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Debug fasta and fastq writer when the first sequence is hudge

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Former-commit-id: d208ff838abb7e19e117067f6243298492d60f14
This commit is contained in:
Eric Coissac
2024-06-26 18:39:42 +02:00
parent 1835cb2cf3
commit e40d0bfbe7
7 changed files with 78 additions and 17 deletions
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28
pkg/obioptions/options.go
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@ -23,6 +23,8 @@ var _ParallelFilesRead = 0
var _MaxAllowedCPU = runtime.NumCPU()
var _BatchSize = 2000
var _Pprof = false
var _PprofMudex = 10
var _PprofGoroutine = 6060
var _Quality_Shift_Input = byte(33)
var _Quality_Shift_Output = byte(33)
@ -56,6 +58,14 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
options.BoolVar(&_Pprof, "force-one-cpu", false,
options.Description("Force to use only one cpu core for parallel processing"))
options.IntVar(&_PprofMudex, "pprof-mutex", _PprofMudex,
options.GetEnv("OBIPPROFMUTEX"),
options.Description("Enable profiling of mutex lock."))
options.IntVar(&_PprofGoroutine, "pprof-goroutine", _PprofGoroutine,
options.GetEnv("OBIPPROFGOROUTINE"),
options.Description("Enable profiling of goroutine blocking profile."))
options.IntVar(&_BatchSize, "batch-size", _BatchSize,
options.GetEnv("OBIBATCHSIZE"),
options.Description("Number of sequence per batch for paralelle processing"))
@ -96,6 +106,24 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
log.Info(" go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/profile?seconds=30'")
}
if options.Called("pprof-mutex") {
url := "localhost:6060"
go http.ListenAndServe(url, nil)
runtime.SetMutexProfileFraction(_PprofMudex)
log.Infof("Start a pprof server at address %s/debug/pprof", url)
log.Info("Profil can be followed running concurrently the command :")
log.Info(" go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/mutex'")
}
if options.Called("pprof-goroutine") {
url := "localhost:6060"
go http.ListenAndServe(url, nil)
runtime.SetBlockProfileRate(_PprofGoroutine)
log.Infof("Start a pprof server at address %s/debug/pprof", url)
log.Info("Profil can be followed running concurrently the command :")
log.Info(" go tool pprof -http=127.0.0.1:8080 'http://localhost:6060/debug/pprof/block'")
}
// Handle user errors
if err != nil {
fmt.Fprintf(os.Stderr, "ERROR: %s\n\n", err)