Update fileset index format to sorted string order with summaries and bloom filter #395

robskillington · 2017-11-10T04:18:48Z

This is the beginning of a set of changes to move to remove all block references from memory except those that are being written to and those that have been loaded in recently as cached blocks due to reads.

This will write out the new file format and support reading it.

For now the seeker still loads the ID and offsets into memory, the next change will update it to load the summaries file and resolve IDs by reading the index entries on disk after searching the summaries for a jumping off point.

coveralls · 2017-11-10T05:23:53Z

Coverage decreased (-0.5%) to 77.591% when pulling 1c0864efbb7a757e1492ecff28cf51488934e160 on r/sorted-string-index-with-summaries-with-bloom-filter into c6b20ed on master.

coveralls · 2017-11-10T05:23:53Z

Coverage decreased (-0.5%) to 77.532% when pulling 1c0864efbb7a757e1492ecff28cf51488934e160 on r/sorted-string-index-with-summaries-with-bloom-filter into c6b20ed on master.

richardartoul · 2017-11-10T15:24:39Z

persist/encoding/decoder.go

@@ -42,3 +51,110 @@ type Decoder interface {
 	// DecodeLogEntry decodes commit log entry
 	DecodeLogEntry() (schema.LogEntry, error)
 }
+
+// DecoderStream is a data stream that is read by the decoder,


This comment is a little confusing. The comment seems like its saying that this interface is meant to be composable with other Reader interface, and I expected the constructor for DecoderStream to look like:

NewDecoderStream(b []byte, r io.Reader) DecoderStream {}

but instead it only accepts []byte, and the type of the internal reader is *bytes.Reader which is not an interface.

How would you use this interface with a ReaderWithDigest interface?

NewDecoderStream(...) in this package is just a default offering for users to use if they don't need to provide the reader themselves.

There is a private newDecoderStream(...) in the persist/fs package for that use case. This is so that users who don't need to and already have just a byte slice can still easily pass a buffer to decode into the msgpack decoder.

richardartoul · 2017-11-10T15:30:06Z

persist/encoding/msgpack/decoder.go

@@ -141,13 +153,45 @@ func (dec *decoder) decodeIndexInfo() schema.IndexInfo {
 	indexInfo.Start = dec.decodeVarint()
 	indexInfo.BlockSize = dec.decodeVarint()
 	indexInfo.Entries = dec.decodeVarint()
+	indexInfo.MajorVersion = dec.decodeVarint()
+	indexInfo.Summaries = dec.decodeIndexSummariesInfo()
+	indexInfo.BloomFilter = dec.decodeIndexBloomFilterInfo()


index files are per shard / block so we have a bloomfilter per shard/block right?

Correct yup.

richardartoul · 2017-11-10T15:41:08Z

persist/fs/commitlog/commit_log_test.go

@@ -372,9 +360,11 @@ func TestReadCommitLogMissingMetadata(t *testing.T) {
 	for i := 0; i < 200; i++ {
 		willNotHaveMetadata := !(i%2 == 0)
 		allSeries = append(allSeries, testSeries(uint64(i), "hax", uint32(i%100)))
-		mockBitSet.indexTestReturn[uint(i)] = willNotHaveMetadata
+		if willNotHaveMetadata {
+			bitSet.Set(uint(i))


good call, I probably should have realized this myself

richardartoul · 2017-11-10T15:42:08Z

persist/fs/commitlog/writer.go

@@ -90,7 +91,7 @@ type writer struct {
 	chunkReserveHeader []byte
 	buffer             *bufio.Writer
 	sizeBuffer         []byte
-	seen               bitSet
+	seen               *xsets.BitSet


were you worried about the performance impact of having an interface here, or it just wasn't necessary?

I was thinking that this might get moved to m3x at some point and if so to help avoid breaking changes when we add methods to things it might be worth keeping the pretty simple data structures that don't need to get mocked out as just structs.

So this choice was mainly for reducing cross repo breaking changes.

If it was a more complicated/logic based structured then we probably would've want to mock it.

richardartoul · 2017-11-10T15:50:00Z

persist/fs/mmap.go

+
+type mmapFileDesc struct {
+	// file is the *os.File ref to store
+	file **os.File


why is this a double ref?

