COMPUTE-15 Prefetch cache truncated read fix (#86)

Modify isDataInCache() such that if there is a covered range in the cache, but the read request extends beyond the last vector in the cache, treat it as DATA_OUTSIDE_CACHE

.github/workflows/build-packages.yml

@@ -20,7 +20,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-go@v2
         with:
-          go-version: '1.16.10'
+          go-version: '1.22.6'
       - name: Build Linux executable
         run: |
           set -x
@@ -51,7 +51,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-go@v2
         with:
-          go-version: '1.16.10'
+          go-version: '1.22.6'
       - name: Build Macos executable
         run: |
           set -x

.github/workflows/master.yml

@@ -20,7 +20,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-go@v2
         with:
-          go-version: '1.16.10'
+          go-version: '1.22.6'
 
       - name: Install & build
         run: |
@@ -33,7 +33,7 @@ jobs:
           python3 python3-pip python3-dev
 
           # Install printing with colors python package
-          python3 -m pip install --upgrade setuptools wheel pyOpenSSL
+          python3 -m pip install --upgrade 'setuptools<71.0.0' wheel
           wget https://raw.githubusercontent.com/dnanexus/dx-toolkit/master/src/python/requirements.txt
           python3 -m pip install -r requirements.txt
 
@@ -63,7 +63,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-go@v2
         with:
-          go-version: '1.16.10'
+          go-version: '1.22.6'
 
       - name: Install & build
         run: |
@@ -75,7 +75,7 @@ jobs:
           openssl libssl-dev zip unzip libffi-dev \
           python3 python3-pip python3-dev
           # Install printing with colors python package
-          python3 -m pip install --upgrade setuptools wheel pyOpenSSL
+          python3 -m pip install --upgrade 'setuptools<71.0.0' wheel
           wget https://raw.githubusercontent.com/dnanexus/dx-toolkit/master/src/python/requirements.txt
           python3 -m pip install -r requirements.txt
 
@@ -105,7 +105,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-go@v2
         with:
-          go-version: '1.16.10'
+          go-version: '1.22.6'
       - name: Install & build
         run: |
           set -x

dxfuse.go

@@ -720,7 +720,6 @@ func (fsys *Filesys) RmDir(ctx context.Context, op *fuseops.RmDirOp) error {
 //
 // Note: We want to have a guarantied O(1) algorithm, otherwise, we would use a
 // randomized approach.
-//
 func (fsys *Filesys) insertIntoFileHandleTable(fh *FileHandle) fuseops.HandleID {
 	fsys.fhCounter++
 	hid := fuseops.HandleID(fsys.fhCounter)
@@ -738,7 +737,6 @@ func (fsys *Filesys) insertIntoDirHandleTable(dh *DirHandle) fuseops.HandleID {
 }
 
 // A CreateRequest asks to create and open a file (not a directory).
-//
 func (fsys *Filesys) CreateFile(ctx context.Context, op *fuseops.CreateFileOp) error {
 	fsys.mutex.Lock()
 	defer fsys.mutex.Unlock()
@@ -1258,7 +1256,6 @@ func (fsys *Filesys) ReleaseDirHandle(ctx context.Context, op *fuseops.ReleaseDi
 
 // ===
 // File handling
-//
 func (fsys *Filesys) openRegularFile(
 	ctx context.Context,
 	oph *OpHandle,
@@ -1317,7 +1314,6 @@ func (fsys *Filesys) openRegularFile(
 }
 
 // Note: What happens if the file is opened for writing?
-//
 func (fsys *Filesys) OpenFile(ctx context.Context, op *fuseops.OpenFileOp) error {
 	fsys.mutex.Lock()
 	defer fsys.mutex.Unlock()
@@ -1415,6 +1411,10 @@ func (fsys *Filesys) readRemoteFile(ctx context.Context, op *fuseops.ReadFileOp,
 	// See if the data has already been prefetched.
 	// This call will wait, if a prefetch IO is in progress.
 	len := fsys.pgs.CacheLookup(fh.hid, op.Offset, endOfs, op.Dst)
+	// log received length if less than requested
+	if fsys.options.Verbose && int64(len) < reqSize {
+		fsys.log("ReadFile: CacheLookup returned %d, requested %d", len, reqSize)
+	}
 	if len > 0 {
 		op.BytesRead = len
 		return nil

