Performance degradation over time

Performance degradation over time

[Marcin Deranek]

Hi,

We are running XFS filesystem on one of out machines which is a big
store (~3TB) of different data files (mostly images). Quite recently we
experienced some performance problems - machine wasn't able to keep up
with updates. After some investigation it turned out that open()
syscalls (open for writing) were taking significantly more time than
they should eg. 15-20ms vs 100-150us.
Some more info about our workload as I think it's important here:
our XFS filesystem is exclusively used as data store, so we only
read and write our data (we mostly write). When new update comes it's
written to a temporary file eg.

/mountpoint/some/path/.tmp/file

When file is completely stored we move it to final location eg.

/mountpoint/some/path/different/subdir/newname

That means that we create lots of files in /mountpoint/some/path/.tmp
directory, but directory is empty as they are moved (rename() syscall)
shortly after file creation to a different directory on the same
filesystem.
The workaround which I found so far is to remove that directory
(/mountpoint/some/path/.tmp in our case) with its content and re-create
it. After this operation open() syscall goes down to 100-150us again.
Is this a known problem ?
Information regarding our system:
CentOS 5.8 / kernel 2.6.18-308.el5 / kmod-xfs-0.4-2
Let me know if you need to know anything more.
Cheers,

Marcin

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Re: Performance degradation over time

[Stan Hoeppner]

On 10/10/2012 3:51 AM, Marcin Deranek wrote:
> Hi,
> 
> We are running XFS filesystem on one of out machines which is a big
> store (~3TB) of different data files (mostly images). Quite recently we
> experienced some performance problems - machine wasn't able to keep up
> with updates. After some investigation it turned out that open()
> syscalls (open for writing) were taking significantly more time than
> they should eg. 15-20ms vs 100-150us.
> Some more info about our workload as I think it's important here:
> our XFS filesystem is exclusively used as data store, so we only
> read and write our data (we mostly write). When new update comes it's
> written to a temporary file eg.
> 
> /mountpoint/some/path/.tmp/file
> 
> When file is completely stored we move it to final location eg.
> 
> /mountpoint/some/path/different/subdir/newname
> 
> That means that we create lots of files in /mountpoint/some/path/.tmp
> directory, but directory is empty as they are moved (rename() syscall)
> shortly after file creation to a different directory on the same
> filesystem.
> The workaround which I found so far is to remove that directory
> (/mountpoint/some/path/.tmp in our case) with its content and re-create
> it. After this operation open() syscall goes down to 100-150us again.
> Is this a known problem ?
> Information regarding our system:
> CentOS 5.8 / kernel 2.6.18-308.el5 / kmod-xfs-0.4-2
> Let me know if you need to know anything more.

Hi Marcin,

I'll begin where you ended:  kmod-xfs.  DO NOT USE THAT.  Use the kernel
driver.  Eric Sandeen can point you to the why.  AIUI that XFS module
hasn't been supported for many many years.

Regarding your problem, I can't state some of the following with
authority, though it might read that way.  I'm making an educated guess
based on what I do know of XFS and the behavior you're seeing.  Dave
will clobber and correct me if I'm wrong here. ;)

XFS filesystems are divided into multiple equal sized allocation groups
on the underlying storage device (single disk, RAID, LVM volume, etc).
With inode32 each directory that is created has its files store in only
one AG, with some exceptions, which you appear to bumping up against.
If you're using inode64 the directories, along with their files, go into
the AGs round robin.

Educated guessing:  When you use rename(2) to move the files, the file
contents are not being moved, only the directory entry, as with EXTx
etc.  Thus the file data is still in the ".tmp" directory AG, but that
AG is no longer its home.  Once this temp dir AG gets full of these
"phantom" file contents (you can only see them with XFS tools), the AG
spills over.  At that point XFS starts moving the phantom contents of
the rename(2) files into the AG which owns the directory of the
rename(2) target.  I believe this is the source of your additional
latency.  Each time you do an open(2) call to write a new file, XFS is
moving a file's contents (extents) to its new/correct parent AG, causing
much additional IO, especially if these are large files.

As you are witnessing, if XFS did the move to the new AG in real time,
the performance of rename(2) would be horrible on the front end.  I'd
guess the developers never imagined that a user would fill an entire AG
using rename(2) calls.  Your deleting and recreating of the .tmp
directory which fixes the performance seems to be evidence of this.
Each time you delete/create that directory it is put into a different AG
in the filesystem, in a round robin fashion.  If you do this enough
times, you should eventually create the directory in the original AG
that's full of the rename(2) file extents, and performance will suffer
again.