This is so you can pass in the ptr you wish to have set.

richardartoul · 2017-11-10T15:50:29Z

persist/fs/mmap.go

+	// file is the *os.File ref to store
+	file **os.File
+	// bytes is the []byte slice ref to store the mmap'd address
+	bytes *[]byte


same here, confused why we're using a pointer to a "pointer type"

Yeah this is so that the API call to mmapFiles(...) can populate refs for you.

richardartoul · 2017-11-10T16:15:18Z

persist/fs/mmap_linux.go

-func (b *bitSetImpl) clearAll() {
-	for i := range b.values {
-		b.values[i] = 0
+	if err := syscall.Madvise(b, syscall.MADV_HUGEPAGE); err != nil {


A comment explaining this would be nice. I found these two links helpful personally:

http://man7.org/linux/man-pages/man2/madvise.2.html

https://www.kernel.org/doc/Documentation/vm/transhuge.txt

Seems like the gist of it is that you can reduce TLB misses by making the pages larger, at the risk of wasting a little extra memory. Is that basically it?

Also just out of curiosity, did this make a big difference in your benchmarks or is it just kind of a "best practices" thing?

Seems like the gist of it is that you can reduce TLB misses by making the pages larger, at the risk of wasting a little extra memory. Is that basically it?

That's it yeah. Also we're mmap'ing really large data files and in case of the index file might use the summary table to jump close to a record but still need to scan a reasonable way forward to find the exact entry, the amount of pages that need to cause a page fault will matter when we do these scans.

I can add a comment, sounds good.

richardartoul · 2017-11-10T17:58:40Z

persist/fs/options.go

@@ -30,6 +31,12 @@ import (
 )

 const (
+	// defaultIndexSummariesPercent is the default percent to save summaries for when writing summary files


This comment could be a little more clear: "defaultIndexSummariesPercent is the default percent of series for which an entry will be written into the metadata summary" or something like that. It took me awhile to figure out what this was until you explained it in person in the meeting

For sure, will update the comment. Thanks for the note.

richardartoul · 2017-11-10T18:16:56Z

persist/fs/write.go

@@ -54,25 +64,55 @@ type writer struct {
 	err        error
 }

+type indexEntry struct {


Is there any benefit in optimizing the size of this struct?

From what I can tell, offsetForSummary never stores a value that is different than offset, so you could probably replace it with a bool. That doesn't actually change the size of the struct, but if you then replace size (or offset but size seems safer) with uint32 and re-order the fields, you can save 8 bytes per struct making it 40 bytes instead of 48 (if this is meaningful at all):

https://play.golang.org/p/dXGawT5YxL

Might be premature, I don't know how hot this is

Although it might make your sort faster too just by virtue of being able to fit more of them in the cache lines

The two offset values are actually different. One is the offset into the data file, the offsetForSummary is the offset of this record in the index file that the summary entry will point to. I'll update these to be dataOffset and indexOffset perhaps.

Yeah size could be reduced to be a uint32 for sure, offsets probably shouldn't be in case we ever have a file >4gb.

I'm pretty sure that the size of the struct won't benefit from just a single field being a uint32 though due to alignment.

Although if I make checksum a uint32 as well then it seems it can help if I place the two fields together, but not if they're apart (which makes sense due to alignment):
https://play.golang.org/p/7RRrGG6y10

https://github.com/dominikh/go-tools/tree/master/cmd/structlayout might be helpful if you wanna go down this road

This one is optimized, in future we can always look at this - agreed.

richardartoul · 2017-11-10T18:33:44Z

persist/fs/write.go

@@ -21,14 +21,18 @@
 package fs


There is a lot going on in this file. I count 6 different file descriptors. Seems like generally speaking now (or sometime soon with the subsequent P.R's) would be a good time to write a few paragraphs about our new file formats (kind of what we have in commitlog.md) and then link to that documentation at the top of this page.

Otherwise as someone unfamiliar with the codebase its pretty difficult to decipher the what / why from code that is just manipulating bytes on disk if that makes sense.

Yup sounds good, I'll write a storage.md and reference it from this module. And maybe a short paragraph in the source file itself.

+1, I found this helpful while reviewing:

┌─────────────────────┐ ┌─────────────────────┐ │ Index File │ ┌─────────────────────┐ │ Summaries File │ │ (sorted by ID) │ │ Data File │ │ (sorted by ID) │ ├─────────────────────┤ ├─────────────────────┤ ├─────────────────────┤ ┌────────▶│- Idx │ │List of: │ ┌─────────────────────┐ │- Idx │ │ │- ID │ ┌────▶│ - Marker (16 bytes)│ │ Info File │ │- ID │ │ │- Size │ │ │ - ID │ ├─────────────────────┤ │- Index Entry Offset ├───────┘ │- Checksum │ │ │ - Data (size bytes)│ │- Block Start │ └─────────────────────┘ │- Data Entry Offset ├────┘ └─────────────────────┘ │- Block Size │ └─────────────────────┘ │- Entries (Num) │ │- Major Version │ ┌─────────────────────┐ │- Summaries (Num) │ │ Bloom_Filter File │ │- BloomFilter (K/M) │ ├─────────────────────┤ └─────────────────────┘ │- N: # elems │ │- P: P(false +ve) │ └─────────────────────┘

