git-diff opens too many files?

git-diff opens too many files?

[Nguyen Thai Ngoc Duy]

I got this error in a quite big (in files) repository:
error: open("vnexpress.net/Suc-khoe/2001/04/3B9AF976"): Too many open
files in system
fatal: cannot hash vnexpress.net/Suc-khoe/2001/04/3B9AF976

The repository contained about 67.000 files and probably all were modified.
git version 1.4.4.rc1.g2bba
-- 

Re: git-diff opens too many files?

[Johannes Schindelin]

Hi,

On Mon, 20 Nov 2006, Nguyen Thai Ngoc Duy wrote:

> I got this error in a quite big (in files) repository:
> error: open("vnexpress.net/Suc-khoe/2001/04/3B9AF976"): Too many open
> files in system
> fatal: cannot hash vnexpress.net/Suc-khoe/2001/04/3B9AF976
> 
> The repository contained about 67.000 files and probably all were modified.
> git version 1.4.4.rc1.g2bba

What was the command line? "git diff" really is a wrapper around different 
programs...

Ciao,
Dscho

Re: git-diff opens too many files?

[Nguyen Thai Ngoc Duy]

On 11/20/06, Johannes Schindelin <Johannes.Schindelin@gmx.de> wrote:
> Hi,
>
> On Mon, 20 Nov 2006, Nguyen Thai Ngoc Duy wrote:
>
> > I got this error in a quite big (in files) repository:
> > error: open("vnexpress.net/Suc-khoe/2001/04/3B9AF976"): Too many open
> > files in system
> > fatal: cannot hash vnexpress.net/Suc-khoe/2001/04/3B9AF976
> >
> > The repository contained about 67.000 files and probably all were modified.
> > git version 1.4.4.rc1.g2bba
>
> What was the command line? "git diff" really is a wrapper around different
> programs...

"git diff" from working directory with no argument. The real command is

git diff |LANG=C grep '^-'|LANG=C grep -v '^--'|LANG=C sort|LANG=C uniq -c

(I squeezed blank lines, so I wanted to check that it just did that,
nothing else)

> Ciao,
> Dscho
>
>


-- 

Re: git-diff opens too many files?

[Johannes Schindelin]

Hi,

On Mon, 20 Nov 2006, Nguyen Thai Ngoc Duy wrote:

> git diff |LANG=C grep '^-'|LANG=C grep -v '^--'|LANG=C sort|LANG=C uniq -c

I looked in the code, but nothing jumps into my eyes. There is a place 
where files are mmap()ed, but AFAICT they are unmmap()ed just after 
diffing. Could you run it with strace and find unclosed open calls?

Ciao,
Dscho

Re: git-diff opens too many files?

[Linus Torvalds]

On Mon, 20 Nov 2006, Nguyen Thai Ngoc Duy wrote:
>
> I got this error in a quite big (in files) repository:
> error: open("vnexpress.net/Suc-khoe/2001/04/3B9AF976"): Too many open
> files in system

Ok, "too many open files in system" is ENFILE - you haven't run out of 
file descriptors in _one_ process, but you've exceeded the total number of 
file descriptors in the whole system.

Which is not because we forget to close() something, but because we're 
keeping file descriptors busy another way.

> fatal: cannot hash vnexpress.net/Suc-khoe/2001/04/3B9AF976

Hmm. We keep files mmap'ed in "git diff" for possibly too long. What 
happens is that we mmap a file that we want to diff when we start the 
whole thing, and keep it mapped over the whole diff session, because we're 
potentially going to need to compare it against other files (ie rename 
detection etc). And then we unmap it only at the end (in "diff_flush()" -> 
"diff_free_filepair()" -> "diff_free_filespec_data()").

And that's normally great, and means that we don't need to worry about the 
file data (we map it once, and can keep it in memory), but yeah, if you 
have thousands of files changed, you'll have thousands of mappings. And 
each one will have a pointer to a "struct file" inside the kernel. 

What OS/distro is this? Normally, you shouldn't have that low a limit on 
number of files open, but we do end up potentially opening thousands.

For example, under Linux, you can do this:

	# in one terminal window, do:
	while : ; do cat /proc/sys/fs/file-nr ; sleep 1; done

	# in another one:
	cd linux-repo
	git ls-files '*.c' | xargs touch
	git diff

and if it looks anything like mine, it could be:

	2464    0       349662
	2464    0       349662
	2464    0       349662
*	5920    0       349662
**	7616    0       349662
***	9024    0       349662
****	10944   0       349662
	2464    0       349662
	2464    0       349662


(see how the numnber of active files grows by thousands).

Anyway, there's two possible solutions:

 - simply make sure that you can have that many open files. 

   If it's a Linux system, just increase the value of the file
   /proc/sys/fs/file-max, and you're done. Of course, if you're not the 
   admin of the box, you may need to ask somebody else to do it for you..

 - we could try to make git not keep them mmap'ed for the whole time. 

Junio? This is your speciality, I'm not sure how painful it would be to 
unmap and remap on demand.. (or switch it to some kind of "keep the last 
<n> mmaps active" kind of thing to avoid having thousands and thousands of 
mmaps active).

