Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 750000000000,
- VCPUs: 32,
+ RAM: 1600000000000,
+ VCPUs: 64,
Priority: *priority,
}
err = runner.TranslatePaths(inputFilename)
Priority: *priority,
}
err = runner.TranslatePaths(inputFilename)
return fmt.Errorf("%d needed tiles are missing from library", len(missing))
}
return fmt.Errorf("%d needed tiles are missing from library", len(missing))
}
+ if true {
+ // low memory mode
+ for _, seqname := range seqnames {
+ log.Infof("assembling %q", seqname)
+ cmd.exportSeq(out, bedout, tilelib.taglib.keylen, seqname, refseq[seqname], tileVariant, cgs)
+ log.Infof("assembled %q", seqname)
+ }
+ return nil
+ }
+
outbuf := make([]bytes.Buffer, len(seqnames))
bedbuf := make([]bytes.Buffer, len(seqnames))
ready := make([]chan struct{}, len(seqnames))
outbuf := make([]bytes.Buffer, len(seqnames))
bedbuf := make([]bytes.Buffer, len(seqnames))
ready := make([]chan struct{}, len(seqnames))
- throttle := throttle{Max: 4}
+ throttle := throttle{Max: 8}
log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
for seqidx, seqname := range seqnames {
seqidx, seqname := seqidx, seqname
log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
for seqidx, seqname := range seqnames {
seqidx, seqname := seqidx, seqname