slice.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bufio"
   9         "encoding/gob"
  10         "flag"
  11         "fmt"
  12         "io"
  13         "net/http"
  14         _ "net/http/pprof"
  15         "os"
  16         "runtime"
  17         "strings"
  18         "sync"
  19
  20         "git.arvados.org/arvados.git/sdk/go/arvados"
  21         "github.com/klauspost/pgzip"
  22         log "github.com/sirupsen/logrus"
  23 )
  24
  25 type slicecmd struct{}
  26
  27 func (cmd *slicecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  28         var err error
  29         defer func() {
  30                 if err != nil {
  31                         fmt.Fprintf(stderr, "%s\n", err)
  32                 }
  33         }()
  34         flags := flag.NewFlagSet("", flag.ContinueOnError)
  35         flags.SetOutput(stderr)
  36         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  37         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  38         projectUUID := flags.String("project", "", "project `UUID` for output data")
  39         priority := flags.Int("priority", 500, "container request priority")
  40         inputDir := flags.String("input-dir", "./in", "input `directory`")
  41         outputDir := flags.String("output-dir", "./out", "output `directory`")
  42         tagsPerFile := flags.Int("tags-per-file", 50000, "tags per file (nfiles will be ~10M÷x)")
  43         err = flags.Parse(args)
  44         if err == flag.ErrHelp {
  45                 err = nil
  46                 return 0
  47         } else if err != nil {
  48                 return 2
  49         }
  50
  51         if *pprof != "" {
  52                 go func() {
  53                         log.Println(http.ListenAndServe(*pprof, nil))
  54                 }()
  55         }
  56
  57         if !*runlocal {
  58                 runner := arvadosContainerRunner{
  59                         Name:        "lightning slice",
  60                         Client:      arvados.NewClientFromEnv(),
  61                         ProjectUUID: *projectUUID,
  62                         RAM:         200000000000,
  63                         VCPUs:       32,
  64                         Priority:    *priority,
  65                         KeepCache:   50,
  66                         APIAccess:   true,
  67                 }
  68                 err = runner.TranslatePaths(inputDir)
  69                 if err != nil {
  70                         return 1
  71                 }
  72                 runner.Args = []string{"slice", "-local=true",
  73                         "-pprof", ":6060",
  74                         "-input-dir", *inputDir,
  75                         "-output-dir", "/mnt/output",
  76                 }
  77                 var output string
  78                 output, err = runner.Run()
  79                 if err != nil {
  80                         return 1
  81                 }
  82                 fmt.Fprintln(stdout, output)
  83                 return 0
  84         }
  85
  86         err = Slice(*outputDir, *inputDir, *tagsPerFile)
  87         if err != nil {
  88                 return 1
  89         }
  90         return 0
  91 }
  92
  93 // Read tags+tiles+genomes from srcdir, write to dstdir with (up to)
  94 // the specified number of tags per file.
  95 func Slice(dstdir, srcdir string, tagsPerFile int) error {
  96         infiles, err := allGobFiles(srcdir)
  97         if err != nil {
  98                 return err
  99         }
 100
 101         var (
 102                 tagset     [][]byte
 103                 tagsetOnce sync.Once
 104                 fs         []*os.File
 105                 bufws      []*bufio.Writer
 106                 gzws       []*pgzip.Writer
 107                 encs       []*gob.Encoder
 108         )
 109
 110         throttle := throttle{Max: runtime.GOMAXPROCS(0)}
 111         for _, path := range infiles {
 112                 path := path
 113                 throttle.Acquire()
 114                 go func() {
 115                         defer throttle.Release()
 116                         f, err := open(path)
 117                         if err != nil {
 118                                 throttle.Report(err)
 119                                 return
 120                         }
 121                         defer f.Close()
 122                         log.Printf("reading %s", path)
 123                         err = DecodeLibrary(f, strings.HasSuffix(path, ".gz"), func(ent *LibraryEntry) error {
 124                                 if err := throttle.Err(); err != nil {
 125                                         return err
 126                                 }
 127                                 if len(ent.TagSet) > 0 {
 128                                         tagsetOnce.Do(func() {
 129                                                 tagset = ent.TagSet
 130                                                 var err error
 131                                                 fs, bufws, gzws, encs, err = openOutFiles(dstdir, len(ent.TagSet), tagsPerFile)
 132                                                 if err != nil {
 133                                                         throttle.Report(err)
 134                                                         return
 135                                                 }
 136                                                 for _, enc := range encs {
 137                                                         err = enc.Encode(LibraryEntry{TagSet: tagset})
 138                                                         if err != nil {
 139                                                                 throttle.Report(err)
 140                                                                 return
 141                                                         }
 142                                                 }
 143                                         })
 144                                 }
 145                                 if err := throttle.Err(); err != nil {
 146                                         return err
 147                                 }
 148                                 for _, tv := range ent.TileVariants {
 149                                         err := encs[int(tv.Tag)/tagsPerFile].Encode(LibraryEntry{
 150                                                 TileVariants: []TileVariant{tv},
 151                                         })
 152                                         if err != nil {
 153                                                 return err
 154                                         }
 155                                 }
 156                                 // Here, each output file gets a
 157                                 // CompactGenome entry for each
 158                                 // genome, even if there are no
 159                                 // variants in the relevant range.
