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From Benedict Elliott Smith <bened...@apache.org>
Subject Re: JVM safepoints, mmap, and slow disks
Date Sun, 09 Oct 2016 21:07:53 GMT
Well, you seem to be assuming:

1) read ahead is done unconditionally, with an equal claim to disk resources
2) read ahead is actually enabled (tuning recommendations are that it be
disabled, or at least drastically reduced, to my knowledge)
3) read ahead happens synchronously (even if you burn some bandwidth, not
waiting the increased latency for all blocks means a faster turn around to
client)

Ignoring all of this, 64kb is 1/3 default read ahead in Linux, so you're
talking a ~50% increase, which is not an amount I would readily dismiss.

On Sunday, 9 October 2016, Ariel Weisberg <ariel@weisberg.ws> wrote:

> Hi,
>
> Even with memory mapped IO the kernel is going to do read ahead. It seems
> like if the issue is reading to much from the device it isn't going to help
> to use memory mapped files or smaller buffered reads. Maybe helps by some
> percentage, but it's still going to read quite a bit extra.
>
> Ariel
>
> On Sun, Oct 9, 2016, at 05:39 AM, Benedict Elliott Smith wrote:
>
> The biggest problem with pread was the issue of over reading (reading 64k
> where 4k would suffice), which was significantly improved in 2.2 iirc. I
> don't think the penalty is very significant anymore, and if you are
> experiencing time to safe point issues it's very likely a worthwhile
> switch to flip.
>
> On Sunday, 9 October 2016, Graham Sanderson <graham@vast.com
> <javascript:_e(%7B%7D,'cvml','graham@vast.com');>> wrote:
>
> I was using the term “touch” loosely to hopefully mean pre-fetch, though I
> suspect (I think intel has been de-emphasizing) you can still do a sensible
> prefetch instruction in native code. Even if not you are still better
> blocking in JNI code - I haven’t looked at the link to see if the correct
> barriers are enforced by the sun-misc-unsafe method.
>
> I do suspect that you’ll see up to about 5-10% sys call overhead if you
> hit pread.
>
> > On Oct 8, 2016, at 11:02 PM, Ariel Weisberg <ariel@weisberg.ws> wrote:
> >
> > Hi,
> >
> > This is starting to get into dev list territory.
> >
> > Interesting idea to touch every 4K page you are going to read.
> >
> > You could use this to minimize the cost.
> > http://stackoverflow.com/questions/36298111/is-it-possible-
> to-use-sun-misc-unsafe-to-call-c-functions-without-jni/36309652#36309652
> >
> > Maybe faster than doing buffered IO. It's a lot of cache and TLB misses
> > with out prefetching though.
> >
> > There is a system call to page the memory in which might be better for
> > larger reads. Still no guarantee things stay cached though.
> >
> > Ariel
> >
> >
> > On Sat, Oct 8, 2016, at 08:21 PM, Graham Sanderson wrote:
> >> I haven’t studied the read path that carefully, but there might be a
> spot at the C* level rather than JVM level where you could effectively do a
> JNI touch of the mmap region you’re going to need next.
> >>
> >>> On Oct 8, 2016, at 7:17 PM, Graham Sanderson <graham@vast.com> wrote:
> >>>
> >>> We don’t use Azul’s Zing, but it does have the nice feature that all
> threads don’t have to reach safepoints at the same time. That said we make
> heavy use of Cassandra (with off heap memtables - not directly related but
> allows us a lot more GC headroom) and SOLR where we switched to mmap
> because it FAR out performed pread variants - in no cases have we noticed
> long time to safe point (then again our IO is lightning fast).
> >>>
> >>>> On Oct 8, 2016, at 1:20 PM, Jonathan Haddad <jon@jonhaddad.com>
> wrote:
> >>>>
> >>>> Linux automatically uses free memory as cache.  It's not swap.
> >>>>
> >>>> http://www.tldp.org/LDP/lki/lki-4.html
> >>>>
> >>>> On Sat, Oct 8, 2016 at 11:12 AM Vladimir Yudovin <
> vladyu@winguzone.com> wrote:
> >>>>> __
> >>>>> Sorry, I don't catch something. What page (memory) cache can exist
> if there is no swap file.
> >>>>> Where are those page written/read?
> >>>>>
> >>>>>
> >>>>> Best regards, Vladimir Yudovin,
> >>>>> *Winguzone[https://winguzone.com/?from=list] - Hosted Cloud
> Cassandra on Azure and SoftLayer.