go.mod

@@ -1,18 +1,22 @@
 module github.com/dnanexus/dxfuse
 
-go 1.16
+go 1.22.6
 
 require (
-	github.com/StackExchange/wmi v1.2.1 // indirect
-	github.com/dnanexus/dxda v0.5.8
-	github.com/go-ole/go-ole v1.2.6 // indirect
-	github.com/jacobsa/fuse v0.0.0-20211019165009-c75d3f26fceb
-	github.com/mattn/go-sqlite3 v1.14.9
+	github.com/dnanexus/dxda v0.6.2
+	github.com/jacobsa/fuse v0.0.0-20240721083925-faebccf4c6c6
+	github.com/mattn/go-sqlite3 v1.14.22
+	github.com/shirou/gopsutil v3.21.11+incompatible
+	golang.org/x/exp v0.0.0-20200513190911-00229845015e
+	golang.org/x/sync v0.8.0
+)
+
+require (
+	github.com/go-ole/go-ole v1.3.0 // indirect
 	github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58 // indirect
-	github.com/shirou/gopsutil v3.21.9+incompatible
 	github.com/stretchr/testify v1.7.0 // indirect
-	github.com/tklauser/go-sysconf v0.3.9 // indirect
-	golang.org/x/exp v0.0.0-20200513190911-00229845015e
-	golang.org/x/sync v0.0.0-20210220032951-036812b2e83c
-	golang.org/x/sys v0.0.0-20211019181941-9d821ace8654 // indirect
+	github.com/tklauser/go-sysconf v0.3.14 // indirect
+	github.com/tklauser/numcpus v0.8.0 // indirect
+	github.com/yusufpapurcu/wmi v1.2.4 // indirect
+	golang.org/x/sys v0.24.0 // indirect
 )

go.sum

@@ -1,46 +1,34 @@
 dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU=
 github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo=
-github.com/PuerkitoBio/goquery v1.5.1/go.mod h1:GsLWisAFVj4WgDibEWF4pvYnkVQBpKBKeU+7zCJoLcc=
-github.com/StackExchange/wmi v1.2.1 h1:VIkavFPXSjcnS+O8yTq7NI32k0R5Aj+v39y29VYDOSA=
-github.com/StackExchange/wmi v1.2.1/go.mod h1:rcmrprowKIVzvc+NUiLncP2uuArMWLCbu9SBzvHz7e8=
-github.com/andybalholm/cascadia v1.1.0/go.mod h1:GsXiBklL0woXo1j/WYWtSYYC4ouU9PqHO0sqidkEA4Y=
 github.com/davecgh/go-spew v1.1.0 h1:ZDRjVQ15GmhC3fiQ8ni8+OwkZQO4DARzQgrnXU1Liz8=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/detailyang/go-fallocate v0.0.0-20180908115635-432fa640bd2e/go.mod h1:3ZQK6DMPSz/QZ73jlWxBtUhNA8xZx7LzUFSq/OfP8vk=
-github.com/dnanexus/dxda v0.5.8 h1:sz1W8WqlSoc6rp4eeZ19JniMx6RLrqX96K+Lpp/Lv6c=
-github.com/dnanexus/dxda v0.5.8/go.mod h1:UeYZ7DMtJGGQ13owVEeAbUSFWXkCj97xZEzoBebZP68=
+github.com/dnanexus/dxda v0.6.2 h1:qmpYDJaqd7wgbIiwdgzpCvCvRs/qBr6FCPTm2vD8pNg=
+github.com/dnanexus/dxda v0.6.2/go.mod h1:NSycIpaP43ilDCoE0WXUFuPmAewkwgqEHU3JuyZY8ZQ=
 github.com/go-gl/glfw/v3.3/glfw v0.0.0-20200222043503-6f7a984d4dc4/go.mod h1:tQ2UAYgL5IevRw8kRxooKSPJfGvJ9fJQFa0TUsXzTg8=
-github.com/go-ole/go-ole v1.2.5/go.mod h1:pprOEPIfldk/42T2oK7lQ4v4JSDwmV0As9GaiUsvbm0=
-github.com/go-ole/go-ole v1.2.6 h1:/Fpf6oFPoeFik9ty7siob0G6Ke8QvQEuVcuChpwXzpY=
 github.com/go-ole/go-ole v1.2.6/go.mod h1:pprOEPIfldk/42T2oK7lQ4v4JSDwmV0As9GaiUsvbm0=
-github.com/google/subcommands v1.2.0/go.mod h1:ZjhPrFU+Olkh9WazFPsl27BQ4UPiG37m3yTrtFlrHVk=
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 github.com/kylelemons/godebug v1.1.0 h1:RPNrshWIDI6G2gRW9EHilWtl7Z6Sb1BR0xunSBf0SNc=
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-github.com/pbnjay/memory v0.0.0-20190104145345-974d429e7ae4/go.mod h1:RMU2gJXhratVxBDTFeOdNhd540tG57lt9FIUV0YLvIQ=
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 github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58/go.mod h1:DXv8WO4yhMYhSNPKjeNKa5WY9YCIEBRbNzFFPJbWO6Y=
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+github.com/tklauser/numcpus v0.8.0/go.mod h1:ZJZlAY+dmR4eut8epnzf0u/VwodKmryxR8txiloSqBE=
+github.com/yusufpapurcu/wmi v1.2.4 h1:zFUKzehAFReQwLys1b/iSMl+JQGSCSjtVqQn9bBrPo0=
+github.com/yusufpapurcu/wmi v1.2.4/go.mod h1:SBZ9tNy3G9/m5Oi98Zks0QjeHVDvuK0qfxQmPyzfmi0=
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
 golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
@@ -51,25 +39,19 @@ golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+o
 golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o=
 golang.org/x/mod v0.1.1-0.20191105210325-c90efee705ee/go.mod h1:QqPTAvyqsEbceGzBzNggFXnrqF1CaUcvgkdR5Ot7KZg=
 golang.org/x/mod v0.1.1-0.20191107180719-034126e5016b/go.mod h1:QqPTAvyqsEbceGzBzNggFXnrqF1CaUcvgkdR5Ot7KZg=
-golang.org/x/net v0.0.0-20180218175443-cbe0f9307d01/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4=
 golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
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-golang.org/x/net v0.0.0-20200202094626-16171245cfb2/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
-golang.org/x/net v0.0.0-20200301022130-244492dfa37a/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
-golang.org/x/net v0.0.0-20200324143707-d3edc9973b7e/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A=
 golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
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-golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
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 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/tools v0.0.0-20200207183749-b753a1ba74fa/go.mod h1:TB2adYChydJhpapKDTa4BR/hXlZSLoq2Wpct/0txZ28=
 golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=

