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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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Running Cactus on AWS - Memory Issue #1322

Open tinaveit opened 8 months ago

tinaveit commented 8 months ago

Hi @glennhickey! Following up with: https://github.com/DataBiosphere/toil/issues/4773

I ran cactus with the following command-line for 2 species (following your suggestions from the previous thread), and it worked successfully:

cactus --consCores 32 --nodeTypes c4.8xlarge,r4.8xlarge --minNodes 0,0 --maxNodes 20,1 --nodeStorage 250 --provisioner aws --batchSystem mesos --metrics aws:us-east-1:xtremo-devo-cactus --defaultMemory 2000000000 --maxMemory 256000000000  --logFile cactus.log seqFile.txt output.hal

However, when I used the same command line to run 8 species, the cactus run crashed at the beginning and produced the attached cactus.log. It looks like a memory issue, but I am not quite sure how to solve it. Any help is appreciated!

Thanks! cactus.log

glennhickey commented 8 months ago

You need to stick to released versions of cactus. This could be the AWS documentation being a little dated (I think it tells you to clone the master branch). Your workaround is either