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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Maxcore did not work #1315

Closed gotouerina closed 4 months ago

gotouerina commented 6 months ago

Hi I used 7 genome for cactus alignment.

I set --maxCore = 224 and --defaultcore = 200

but it only used about 10 core .

what should I do to use all cores?

glennhickey commented 6 months ago

don't set --defaultcore

gotouerina commented 6 months ago

I did not set --defaultcore but it did not works

I use docker image version 2.8.0

gotouerina commented 6 months ago

I meet a new problem, the restart did not work and the cactus did not continue to work, what did this happen?

gotouerina commented 6 months ago

[2024-03-20T11:12:19+0000] [MainThread] [I] [toil.statsAndLogging] Enabling realtime logging in Toil
[2024-03-20T11:12:19+0000] [MainThread] [W] [toil.lib.humanize] Deprecated toil method. Please use "toil.lib.conversions.human2bytes()" instead." [2024-03-20T11:12:19+0000] [MainThread] [W] [toil.lib.humanize] Deprecated toil method. Please use "toil.lib.conversions.human2bytes()" instead."
[2024-03-20T11:12:19+0000] [MainThread] [I] [toil.statsAndLogging] Cactus Command: /home/cactus/cactus_env/bin/cactus ./test species.tree3 test.hal --workDir ./ --targetTime 1000 --maxCores 150 --restart [2024-03-20T11:12:19+0000] [MainThread] [I] [toil.statsAndLogging] Cactus Commit: 7286b49b264896f43cc64aa405b39f914d43f75b

Then the work stop working. Does the restart would take longer than 1 hour ?

gotouerina commented 6 months ago

don't set --defaultcore

The max core only work in some process, but many process only use 8 CPU, Could this be improved?

gotouerina commented 4 months ago

Close for not responsible authors