Memory tweaks.

refs #17562

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/export.go b/export.go
index 1ef8a074b26645f88747cd9d3d0decf8f046d8b6..6bc1007b235cadffdcdda86ef7d5d0c65bc90468 100644 (file)
--- a/export.go
+++ b/export.go
@@ -697,10 +697,11 @@ func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVarian
 
 type formatHGVSNumpy struct {
        sync.Mutex
-       alleles map[string][][]bool // alleles[seqname][variantidx][genomeidx*2+phase]
+       writelock sync.Mutex
+       alleles   map[string][][]bool // alleles[seqname][variantidx][genomeidx*2+phase]
 }
 
-func (*formatHGVSNumpy) MaxGoroutines() int                            { return 8 }
+func (*formatHGVSNumpy) MaxGoroutines() int                            { return 4 }
 func (*formatHGVSNumpy) Filename() string                              { return "annotations.csv" }
 func (*formatHGVSNumpy) PadLeft() bool                                 { return false }
 func (*formatHGVSNumpy) Head(out io.Writer, cgs []CompactGenome) error { return nil }
@@ -785,7 +786,9 @@ func (f *formatHGVSNumpy) Finish(outdir string, _ io.Writer, seqname string) err
                "cols":    cols,
        }).Info("writing numpy")
        npw.Shape = []int{rows, cols}
+       f.writelock.Lock() // serialize because WriteInt8 uses lots of memory
        npw.WriteInt8(out)
+       f.writelock.Unlock()
        err = bufw.Flush()
        if err != nil {
                return err