Ha thanks for that, removed the URL from your comment and replaced with the actual content though to avoid leakage of non-public assets.

richardartoul · 2017-11-10T18:43:14Z

persist/fs/write.go

+	// Write the index entries and calculate the bloom filter
+	n, p := uint(w.currIdx), w.bloomFilterFalsePositivePercent
+	m, k := xsets.BloomFilterEstimate(n, p)
+	bloomFilter := xsets.NewBloomFilter(m, k)


Ok interesting so we don't even create the bloom filter until we're ready to flush to disk? I guess I thought we'd be creating it as we saw things, but I guess we don't need it until data has been flushed to disk, because if its still in memory we can just check.

Right yeah. We'll experiment with how much time this takes to do sequentially all during a flush vs amortizing it during series insertions.

richardartoul · 2017-11-10T18:49:15Z

persist/fs/write.go

+	for i := range w.indexEntries {
+		id := w.indexEntries[i].id.Data().Get()
+
+		entry := schema.IndexEntry{


Kind of annoying we have to do this conversion because of a single field difference but I dont know if there is much that can be done about it

Yeah, not too big a deal it'll just be a memcopy to a stack allocated piece of memory though.

richardartoul · 2017-11-10T18:54:01Z

persist/fs/write.go

 	w.currIdx++

 	return nil
 }

-func (w *writer) close() error {
+func (w *writer) writeIndexEntriesSummariesBloomFilter() error {


Seems like this function does more than the name implies. Maybe: "writeIndexEntriesAndIndexSummaryAndBloomFilter" or something. I know that's verbose but the existing name makes it seem like its writing one file when its writing 3

Yeah I might break some of this up into smaller fns and have a second attempt at naming this.

+1, breaking into smaller fns would help readability.

richardartoul · 2017-11-10T18:56:02Z

persist/fs/write.go

 	}

 	w.encoder.Reset()
 	if err := w.encoder.EncodeIndexInfo(info); err != nil {
 		return err
 	}

-	if _, err := w.infoFdWithDigest.WriteBytes(w.encoder.Bytes()); err != nil {
+	_, err = w.infoFdWithDigest.Write(w.encoder.Bytes())


So the info about the index is stored in a separate file than the index itself?

Correct, right now all files are either just repeated records or a single record. i.e. always a single type in one file.

Probably worth continuing this for simplicity, in the future if its important enough we can combine them. The thing is there's data in the info file that you don't have ahead of time when you write the index file (i.e. number of summaries), although we could probably do some maths to calculate that rather than keep a counter potentially.

richardartoul · 2017-11-10T18:56:21Z

persist/fs/write.go

+	if err != nil {
+		return err
+	}
+
 	info := schema.IndexInfo{


Should we have constructors for these msgpack structs? Seems like it would be easy to leave out a field by accident and corrupt the whole thing

There's usually only a single place where we ever construct these and the unit tests are pretty rigorous. Since there's only one piece of code constructing these msgpack structs I'd prefer the readability when setting the fields rather than the safety added of a constructor (where you don't know what each arg is when reading the code necessarily and maybe you specify the wrong local variable to the wrong argument).

If tons of different places constructed these types then I would agree with you.

richardartoul · 2017-11-10T19:05:12Z

x/sets/bloom_filter.go

+// NewBloomFilter creates a new bloom filter that can represent
+// m elements with k hashes.
+func NewBloomFilter(m uint, k uint) *BloomFilter {
+	if m < 1 {


I wonder if it should return an error if these values are invalid...might be annoying to add the error value everywhere though

Possibly, although am definitely trying to keep the generic datastructures as simple as possible to use so its more ergonomic. I think in this case keeping both bitset and bloomfilter without an error is more ergonomic currently. If there was some other args that could truly screw up things then at that point I'd lean towards an error here.