prefetch.go

@@ -148,7 +148,7 @@ func (iov Iovec) intersectBuffer(startOfs int64, endOfs int64) []byte {
 	bgnByte := MaxInt64(iov.startByte, startOfs)
 	endByte := MinInt64(iov.endByte, endOfs)
 
-	// normalize, to offets inside the buffer
+	// normalize, to offsets inside the buffer
 	bgnByte -= iov.startByte
 	endByte -= iov.startByte
 
@@ -724,6 +724,7 @@ func (pgs *PrefetchGlobalState) findCoveredRange(
 	pfm *PrefetchFileMetadata,
 	startOfs int64,
 	endOfs int64) (int, int) {
+
 	// check if there is ANY intersection with cache
 	if endOfs < pfm.cache.startByte ||
 		pfm.cache.endByte < startOfs {
@@ -769,11 +770,15 @@ func (pgs *PrefetchGlobalState) findCoveredRange(
 // For example, if there are currently 2 chunks in cache, and the current IO falls
 // in the second location then:
 // assuming
-//     maxNumIovecs = 2
+//
+//	maxNumIovecs = 2
+//
 // calculate
-//     iovIndex = 1
-//     nReadAheadChunks = iovIndex + maxNumIovecs - nIovec
-//                      =  1       + 2            - 2      = 1
+//
+//	iovIndex = 1
+//	nReadAheadChunks = iovIndex + maxNumIovecs - nIovec
+//	                 =  1       + 2            - 2      = 1
+//
 // If the IO landed on the first location, then iovIndex=0, and we will not issue
 // additional readahead IOs.
 func (pgs *PrefetchGlobalState) moveCacheWindow(pfm *PrefetchFileMetadata, iovIndex int) {
@@ -951,6 +956,14 @@ func (pgs *PrefetchGlobalState) isDataInCache(
 		// the cached area.
 		return DATA_OUTSIDE_CACHE
 	}
+	// if the end offset is greater than the last byte iov, then we are outside the cache
+	// If access were deemed sequential, we would have prefetched the data
+	if endOfs > pfm.cache.iovecs[last].endByte {
+		if pgs.verboseLevel >= 2 {
+			pfm.log("isDataInCache: endOfs=%d  last=%d  endByte=%d", endOfs, last, pfm.cache.iovecs[last].endByte)
+		}
+		return DATA_OUTSIDE_CACHE
+	}
 
 	for i := first; i <= last; i++ {
 		iov := pfm.cache.iovecs[i]
@@ -1044,7 +1057,6 @@ func (pgs *PrefetchGlobalState) getDataFromCache(
 
 // This is done on behalf of a user read request. If this range has been prefetched, copy the data.
 // Return how much data was copied. Return zero length if the data isn't in cache.
-//
 func (pgs *PrefetchGlobalState) CacheLookup(hid fuseops.HandleID, startOfs int64, endOfs int64, data []byte) int {
 	pfm := pgs.getAndLockPfm(hid)
 	if pfm == nil {