> >>>>> Launch your cluster in minutes.
> > *
> >>>>>
> >>>>> ---- On Sat, 08 Oct 2016 14:09:50 -0400 *Ariel Weisberg<
> ariel@weisberg.ws>* wrote ----
> >>>>>> Hi,
> >>>>>>
> >>>>>> Nope I mean page cache. Linux doesn't call the cache it maintains
> using free memory a file cache. It uses free (and some of the time not so
> free!) memory to buffer writes and to cache recently written/read data.
> >>>>>>
> >>>>>> http://www.tldp.org/LDP/lki/lki-4.html
> >>>>>>
> >>>>>> When Linux decides it needs free memory it can either evict
stuff
> from the page cache, flush dirty pages and then evict, or swap anonymous
> memory out. When you disable swap you only disable the last behavior.
> >>>>>>
> >>>>>> Maybe we are talking at cross purposes? What I meant is that
> increasing the heap size to reduce GC frequency is a legitimate thing to do
> and it does have an impact on the performance of the page cache even if you
> have swap disabled?
> >>>>>>
> >>>>>> Ariel
> >>>>>>
> >>>>>>
> >>>>>> On Sat, Oct 8, 2016, at 01:54 PM, Vladimir Yudovin wrote:
> >>>>>>>> Page cache is data pending flush to disk and data cached
from
> disk.
> >>>>>>>
> >>>>>>> Do you mean file cache?
> >>>>>>>
> >>>>>>>
> >>>>>>> Best regards, Vladimir Yudovin,
> >>>>>>> *Winguzone[https://winguzone.com/?from=list] - Hosted Cloud
> Cassandra on Azure and SoftLayer.
> >>>>>>> Launch your cluster in minutes.*
> >>>>>>>
> >>>>>>>
> >>>>>>> ---- On Sat, 08 Oct 2016 13:40:19 -0400 *Ariel Weisberg
<
> ariel@weisberg.ws>* wrote ----
> >>>>>>>> Hi,
> >>>>>>>>
> >>>>>>>> Page cache is in use even if you disable swap. Swap
is anonymous
> memory, and whatever else the Linux kernel supports paging out. Page cache
> is data pending flush to disk and data cached from disk.
> >>>>>>>>
> >>>>>>>> Given how bad the GC pauses are in C* I think it's not
the high
> pole in the tent. Until key things are off heap and C* can run with CMS and
> get 10 millisecond GCs all day long.
> >>>>>>>>
> >>>>>>>> You can go through tuning and hardware selection try
to get more
> consistent IO pauses and remove outliers as you mention and as a user I
> think this is your best bet. Generally it's either bad device or filesystem
> behavior if you get page faults taking more than 200 milliseconds O(G1 gc
> collection).
> >>>>>>>>
> >>>>>>>> I think a JVM change to allow safe points around memory
mapped
> file access is really unlikely although I agree it would be great. I think
> the best hack around it is to code up your memory mapped file access into
> JNI methods and find some way to get that to work. Right now if you want to
> create a safe point a JNI method is the way to do it. The problem is that
> JNI methods and POJOs don't get along well.
> >>>>>>>>
> >>>>>>>> If you think about it the reason non-memory mapped IO
works well
> is that it's all JNI methods so they don't impact time to safe point. I
> think there is a tradeoff between tolerance for outliers and performance.
> >>>>>>>>
> >>>>>>>> I don't know the state of the non-memory mapped path
and how
> reliable that is. If it were reliable and I couldn't tolerate the outliers
> I would use that. I have to ask though, why are you not able to tolerate
> the outliers? If you are reading and writing at quorum how is this
> impacting you?
> >>>>>>>>
> >>>>>>>> Regards,
> >>>>>>>> Ariel
> >>>>>>>>
> >>>>>>>> On Sat, Oct 8, 2016, at 12:54 AM, Vladimir Yudovin wrote:
> >>>>>>>>> Hi Josh,
> >>>>>>>>>
> >>>>>>>>>> Running with increased heap size would reduce
GC frequency, at
> the cost of page cache.
> >>>>>>>>>
> >>>>>>>>> Actually  it's recommended to run C* without virtual
memory
> enabled. So if there  is no enough memory JVM fails instead of blocking
> >>>>>>>>>
> >>>>>>>>> Best regards, Vladimir Yudovin,
> >>>>>>>>> *Winguzone[https://winguzone.com/?from=list] - Hosted
Cloud
> Cassandra on Azure and SoftLayer.