One of the devs probably has some tricks/tools up his sleeve to force
those extents to their new parent AG.  You might be able to run a
nightly script to do this housekeeping.  Or you could always put the
.tmp directory on a different filesystem on a scratch disk.

This problem could also be a free space fragmentation issue, but given
that recreating the .tmp directory fixes it, I doubt free space frag is
the problem.

-- 
Stan

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Re: Performance degradation over time

[Eric Sandeen]

On 10/10/12 8:17 AM, Stan Hoeppner wrote:
> On 10/10/2012 3:51 AM, Marcin Deranek wrote:
>> Hi,
>>
>> We are running XFS filesystem on one of out machines which is a big
>> store (~3TB) of different data files (mostly images). Quite recently we
>> experienced some performance problems - machine wasn't able to keep up
>> with updates. After some investigation it turned out that open()
>> syscalls (open for writing) were taking significantly more time than
>> they should eg. 15-20ms vs 100-150us.
>> Some more info about our workload as I think it's important here:
>> our XFS filesystem is exclusively used as data store, so we only
>> read and write our data (we mostly write). When new update comes it's
>> written to a temporary file eg.
>>
>> /mountpoint/some/path/.tmp/file
>>
>> When file is completely stored we move it to final location eg.
>>
>> /mountpoint/some/path/different/subdir/newname
>>
>> That means that we create lots of files in /mountpoint/some/path/.tmp
>> directory, but directory is empty as they are moved (rename() syscall)
>> shortly after file creation to a different directory on the same
>> filesystem.
>> The workaround which I found so far is to remove that directory
>> (/mountpoint/some/path/.tmp in our case) with its content and re-create
>> it. After this operation open() syscall goes down to 100-150us again.
>> Is this a known problem ?
>> Information regarding our system:
>> CentOS 5.8 / kernel 2.6.18-308.el5 / kmod-xfs-0.4-2
>> Let me know if you need to know anything more.
> 
> Hi Marcin,
> 
> I'll begin where you ended:  kmod-xfs.  DO NOT USE THAT.  Use the kernel
> driver.  Eric Sandeen can point you to the why.  AIUI that XFS module
> hasn't been supported for many many years.

Yep.  Ditch that; it overrides the maintained module that comes with the
kernel itself.  See if that helps, first, I suppose.

I've been asking Centos for a while to find some way to deprecate that,
but it's like night of the living dead xfs modules.

(modinfo xfs will tell you for sure which xfs.ko is getting loaded I suppose).

> Regarding your problem, I can't state some of the following with
> authority, though it might read that way.  I'm making an educated guess
> based on what I do know of XFS and the behavior you're seeing.  Dave
> will clobber and correct me if I'm wrong here. ;)
> 
> XFS filesystems are divided into multiple equal sized allocation groups
> on the underlying storage device (single disk, RAID, LVM volume, etc).
> With inode32 each directory that is created has its files store in only
> one AG, with some exceptions, which you appear to bumping up against.
> If you're using inode64 the directories, along with their files, go into
> the AGs round robin.

Agreed that it would be good to know whether inode64 is in use.

Let's start there (and with a modern xfs.ko) before we speculate further.

> Educated guessing:  When you use rename(2) to move the files, the file
> contents are not being moved, only the directory entry, as with EXTx
> etc.  Thus the file data is still in the ".tmp" directory AG, but that
> AG is no longer its home.  Once this temp dir AG gets full of these
> "phantom" file contents (you can only see them with XFS tools), the AG
> spills over.  At that point XFS starts moving the phantom contents of
> the rename(2) files into the AG which owns the directory of the
> rename(2) target.  I believe this is the source of your additional
> latency.  Each time you do an open(2) call to write a new file, XFS is
> moving a file's contents (extents) to its new/correct parent AG, causing
> much additional IO, especially if these are large files.

Nope, don't think so ;) Nothing is going to be moving file contents
behind your back on a rename.

<snip>

-Eric

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Re: Performance degradation over time

[Marcin Deranek]

Hi Eric,

On Wed, 10 Oct 2012 09:31:16 -0500
Eric Sandeen <sandeen@sandeen.net> wrote:

> Yep.  Ditch that; it overrides the maintained module that comes with
> the kernel itself.  See if that helps, first, I suppose.

I wasn't aware that stock kernel comes with xfs module. From my testing
looks like stock kernel module is still preferred over kmod-xfs:

# modinfo xfs
filename:       /lib/modules/2.6.18-308.el5/kernel/fs/xfs/xfs.ko
license:        GPL
description:    SGI XFS with ACLs, security attributes, large block/inode numbers, no debug enabled
author:         Silicon Graphics, Inc.
srcversion:     D37A003AFEE1A42BDD4DD56
depends:        
vermagic:       2.6.18-308.el5 SMP mod_unload gcc-4.1
module_sig:
883f3504f44471c48d0a1fbae482c4c11225a009e3fa1179850eea96ab882c910d750e88743fec5309d1ca09de3d81add6999f9dedc65f84a0d1e21293

Most likely due to historical reasons we still install kmod-xfs on our 
systems.
To be sure I have removed kmod-xfs, unmounted filesystem and removed
kernel module and them mounted filesystem again. Still seeing the very same
behaviour.

