.s.GNU parallel, execution of commands from file few at a time

问题

I have a file called macse.cmd which contains 1000 commands to execute, 1 command per line.

I want to use parallel to execute 30 at a time. I don't care in what order they are executed as long as all are.

I tried "parallel -j 30 ./macse.cmd" but this caused them to run 1 by 1 and I am not even sure how to stop them.

Adrian

p.s.

Commands look like:

java -jar -Xmx5000m ~/programs/macse_v1.01b.jar -prog alignSequences -seq M715_2100035271/all_unaligned.fasta -out_NT M715_2100035271/aligned_nt.fasta -out_AA M715_2100035271/aligned_aa.fasta
java -jar -Xmx5000m ~/programs/macse_v1.01b.jar -prog alignSequences -seq M715_100078281/all_unaligned.fasta -out_NT M715_100078281/aligned_nt.fasta -out_AA M715_100078281/aligned_aa.fasta
java -jar -Xmx5000m ~/programs/macse_v1.01b.jar -prog alignSequences -seq M715_510001221/all_unaligned.fasta -out_NT M715_510001221/aligned_nt.fasta -out_AA M715_510001221/aligned_aa.fasta
java -jar -Xmx5000m ~/programs/macse_v1.01b.jar -prog alignSequences -seq M715_100094159/all_unaligned.fasta -out_NT M715_100094159/aligned_nt.fasta -out_AA M715_100094159/aligned_aa.fasta

So it's only the M715_ number that changes between commands.

回答1:

Is the command always the same? As in

echo "A"
echo "B"
echo "C"

?

Then you should change it to:

"A"
"B"
"C"

and run: parallel -j 30 -a macse.cmd echo where of course echo is your actuall command.

回答2:

parallel -j 30 < ./macse.cmd

or:

parallel java -jar -Xmx5000m ~/programs/macse_v1.01b.jar -prog alignSequences -seq {}/all_unaligned.fasta -out_NT {}/aligned_nt.fasta -out_AA {}/aligned_aa.fasta ::: M*/

Walk through the tutorial:

man parallel_tutorial

来源：https://stackoverflow.com/questions/28072857/s-gnu-parallel-execution-of-commands-from-file-few-at-a-time