bugs.python.org/issue21638' versions = ['Python 2.7'] ```

[1134efe2-03f1-4cfc-baa6-68518adc5830]

I noticed this problem when I run a Python2 program (MACS: http://liulab.dfci.harvard.edu/MACS/) very inefficiently on a large storage on a high performace server (64-bit Linux). It was much slower (more than two days) than running it on a normal PC (less than two hours).

After ruling out many optimizing conditions, I finally located the problem on the seek() function of Python2. Now I can reproduce the problem in a very simple example:

#!/usr/bin/python2
f = open("Input.sort.bam", "rb")
f.seek(0, 2)
f.close()

Here, the size of file 'Input.sort.bam' is 4,110,535,920 bytes. When I run the program with 'strace' to see the system calls on Linux:

$ strace python2 foo.py
...
open("Input.sort.bam", O_RDONLY)        = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=4110535920, ...}) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=4110535920, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f23d4492000
fstat(3, {st_mode=S_IFREG|0644, st_size=4110535920, ...}) = 0
lseek(3, 4110532608, SEEK_SET)          = 4110532608
read(3, "f\203\337<\334\350\313\315\345&T\227\211\fC\212a\260\204P\235\366\326\353\230\327>\373\361\221\357\373"..., 3312) = 3312
close(3)                                = 0
...

It seems that python2 just move file cursor to a specific position (4110532608 in this case) and read ahead the rest bytes, rather than seek to the file end directly. I tried to run the exact the same program on the large storage, the position changed to 1073741824, left 889310448 bytes to read to reach the file end, which reduced the performance a lot!

[vstinner]

I don't think that Python calls directly read(). Python 2 uses fopen / fread.

Python 3 doesn't use buffered files, but call open / read directly.

[1134efe2-03f1-4cfc-baa6-68518adc5830]

I agree that Python 2 should use fopen / fread rather than directly read(). But you may misunderstand this. The 'strace' tool reports Linux system calls, including read() rather than fread(), and I guess that read() should be finally called in fread() implementation.

What I mean is that Python 2's seek(0, 2) does not use fseek(0, SEEK_END), but fseek(somewhere, SEEK_SET) and fread(rest-bytes) instead, which is too inefficient in some kind of storage.

By the way, Python 3 does not behavior like this.

On Tue, Jun 3, 2014 at 4:35 AM, STINNER Victor \report@bugs.python.org\ wrote:

STINNER Victor added the comment:

I don't think that Python calls directly read(). Python 2 uses fopen / fread.

Python 3 doesn't use buffered files, but call open / read directly.

---------- nosy: +haypo, neologix

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Python tracker \report@bugs.python.org\ \http://bugs.python.org/issue21638\

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[79528080-9d85-4d18-8a2a-8b1f07640dd7]

I agree that Python 2 should use fopen / fread rather than directly read(). But you may misunderstand this. The 'strace' tool reports Linux system calls, including read() rather than fread(), and I guess that read() should be finally called in fread() implementation.

What I mean is that Python 2's seek(0, 2) does not use fseek(0, SEEK_END), but fseek(somewhere, SEEK_SET) and fread(rest-bytes) instead, which is too inefficient in some kind of storage.

Actually, Python does use fopen(), and fseek(): the culprit is the libc: $ cat /tmp/test.c; gcc -o /tmp/test /tmp/test.c -Wall; strace /tmp/test open("/etc/fstab", O_RDONLY) = 3 fstat64(3, {st_mode=S_IFREG|0644, st_size=809, ...}) = 0 mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb77ae000 fstat64(3, {st_mode=S_IFREG|0644, st_size=809, ...}) = 0 _llseek(3, 0, [0], SEEK_SET) = 0 read(3, "# /etc/fstab: static file system"..., 809) = 809 close(3) = 0

By the way, Python 3 does not behavior like this.

That's because in Python 3, the IO stack is implemented directly on top of open()/read()/lseek().

It's not the first time we stumble upon glibc stdio bugs.

I'd suggest closing this.

[1134efe2-03f1-4cfc-baa6-68518adc5830]

Thanks! I agree with that.

[1134efe2-03f1-4cfc-baa6-68518adc5830]

I ensured that the problem is in libc. I will try to figure out it by updating libc or optimizing some related parameters.