One simple thing that might be worth it is to simply _not_ use mmap() at 
all for small files. If a file is less than 1kB, it might be better to do 
a malloc() and a read() - partly because it avoids having tons of file 
descriptors, but partly because it's also more efficient from a virtual 
memory usage perspective (not that you're probably very likely to ever 
really hit that problem in practice).

Nguyen - that "use malloc+read" thing might be a quick workaround, but 
only if you have tons of _small_ files (and if you can't easily just 
increase file-max). 

Re: git-diff opens too many files?

[Junio C Hamano]

Linus Torvalds <torvalds@osdl.org> writes:

> Anyway, there's two possible solutions:
>
>  - simply make sure that you can have that many open files. 
>
>    If it's a Linux system, just increase the value of the file
>    /proc/sys/fs/file-max, and you're done. Of course, if you're not the 
>    admin of the box, you may need to ask somebody else to do it for you..
>
>  - we could try to make git not keep them mmap'ed for the whole time. 
>
> Junio? This is your speciality, I'm not sure how painful it would be to 
> unmap and remap on demand.. (or switch it to some kind of "keep the last 
> <n> mmaps active" kind of thing to avoid having thousands and thousands of 
> mmaps active).

60,000 files 1kB each is 60MB which is a peanuts these days, but
10kB each would be already nontrivial burden on 32-bit (20%
under 3+1 split), so even if we do the "read in small files
instead of mapping" we would need diff_unpopulate_filespec() calls.

I think after diffcore_rename() runs, the data in filespec is
used only once during final textual diff generation.  We would
use once more before diff generation if diffcore_pickaxe() is in
use.  These codepaths begin with diff_populate_filespec(), so if
we unpopulate them after diffcore_rename() runs nobody would
notice (other than performance degradation and strace showing us
reading the same thing twice).

The diffcore_rename() matrix code expects all filespecs involved
can be populated at the same time, but it should not be too hard
to change it to keep one dst and all src candidates populated
but others dropped if space gets tight.  I need to look at the
code for the details.

But Nguyen's command line did not have -M; I think the filespecs
are populated only during the text generation in that case, so
the above would not help him while it would be a worthwhile
change.

Because there is _no_ processing that comes after textual diff
generation that looks at the data, I think diff_flush_patch()
after calling run_diff() can unpopulate the data from the
filepair *p before returning without harming performance.

I think diff_flush_stat() and diff_flush_checkdiff() would have
the same issue, though.  Ideally these should be able to do
their processing while the main textual diff holds the data in
memory for its processing but that is currently not the way the
code is structured.

Re: git-diff opens too many files?

[Junio C Hamano]

Linus Torvalds <torvalds@osdl.org> writes:

> Junio? This is your speciality, I'm not sure how painful it would be to 
> unmap and remap on demand.. (or switch it to some kind of "keep the last 
> <n> mmaps active" kind of thing to avoid having thousands and thousands of 
> mmaps active).
>
> One simple thing that might be worth it is to simply _not_ use mmap() at 
> all for small files. If a file is less than 1kB, it might be better to do 
> a malloc() and a read() - partly because it avoids having tons of file 
> descriptors, but partly because it's also more efficient from a virtual 
> memory usage perspective (not that you're probably very likely to ever 
> really hit that problem in practice).
>
> Nguyen - that "use malloc+read" thing might be a quick workaround, but 
> only if you have tons of _small_ files (and if you can't easily just 
> increase file-max). 

So here is a lunch-time hack to get Nguyen unstuck.

-- >8 --
[PATCH] diff.c: avoid mmap() of small files in populate_filespec()

This would hopefully behave better in VM usage.  It is not a
real fix if you are dealing with truly huge diff, in which case
we would have to LRU out the data in memory for filespecs that
are not used in immediate future.

Signed-off-by: Junio C Hamano <junkio@cox.net>
---
diff --git a/diff.c b/diff.c
index 3315378..af50b6f 100644
--- a/diff.c
+++ b/diff.c
@@ -1294,11 +1294,22 @@ int diff_populate_filespec(struct diff_f
 		fd = open(s->path, O_RDONLY);
 		if (fd < 0)
 			goto err_empty;
-		s->data = mmap(NULL, s->size, PROT_READ, MAP_PRIVATE, fd, 0);
+		if (s->size < MINIMUM_MMAP) {
+			s->data = xmalloc(s->size);
+			s->should_free = 1;
+			if (xread(fd, s->data, s->size) != s->size) {
+				free(s->data);
+				goto err_empty;
+			}
+		}
+		else {
+			s->data = mmap(NULL, s->size, PROT_READ, MAP_PRIVATE,
+				       fd, 0);
+			s->should_munmap = 1;
+		}
 		close(fd);
 		if (s->data == MAP_FAILED)
 			goto err_empty;
-		s->should_munmap = 1;
 	}
 	else {
 		char type[20];
diff --git a/diffcore.h b/diffcore.h
index 2249bc2..f129aa0 100644
--- a/diffcore.h
+++ b/diffcore.h
@@ -21,6 +21,7 @@
 #define DEFAULT_MERGE_SCORE  36000 /* maximum for break-merge to happen 60%) */
 
 #define MINIMUM_BREAK_SIZE     400 /* do not break a file smaller than this */
+#define MINIMUM_MMAP	      4096 /* do not mmap a file smaller than this */
 
 struct diff_filespec {
 	unsigned char sha1[20];