> >>>>>>>>> Launch your cluster in minutes.*
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> ---- On Fri, 07 Oct 2016 21:06:24 -0400 *Josh Snyder<
> josh@code406.com>* wrote ----
> >>>>>>>>>> Hello cassandra-users,
> >>>>>>>>>>
> >>>>>>>>>> I'm investigating an issue with JVMs taking
a while to reach a
> safepoint.  I'd
> >>>>>>>>>> like the list's input on confirming my hypothesis
and finding
> mitigations.
> >>>>>>>>>>
> >>>>>>>>>> My hypothesis is that slow block devices are
causing
> Cassandra's JVM to pause
> >>>>>>>>>> completely while attempting to reach a safepoint.
> >>>>>>>>>>
> >>>>>>>>>> Background:
> >>>>>>>>>>
> >>>>>>>>>> Hotspot occasionally performs maintenance tasks
that
> necessitate stopping all
> >>>>>>>>>> of its threads. Threads running JITed code occasionally
read
> from a given
> >>>>>>>>>> safepoint page. If Hotspot has initiated a safepoint,
reading
> from that page
> >>>>>>>>>> essentially catapults the thread into purgatory
until the
> safepoint completes
> >>>>>>>>>> (the mechanism behind this is pretty cool).
Threads performing
> syscalls or
> >>>>>>>>>> executing native code do this check upon their
return into the
> JVM.
> >>>>>>>>>>
> >>>>>>>>>> In this way, during the safepoint Hotspot can
be sure that all
> of its threads
> >>>>>>>>>> are either patiently waiting for safepoint completion
or in a
> system call.
> >>>>>>>>>>
> >>>>>>>>>> Cassandra makes heavy use of mmapped reads in
normal operation.
> When doing
> >>>>>>>>>> mmapped reads, the JVM executes userspace code
to effect a read
> from a file. On
> >>>>>>>>>> the fast path (when the page needed is already
mapped into the
> process), this
> >>>>>>>>>> instruction is very fast. When the page is not
cached, the CPU
> triggers a page
> >>>>>>>>>> fault and asks the OS to go fetch the page.
The JVM doesn't
> even realize that
> >>>>>>>>>> anything interesting is happening: to it, the
thread is just
> executing a mov
> >>>>>>>>>> instruction that happens to take a while.
> >>>>>>>>>>
> >>>>>>>>>> The OS, meanwhile, puts the thread in question
in the D state
> (assuming Linux,
> >>>>>>>>>> here) and goes off to find the desired page.
This may take
> microseconds, this
> >>>>>>>>>> may take milliseconds, or it may take seconds
(or longer). When
> I/O occurs
> >>>>>>>>>> while the JVM is trying to enter a safepoint,
every thread has
> to wait for the
> >>>>>>>>>> laggard I/O to complete.
> >>>>>>>>>>
> >>>>>>>>>> If you log safepoints with the right options
[1], you can see
> these occurrences
> >>>>>>>>>> in the JVM output:
> >>>>>>>>>>
> >>>>>>>>>>> # SafepointSynchronize::begin: Timeout detected:
> >>>>>>>>>>> # SafepointSynchronize::begin: Timed out
while spinning to
> reach a safepoint.
> >>>>>>>>>>> # SafepointSynchronize::begin: Threads which
did not reach the
> safepoint:
> >>>>>>>>>>> # "SharedPool-Worker-5" #468 daemon prio=5
os_prio=0
> tid=0x00007f8785bb1f30 nid=0x4e14 runnable [0x0000000000000000]
> >>>>>>>>>>>   java.lang.Thread.State: RUNNABLE
> >>>>>>>>>>>
> >>>>>>>>>>> # SafepointSynchronize::begin: (End of list)
> >>>>>>>>>>>         vmop                    [threads:
total
> initially_running wait_to_block]    [time: spin block sync cleanup vmop]
> page_trap_count
> >>>>>>>>>>> 58099.941: G1IncCollectionPause        
    [     447
> 1              1    ]      [  3304     0  3305     1   190    ]  1
> >>>>>>>>>>
> >>>>>>>>>> If that safepoint happens to be a garbage collection
(which
> this one was), you
> >>>>>>>>>> can also see it in GC logs:
> >>>>>>>>>>
> >>>>>>>>>>> 2016-10-07T13:19:50.029+0000: 58103.440:
Total time for which
> application threads were stopped: 3.4971808 seconds, Stopping threads took:
> 3.3050644 seconds
> >>>>>>>>>>
> >>>>>>>>>> In this way, JVM safepoints become a powerful
weapon for
> transmuting a single
> >>>>>>>>>> thread's slow I/O into the entire JVM's lockup.
