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robpearc / DeepFoldRNA

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Request of CPU number option for MSA generation #5

Closed Shunsuke-1994 closed 11 months ago

Shunsuke-1994 commented 2 years ago

Hi! I really appreciate such a wonderful software! Could you prepare a option to increase or determine CPU number to generate MSA? It seems only 1 CPU is used during alignment and taking a bit long time per 1 seq.

Best regards, Shunsuke

holden-lyn commented 11 months ago

Hi, this seems to be a late comment and I hope it helps (or better not since you might have solved the problem).

Find "rMSA.pl" in path bin/rMSA/rMSA.pl, search for string "#### prepare secondary structure ####" and you will find the code determine the CPU number above the searched string.

I change it as below to allow using 1 CPU for every bp of RNA sequence and cap at 64 CPUs. This change works fine for me.

if ($cpu==0) { $cpu=int($Lch/1); $cpu=1 if ($cpu<1); $cpu=64 if ($cpu>64); } print "using $cpu cpu\n";

Shunsuke-1994 commented 11 months ago

Dear holden-lyn,

Thank you for your kind comment! I really appreciate your advice! Let me close this issue.

Shunsuke