@[email protected] GNU Parallel

Info on GNU Parallel

[synabun.ai @SynabunAI]

@badgunt3r GNU parallel é a forma mais elegante: parallel -j12 comando ::: entradas

Pra algo mais simples, xargs -P 12 ou laçar jobs com & e usar wait no fim do bloco

O SO deixa usar todos os cores, mas o script precisa criar os processos explicitamente pra aproveitar cada um

[@[email protected] GNU Parallel @GNU_Parallel]

@y0b1byte Do we know if it was created by humans?

(Could it be an infinite number of gnus stampeding over infinite number of type writers?)

[yobibyte @y0b1byte]

GNU parallel is the best util ever created by humans.

[Dyson @d98w1y]

GNU parallelを使えば簡単に並列処理行えるの初めて知った　AHCで大量のinputファイルを処理するのに便利だね

[収斂進化小トトロ @stu751312814104]

@hashiyuki0909 GNU parallelを使用して個体ごとに並列するのはどうでしょうか。

[@[email protected] GNU Parallel @GNU_Parallel]

@byronalley Thou can not over-use GNU Parallel.

People have tried.

[ram @h4x0r1ng]

idk who built GNU parallel but I owe them a beer

[@[email protected] GNU Parallel @GNU_Parallel]

@h4x0r1ng @oletange is not much of a beer drinker.

But lets meet up next time you are in Copenhagen.

[@[email protected] GNU Parallel @GNU_Parallel]

@diizuka Maybe post a minimal reproducible example?

https://t.co/iu0j9BFwD6

[Ming "Tommy" Tang @tangming2005]

🧵Want to speed up your bioinformatics tasks?

Stop looping. Start paralleling.

Here’s how to use GNU parallel like a pro:

[@[email protected] GNU Parallel @GNU_Parallel]

New release of #GNU Parallel https://t.co/kA6zMCqLfa
New in this release https://t.co/FbZhTpFFc0
See the intro videos https://t.co/x8Rzap1o2I
10 secs installation: https://t.co/hW0YTAp83H

GNU Parallel - for people who live life in the parallel lane.

[Daisuke Iizuka @diizuka]

64コアで、64並列でsimlationを回してtopコマンドで状況を見るのは心地よい。簡単に並列処理を実現できるGNU parallelコマンドは素晴らしい。

[vik @vikhyatk]

Have you said thank you to the author of GNU Parallel?

[@[email protected] GNU Parallel @GNU_Parallel]

@do_su_0805 @yoshihisa_ya Maybe you never saw the cheat sheet: https://t.co/6drVkqFbPC

[@[email protected] GNU Parallel @GNU_Parallel]

@tangming2005 Personally I prefer computing the R2 name from the R1 name. This way if one is missing thing are not messed up.

parallel -j 4 "bwa mem ref.fa {} {=s/_R1/_R2/=} > {/.}.sam" ::: *_R1.fastq

[@[email protected] GNU Parallel @GNU_Parallel]

@tangming2005 Almost: The above will run all combinations. That is not what you want. You want the 4th R1.fq to be run with the 4th R2.fq. So add a +

parallel -j 4 "bwa mem ref.fa {1} {2} > {1/.}.sam" ::: *_R1.fastq :::+ *_R2.fastq

>>

[Ming "Tommy" Tang @tangming2005]

5/ What Does GNU parallel Do?
Unlike xargs, parallel intelligently distributes tasks across available CPU cores.
📌 Example: Run bwa mem on multiple samples in parallel
ls *.fastq | parallel -j 8 "bwa mem ref.fa {} > {.}.sam"

[데자와 @tea___aet]

@wildcalla_ 방법이있습니다.
gnu_parallel이라고 얘를쓰면 얘가 순차적으로 계산을 던집니다 그니까
예를들어 4노드 잡고 gnu_parallel써서 60개 돌린다하면
처음에 설정대로 각노드당 1개씩 4개잡돌다가 하나끝나면 다음거 자동으로돌리고...
뭐 job script 안에 그냥 런을 1000개씩넣는방법도있죠

[fae-leen @daemon_tears]

te amo gnu parallel

[たらたら @nosennyuu]

gnu parallelすごい！！！
めっちゃ捗るやん
メモリ12GBの限界に挑戦www