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From Ariel Weisberg <ar...@weisberg.ws>
Subject Re: JVM safepoints, mmap, and slow disks
Date Sat, 08 Oct 2016 18:09:50 GMT
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[1] - 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[2] - 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:PrintSafepointStatisticsCount=1
>>>> [2] https://github.com/brendangregg/perf-tools/blob/master/iosnoop
>>


Links:

  1. https://winguzone.com?from=list
  2. https://winguzone.com?from=list

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