> Agreed that it would be good to know whether inode64 is in use.

No, we don't use any special mount options here.

> Let's start there (and with a modern xfs.ko) before we speculate
> further.

I guess next step would be to use inode64..
Regards,

Marcin

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Re: Performance degradation over time

[Marcin Deranek]

On Thu, 11 Oct 2012 10:33:52 +0200
Marcin Deranek <marcin.deranek@booking.com> wrote:

> I guess next step would be to use inode64..

After mounting XFS with inode64 I see performance improvement (open()
now takes ~3ms vs ~15ms previous) although it's still not something I
would expect (~150us.) On Dave's suggestion I will give a shot CentOS
6.x and see if that makes any difference although this needs to be
monitored over longer period of time to reliably tell if that make a
difference.
Regards,

Marcin

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Re: Performance degradation over time

[Peter Grandi]

>>> [ ... ] open() syscalls (open for writing) were taking
>>> significantly more time than they should eg. 15-20ms vs
>>> 100-150us. [ ... ] That means that we create lots of files in
>>> /mountpoint/some/path/.tmp directory, but directory is empty
>>> as they are moved (rename() syscall) shortly after file
>>> creation to a different directory on the same filesystem.

>>> The workaround which I found so far is to remove that
>>> directory (/mountpoint/some/path/.tmp in our case) with its
>>> content and re-create it. After this operation open() syscall
>>> goes down to 100-150us again.

>>> Is this a known problem ?

Indeed, two known (for several decades) problems: using
filesystems as DBMSes and directories as spool queues.

[ ... ]

> After mounting XFS with inode64 I see performance improvement
> (open() now takes ~3ms vs ~15ms previous) although it's still
> not something I would expect (~150us.)

It would be amusing to know why ever to expect a random metadata
access operation to take 150µs on *average* on a storage system
that seems to have rotating disk with 10-15ms *average* access
time.

The metadata operations may have locality, but unsurprisingly
that decreases with time...

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Re: Performance degradation over time

[Dave Chinner]

On Wed, Oct 10, 2012 at 10:51:42AM +0200, Marcin Deranek wrote:
> Hi,
> 
> We are running XFS filesystem on one of out machines which is a big
> store (~3TB) of different data files (mostly images). Quite recently we
> experienced some performance problems - machine wasn't able to keep up
> with updates. After some investigation it turned out that open()
> syscalls (open for writing) were taking significantly more time than
> they should eg. 15-20ms vs 100-150us.

Which is clearly an IO latency vs cache hit latency.

> Some more info about our workload as I think it's important here:
> our XFS filesystem is exclusively used as data store, so we only
> read and write our data (we mostly write). When new update comes it's
> written to a temporary file eg.
> 
> /mountpoint/some/path/.tmp/file
> 
> When file is completely stored we move it to final location eg.
> 
> /mountpoint/some/path/different/subdir/newname
> 
> That means that we create lots of files in /mountpoint/some/path/.tmp
> directory, but directory is empty as they are moved (rename() syscall)
> shortly after file creation to a different directory on the same
> filesystem.
> The workaround which I found so far is to remove that directory
> (/mountpoint/some/path/.tmp in our case) with its content and re-create
> it. After this operation open() syscall goes down to 100-150us again.
> Is this a known problem ?

By emptying the directory, you are making it smaller and likely
causing it to be cached in memory again as new files are added to
it. Over time, blocks will be removed from the cache due to memory
pressure, and latencies will be seen again.

> Information regarding our system:
> CentOS 5.8 / kernel 2.6.18-308.el5 / kmod-xfs-0.4-2

Use a more recent distro. I reworked the metadata caching algorithms
a couple of years ago to avoid these sorts of problems with memory
reclaim.

Cheers,

Dave.
-- 
Dave Chinner
david@fromorbit.com

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Re: Performance degradation over time

[Marcin Deranek]

On Thu, 11 Oct 2012 10:37:04 +1100
Dave Chinner <david@fromorbit.com> wrote:

> Use a more recent distro. I reworked the metadata caching algorithms
> a couple of years ago to avoid these sorts of problems with memory
> reclaim.

I can give a shot CentOS 6.x although that might take some time..

Marcin

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