 160                                 // Easier for downstream code.
 161                                 for _, cg := range ent.CompactGenomes {
 162                                         for i, enc := range encs {
 163                                                 start := i * tagsPerFile
 164                                                 end := start + tagsPerFile
 165                                                 if max := len(cg.Variants)/2 + int(cg.StartTag); end > max {
 166                                                         end = max
 167                                                 }
 168                                                 if start < int(cg.StartTag) {
 169                                                         start = int(cg.StartTag)
 170                                                 }
 171                                                 var variants []tileVariantID
 172                                                 if start < end {
 173                                                         variants = cg.Variants[(start-int(cg.StartTag))*2 : (end-int(cg.StartTag))*2]
 174                                                 }
 175                                                 err := enc.Encode(LibraryEntry{CompactGenomes: []CompactGenome{{
 176                                                         Name:     cg.Name,
 177                                                         Variants: variants,
 178                                                         StartTag: tagID(start),
 179                                                         EndTag:   tagID(start + tagsPerFile),
 180                                                 }}})
 181                                                 if err != nil {
 182                                                         return err
 183                                                 }
 184                                         }
 185                                 }
 186                                 // Write all ref seqs to the first
 187                                 // slice. Easier for downstream code.
 188                                 if len(ent.CompactSequences) > 0 {
 189                                         err := encs[0].Encode(LibraryEntry{CompactSequences: ent.CompactSequences})
 190                                         if err != nil {
 191                                                 return err
 192                                         }
 193                                 }
 194                                 return nil
 195                         })
 196                         throttle.Report(err)
 197                 }()
 198         }
 199         throttle.Wait()
 200         if throttle.Err() != nil {
 201                 closeOutFiles(fs, bufws, gzws, encs)
 202                 return throttle.Err()
 203         }
 204         return closeOutFiles(fs, bufws, gzws, encs)
 205 }
 206
 207 func openOutFiles(dstdir string, tags, tagsPerFile int) (fs []*os.File, bufws []*bufio.Writer, gzws []*pgzip.Writer, encs []*gob.Encoder, err error) {
 208         nfiles := (tags + tagsPerFile - 1) / tagsPerFile
 209         fs = make([]*os.File, nfiles)
 210         bufws = make([]*bufio.Writer, nfiles)
 211         gzws = make([]*pgzip.Writer, nfiles)
 212         encs = make([]*gob.Encoder, nfiles)
 213         for i := 0; i*tagsPerFile < tags; i++ {
 214                 fs[i], err = os.Create(dstdir + fmt.Sprintf("/library%04d.gob.gz", i))
 215                 if err != nil {
 216                         return
 217                 }
 218                 bufws[i] = bufio.NewWriterSize(fs[i], 1<<26)
 219                 gzws[i] = pgzip.NewWriter(bufws[i])
 220                 encs[i] = gob.NewEncoder(gzws[i])
 221         }
 222         return
 223 }
 224
 225 func closeOutFiles(fs []*os.File, bufws []*bufio.Writer, gzws []*pgzip.Writer, encs []*gob.Encoder) error {
 226         var firstErr error
 227         for _, gzw := range gzws {
 228                 if gzw != nil {
 229                         err := gzw.Close()
 230                         if err != nil && firstErr == nil {
 231                                 firstErr = err
 232                         }
 233                 }
 234         }
 235         for _, bufw := range bufws {
 236                 if bufw != nil {
 237                         err := bufw.Flush()
 238                         if err != nil && firstErr == nil {
 239                                 firstErr = err
 240                         }
 241                 }
 242         }
 243         for _, f := range fs {
 244                 if f != nil {
 245                         err := f.Close()
 246                         if err != nil && firstErr == nil {
 247                                 firstErr = err
 248                         }
 249                 }
 250         }
 251         return firstErr
 252 }