Overall a good comment but I think just for ergonomics we should probably avoid returning an error for this API.

richardartoul · 2017-11-10T19:07:21Z

Looks good to me for the most part. My main feedback is that it would be really nice to document these new file formats and how they interact (even a few paragraphs) and then link to them from the write.go file

coveralls · 2017-11-11T00:16:41Z

Coverage decreased (-0.6%) to 77.45% when pulling ed3a584d8732004124338720e08da2ab02956b0c on r/sorted-string-index-with-summaries-with-bloom-filter into c6b20ed on master.

…filter

prateek · 2017-11-20T17:13:53Z

persist/fs/commitlog/reader.go

@@ -501,7 +509,7 @@ func (r *reader) readInfo() (schema.LogInfo, error) {
 		return emptyLogInfo, err
 	}
 	data.IncRef()
-	r.logDecoder.Reset(data.Get())
+	r.logDecoder.Reset(encoding.NewDecoderStream(data.Get()))


same here, should we pool DecoderStream somehow?

I can reuse the decoderstream for the reader, sure thing.

prateek · 2017-11-20T17:18:29Z

persist/fs/mmap_linux.go

+		return nil, err
+	}
+
+	if length < hugePageSize {


Not sure I follow, why not use a huge page for 1.5MB index file?

Well we definitely don't want to use huge pages for anything less than 4096 or even "a few" 4096 files in length, otherwise you do cause memory fragmentation (it's a problem with huge pages). Maybe I'll use > 32kb which is 8 pages.

Done.

prateek · 2017-11-20T17:19:15Z

persist/fs/mmap.go

+	// close the ones that have been opened.
+	for _, desc := range files {
+		if *desc.file != nil {
+			(*desc.file).Close()


do you also need to munmap here?

prateek · 2017-11-20T18:11:15Z

storage/bootstrap/bootstrapper/fs/source.go

-			r := readerPool.get()
+			r, err := readerPool.get()
+			if err != nil {
+				s.log.Errorf("unable to get reader from pool")


should this be bubbled up so we know that we've bootstrapped from partial data.

Sure thing, restructured this to bubble it up.

prateek · 2017-11-20T18:19:58Z

persist/fs/read.go

 		filesetPathFromTime(shardDir, blockStart, digestFileSuffix): &digestFd,
 	}); err != nil {
 		return err
 	}

 	r.infoFdWithDigest.Reset(infoFd)
-	r.indexFdWithDigest.Reset(indexFd)
-	r.dataFdWithDigest.Reset(dataFd)
 	r.digestFdWithDigestContents.Reset(digestFd)

 	defer func() {
 		// NB(r): We don't need to keep these FDs open as we use these up front
 		r.infoFdWithDigest.Close()


Would it be better to not retain these fds in the struct?

We don't actually retain the fds in the struct, we just retain the fd with digest wrappers so that we don't need to create them every time we open the file again (i.e. pooling the fd with digest wrappers).

ah makes sense. would you mind putting a note down in the struct about the lifecycle of the wrappers

prateek · 2017-11-20T18:26:10Z

persist/fs/read.go

+	indexEntriesByOffsetAsc []schema.IndexEntry
+}
+
+type indexEntriesByOffsetAsc []schema.IndexEntry


nit: move indexEntriesByOffsetAsc and decoderStream to the bottom of the file

Sure thing, I'll move decoderStream to it's own file and indexEntriesByOffsetAsc to the bottom.

prateek · 2017-11-20T18:29:19Z

persist/fs/read.go

-		return err
+func (r *reader) readIndex() error {
+	r.decoder.Reset(r.indexDecoderStream)
+	for i := 0; i < r.entries; i++ {


Looks like we're still keeping all of the index file in memory, is the plan to do this lazily in subsequent PRs?

Correct, however we'll implement this in the seeker and keep the reader as is. We'll just never use the reader outside needing to do batch jobs.

…bloom-filter

coveralls · 2017-11-27T16:04:53Z

Coverage decreased (-0.08%) to 78.027% when pulling 9039699 on r/sorted-string-index-with-summaries-with-bloom-filter into db90243 on master.

prateek · 2017-11-27T17:07:07Z

storage/bootstrap/bootstrapper/fs/source.go

 	bytesPool pool.CheckedBytesPool,
-	decodingOpts msgpack.DecodingOptions,
-) fs.FileSetReader
+	opts fs.Options,


massive +1 for this change

prateek · 2017-11-27T17:08:01Z

storage/bootstrap/bootstrapper/fs/source.go

+			r, err := readerPool.get()
+			if err != nil {
+				s.log.Errorf("unable to get reader from pool")
+				readersCh <- shardReaders{err: err}


do you need a readerPool.put(r) after this?

