Hi, > That StackOverflow headline is interesting. Based on my reading of > Hotspot's > code, it looks like sun.misc.unsafe is used under the hood to > perform mmapped > I/O. I need to learn more about Hotspot's implementation before I can > comment > further. A memory mapped file is "just" memory so it's accessed using a ByteBuffer pointing to off heap memory. Works the same as if you had mapped in some anonymous memory.
> Not sure what you mean here. Aren't there going to be cache and TLB > misses for any I/O, whether via mmap or syscall? > The beauty of memory mapped files can be that if the data is already in the page cache it's just a regular read of memory. If you touch each page and it's all in memory it's going to be a slower operation that blocks the CPU as it has to synchronously load each cache line. It's possible you might be able to touch multiple pages in parallel if you are clever. So if the data is the page cache and you just access it regularly (sequentially) you get all the benefits of the prefetcher. If you go and touch every page first you will not have the latency of prefetching hidden from you. > There is a system call to page the memory in which might be better for > larger reads. Still no guarantee things stay cached though. When you fault a page the kernel has no idea how much you are going to read. If there is a mismatch then you may end up going back and forth to the device several times and for spinning disk this is worse. If you express up front what you want to read either by fadvise/madvise or a buffered read it can do something "smart". Granted IO scheduling ranges from middling to non-existent most of the time, and the fadvise/madvise stuff for this has holes I can't recall right now. Ariel On Mon, Oct 10, 2016, at 02:19 PM, Josh Snyder wrote: > On Sat, Oct 8, 2016 at 9:02 PM, Ariel Weisberg > <ar...@weisberg.ws> wrote: > ... > > > 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 > > That StackOverflow headline is interesting. Based on my reading of > Hotspot's > code, it looks like sun.misc.unsafe is used under the hood to perform > mmapped > I/O. I need to learn more about Hotspot's implementation before I can > comment > further. > > > Maybe faster than doing buffered IO. It's a lot of cache and TLB > > misses > > with out prefetching though. > > Not sure what you mean here. Aren't there going to be cache and TLB > misses for > any I/O, whether via mmap or syscall? > > > There is a system call to page the memory in which might be > > better for > > larger reads. Still no guarantee things stay cached though. > > The approaches I've seen just involve something in userspace going > through and > touching every desired page. It works, especially if you touch > pages in > parallel. > > Thanks for the pointers. If I get anywhere with them, I'll be sure to > let you know. > > Josh > > > 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 <gra...@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 <j...@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 > >>>> <vla...@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<ar...@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 > >>>>>>> <ar...@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<j...@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 > >>>>>>>> > >>>>>> > >> Email had 1 attachment: > > > > > >> * smime.p7s > >> 2k (application/pkcs7-signature)