> >>>>>>>>>>
> >>>>>>>>>> Does all of the above sound correct?
> >>>>>>>>>>
> >>>>>>>>>> Mitigations:
> >>>>>>>>>>
> >>>>>>>>>> 1) don't tolerate block devices that are slow
> >>>>>>>>>>
> >>>>>>>>>> This is easy in theory, and only somewhat difficult
in
> practice. Tools like
> >>>>>>>>>> perf and iosnoop [2] can do pretty good jobs
of letting you
> know when a block
> >>>>>>>>>> device is slow.
> >>>>>>>>>>
> >>>>>>>>>> It is sad, though, because this makes running
Cassandra on
> mixed hardware (e.g.
> >>>>>>>>>> fast SSD and slow disks in a JBOD) quite unappetizing.
> >>>>>>>>>>
> >>>>>>>>>> 2) have fewer safepoints
> >>>>>>>>>>
> >>>>>>>>>> Two of the biggest sources of safepoints are
garbage collection
> and revocation
> >>>>>>>>>> of biased locks. Evidence points toward biased
locking being
> unhelpful for
> >>>>>>>>>> Cassandra's purposes, so turning it off (-XX:-UseBiasedLocking)
> is a quick way
> >>>>>>>>>> to eliminate one source of safepoints.
> >>>>>>>>>>
> >>>>>>>>>> Garbage collection, on the other hand, is unavoidable.
Running
> with increased
> >>>>>>>>>> heap size would reduce GC frequency, at the
cost of page cache.
> But sacrificing
> >>>>>>>>>> page cache would increase page fault frequency,
which is
> another thing we're
> >>>>>>>>>> trying to avoid! I don't view this as a serious
option.
> >>>>>>>>>>
> >>>>>>>>>> 3) use a different IO strategy
> >>>>>>>>>>
> >>>>>>>>>> Looking at the Cassandra source code, there
appears to be an
> un(der)documented
> >>>>>>>>>> configuration parameter called disk_access_mode.
It appears
> that changing this
> >>>>>>>>>> to 'standard' would switch to using pread()
and pwrite() for
> I/O, instead of
> >>>>>>>>>> mmap. I imagine there would be a throughput
penalty here for
> the case when
> >>>>>>>>>> pages are in the disk cache.
> >>>>>>>>>>
> >>>>>>>>>> Is this a serious option? It seems far too underdocumented
to
> be thought of as
> >>>>>>>>>> a contender.
> >>>>>>>>>>
> >>>>>>>>>> 4) modify the JVM
> >>>>>>>>>>
> >>>>>>>>>> This is a longer term option. For the purposes
of safepoints,
> perhaps the JVM
> >>>>>>>>>> could treat reads from an mmapped file in the
same way it
> treats threads that
> >>>>>>>>>> are running JNI code. That is, the safepoint
will proceed even
> though the
> >>>>>>>>>> reading thread has not "joined in". Upon finishing
its mmapped
> read, the
> >>>>>>>>>> reading thread would test the safepoint page
(check whether a
> safepoint is in
> >>>>>>>>>> progress, in other words).
> >>>>>>>>>>
> >>>>>>>>>> Conclusion:
> >>>>>>>>>>
> >>>>>>>>>> I don't imagine there's an easy solution here.
I plan to go
> ahead with
> >>>>>>>>>> mitigation #1: "don't tolerate block devices
that are slow",
> but I'd appreciate
> >>>>>>>>>> any approach that doesn't require my hardware
to be flawless
> all the time.
> >>>>>>>>>>
> >>>>>>>>>> Josh
> >>>>>>>>>>
> >>>>>>>>>> [1] -XX:+SafepointTimeout -XX:SafepointTimeoutDelay=100
> >>>>>>>>>> -XX:+PrintSafepointStatistics -XX:PrintSafepointStatisticsCo
> unt=1
> >>>>>>>>>> [2] https://github.com/brendangregg/perf-tools/blob/master/
> iosnoop
> >>>>>>>>
> >>>>>>
> >> Email had 1 attachment:
> >
> >
> >> * smime.p7s
> >>   2k (application/pkcs7-signature)
>
>
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