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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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use available processor for process not all on host #349

Closed EricDeveaud closed 1 year ago

EricDeveaud commented 1 year ago

Hello

this PR fix probelem mentionned in https://github.com/voutcn/megahit/issues/338

some sample output of megahit in taskset environnement once applied

maestro-builder:megahit/test_data > megahit -t 12 -1 r3_1.fa  -2 r3_2.fa -o out 2>&1| grep  -e cpu -e thread 
2023-01-26 18:21:10 - Start assembly. Number of CPU threads 12

now run with 8 core constrain (using taskset)

maestro-builder:megahit/test_data > taskset -c 1-8 megahit -t 12 -1 r3_1.fa  -2 r3_2.fa -o out2 2>&1| grep  -e cpu -e thread
2023-01-26 18:21:47 - Maximum number of available CPU thread is 8.
2023-01-26 18:21:47 - Number of thread is reset to the 8.
2023-01-26 18:21:47 - Start assembly. Number of CPU threads 8

no diff in the results

maestro-builder:megahit/test_data > diff -q out/final.contigs.fa out2/final.contigs.fa 
maestro-builder:megahit/test_data > echo $?
0

regards

Eric