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Add an option --pprof

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Former-commit-id: 3ca1280e8daddbf1075e3189f9851211ce8882ae
This commit is contained in:
Eric Coissac
2023-03-28 20:07:26 +07:00
parent 988ae79989
commit e863dc456a
3 changed files with 24 additions and 9 deletions
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14
cmd/obitools/obipcr/main.go
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@ -2,8 +2,10 @@ package main
import ( import (
"os" "os"
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert" "git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
@ -12,13 +14,9 @@ import (
func main() { func main() {
// go tool pprof -http=":8000" ./obipairing ./cpu.pprof // go tool pprof -nodefraction=0 -http=:8081 http://localhost:8080/debug/pprof/allocs
// f, err := os.Create("cpu.pprof") // look at http://localhost:8080/debug/pprof for havng the possibilities
// if err != nil { //go http.ListenAndServe("localhost:8080", nil)
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
// go tool trace cpu.trace // go tool trace cpu.trace
// ftrace, err := os.Create("cpu.trace") // ftrace, err := os.Create("cpu.trace")
@ -35,7 +33,7 @@ func main() {
sequences, err := obiconvert.CLIReadBioSequences(args...) sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil { if err != nil {
log.Errorf("Cannot open file (%v)",err) log.Errorf("Cannot open file (%v)", err)
os.Exit(1) os.Exit(1)
} }

11
pkg/obioptions/options.go
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@ -8,12 +8,17 @@ import (
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
"github.com/DavidGamba/go-getoptions" "github.com/DavidGamba/go-getoptions"
"net/http"
_ "net/http/pprof"
) )
var _Debug = false var _Debug = false
var _ParallelWorkers = runtime.NumCPU()*2 - 1 var _ParallelWorkers = runtime.NumCPU()*2 - 1
var _MaxAllowedCPU = runtime.NumCPU() var _MaxAllowedCPU = runtime.NumCPU()
var _BatchSize = 5000 var _BatchSize = 5000
var _Pprof = false
type ArgumentParser func([]string) (*getoptions.GetOpt, []string) type ArgumentParser func([]string) (*getoptions.GetOpt, []string)
@ -24,6 +29,7 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
options.SetUnknownMode(getoptions.Fail) options.SetUnknownMode(getoptions.Fail)
options.Bool("help", false, options.Alias("h", "?")) options.Bool("help", false, options.Alias("h", "?"))
options.BoolVar(&_Debug, "debug", false) options.BoolVar(&_Debug, "debug", false)
options.BoolVar(&_Pprof, "pprof", false)
options.IntVar(&_ParallelWorkers, "workers", _ParallelWorkers, options.IntVar(&_ParallelWorkers, "workers", _ParallelWorkers,
options.Alias("w"), options.Alias("w"),
@ -52,6 +58,11 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
log.Debugln("Switch to debug level logging") log.Debugln("Switch to debug level logging")
} }
if options.Called("pprof") {
go http.ListenAndServe("localhost:8080", nil)
log.Infoln("Start a pprof server at address http://localhost:8080/debug/pprof")
}
// Handle user errors // Handle user errors
if err != nil { if err != nil {
fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err) fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)

8
pkg/obiseq/pool.go
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@ -45,7 +45,13 @@ func GetSlice(capacity int) []byte {
} }
func CopySlice(src []byte) []byte { func CopySlice(src []byte) []byte {
sl := GetSlice(len(src))[0:len(src)] sl := GetSlice(len(src))
if cap(sl) < len(src) {
log.Panicln("Bizarre... j'aurai pourtant cru")
}
sl = sl[0:len(src)]
copy(sl, src) copy(sl, src)