Ah no because reader is nil here (the err was from trying to get it from the pool hehe).

prateek · 2017-11-27T17:12:22Z

storage/bootstrap/bootstrapper/fs/source.go

-		)
+	bytesPool := s.opts.ResultOptions().DatabaseBlockOptions().BytesPool()
+	readerPool := newReaderPool(func() (fs.FileSetReader, error) {
+		return s.newReaderFn(bytesPool, s.fsopts)


Any reason to have this here instead of Options?

Yeah you don't really want to allocate and keep around readers outside of the bootstrapping process, hence why its created on demand each time.

I'll add a comment about this.

prateek · 2017-11-27T17:45:52Z

persist/fs/commitlog/reader.go

@@ -270,7 +272,9 @@ func (r *reader) shutdown() {
 func (r *reader) decoderLoop(inBuf <-chan decoderArg, outBuf chan<- readResponse) {
 	decodingOpts := r.opts.FilesystemOptions().DecodingOptions()


nit: could you put this in a var block

prateek · 2017-11-27T18:17:15Z

persist/fs/read_test.go

+	}
+}
+
+func TestDecoderStreamUnreadByteMultiple(t *testing.T) {


+1 for this keeping this test.

Feels like you're having to test a lot of weird combination of conditions, how would you feel about adding a few property tests for the decoder?

I'll open an issue for it, in the interest of expediting this change we'll look at this later.

Opened #403

prateek · 2017-11-27T18:28:17Z

persist/fs/read_decode_stream.go

+
+var (
+	// Ensure readerDecoderStream implements encoding.DecoderStream
+	_ encoding.DecoderStream = &readerDecoderStream{}


could you avoid this by changing the ctor to the following signature: func newReaderDecoderStream() encoding.DecoderStream {...}

Sounds good, done

prateek · 2017-11-27T19:36:04Z

persist/fs/mmap.go

+			break
+		}
+
+		*desc.file = fd


pretty soon we'll be writing desc->file = fd; 🤣

prateek

LGTM w/ some minor nits

coveralls · 2017-11-27T21:02:46Z

Coverage decreased (-0.08%) to 78.033% when pulling e5ca681 on r/sorted-string-index-with-summaries-with-bloom-filter into db90243 on master.

…ries and bloom filter (m3db#395)" This reverts commit 4afa833.

robskillington added C: Filesystem C: Storage P: Medium T: Feature labels Nov 10, 2017

richardartoul reviewed Nov 10, 2017

View reviewed changes

Rob Skillington added 6 commits November 13, 2017 11:00

The write side for the new sorted string index w/ summaries w/ bloom …

9d3305f

…filter

Fix reader and persist/fs tests

7f032e8

Fix Madvise call in mmap_linux.go

f55c0cd

Fix integration build errors

453624d

Fix tests in affected packages

31faf07

Fix metalint issues

54beadf

prateek reviewed Nov 20, 2017

View reviewed changes

Rob Skillington added 4 commits November 21, 2017 14:25

Address review comments

2495f1b

Parameterize the mmap huge page configuration

ac2cc13

Fix TestConfiguration test and metalint unconvert issue

a648700

Merge branch 'master' into r/sorted-string-index-with-summaries-with-…

9039699

…bloom-filter

m3db deleted a comment from coveralls Nov 27, 2017

prateek reviewed Nov 27, 2017

View reviewed changes

prateek approved these changes Nov 27, 2017

View reviewed changes

robskillington mentioned this pull request Nov 27, 2017

Add some prop tests for the DecoderStream implementations #403

Closed

Rob Skillington added 2 commits November 27, 2017 15:21

Address final round of feedback

0b2f387

Fix reader tests

e5ca681

m3db deleted a comment from coveralls Nov 27, 2017

robskillington merged commit 4afa833 into master Nov 27, 2017

robskillington deleted the r/sorted-string-index-with-summaries-with-bloom-filter branch November 27, 2017 22:18

richardartoul pushed a commit to richardartoul/m3db that referenced this pull request Nov 30, 2017

Revert "Update fileset index format to sorted string order with summa…

330b2bd

…ries and bloom filter (m3db#395)" This reverts commit 4afa833.

		@@ -270,7 +272,9 @@ func (r *reader) shutdown() {
		func (r *reader) decoderLoop(inBuf <-chan decoderArg, outBuf chan<- readResponse) {
		decodingOpts := r.opts.FilesystemOptions().DecodingOptions()

Update fileset index format to sorted string order with summaries and bloom filter #395

Update fileset index format to sorted string order with summaries and bloom filter #395

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