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homogenize worker count

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Former-commit-id: 4352ac6694c08023cdf0e090723fac8af655cea4
This commit is contained in:
Eric Coissac
2023-12-20 08:14:07 +01:00
parent 7a31d5b07b
commit a36e830de3
4 changed files with 10 additions and 6 deletions
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3
pkg/obiapat/pcr.go
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@ -3,6 +3,7 @@ package obiapat
import ( import (
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
) )
@ -103,7 +104,7 @@ func MakeOptions(setters []WithOption) Options {
extension: -1, extension: -1,
fullExtension: false, fullExtension: false,
circular: false, circular: false,
parallelWorkers: 4, parallelWorkers: obioptions.CLIParallelWorkers(),
batchSize: 100, batchSize: 100,
forward: NilApatPattern, forward: NilApatPattern,
cfwd: NilApatPattern, cfwd: NilApatPattern,

6
pkg/obichunk/options.go
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@ -1,5 +1,7 @@
package obichunk package obichunk
import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
type __options__ struct { type __options__ struct {
statsOn []string statsOn []string
categories []string categories []string
@ -24,8 +26,8 @@ func MakeOptions(setters []WithOption) Options {
navalue: "NA", navalue: "NA",
cacheOnDisk: false, cacheOnDisk: false,
batchCount: 100, batchCount: 100,
batchSize: 5000, batchSize: obioptions.CLIBatchSize(),
parallelWorkers: 4, parallelWorkers: obioptions.CLIParallelWorkers(),
noSingleton: false, noSingleton: false,
} }

5
pkg/obingslibrary/worker.go
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@ -1,6 +1,7 @@
package obingslibrary package obingslibrary
import ( import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
) )
@ -125,8 +126,8 @@ func MakeOptions(setters []WithOption) Options {
allowedMismatch: 0, allowedMismatch: 0,
allowsIndel: false, allowsIndel: false,
withProgressBar: false, withProgressBar: false,
parallelWorkers: 4, parallelWorkers: obioptions.CLIParallelWorkers(),
batchSize: 1000, batchSize: obioptions.CLIBatchSize(),
} }
opt := Options{&o} opt := Options{&o}

2
pkg/obitools/obipairing/pairing.go
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@ -221,7 +221,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
log.Fatalln("Sequence data must be paired") log.Fatalln("Sequence data must be paired")
} }
nworkers := obioptions.CLIMaxCPU() * 3 / 2 nworkers := obioptions.CLIParallelWorkers()
if len(sizes) > 0 { if len(sizes) > 0 {
nworkers = sizes[0] nworkers = sizes[0]