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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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maxMemory problems #1152

Open shuifeng1988 opened 10 months ago

shuifeng1988 commented 10 months ago

I run quay.io/comparative-genomics-toolkit/cactus:v2.6.7-gpu in our server， our server has 384G memory and 4 Tesla V100 GPUs. So I set --maxMemory=300G, howerver it prompts momoery not enough, "The job 'cactus_cons' kind-cactus_cons/instance-_tlpq4of v1 is requesting 404642332672 bytes of memory, more than the maximum of 300000000000 bytes of memory that SingleMachineBatchSystem was configured with, or enforced by --maxMemory. Scale is set to 1.0.". I have set the --maxMomery, why it still has maxMomery error? I also want to know how many memeory, disk and time is need for aligning 4 mammals using 3 Tesla V100 GPUs and 360G memory (for testing)? what's about 137 mammals?

#######################################my commands for aligning 4 mammals for testing): step 1: docker run -p 9001:22 --gpus='"device=0,1,2"' --name cactus -v /gpfs/home/mays/MGA_cactus/test.docker.gpu:/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7-gpu /bin/bash step 2: mkdir tmp step 3: cactus /data/jobStore /data/tree_sequence_info /data/evolverMammals.hal --maxCores 28 --maxMemory 300G --maxDisk 3000G --maxJobDuration 20000000 --writeLogs LOGS --workDir=/data/tmp 1>stdout 2>stderr

logs for cactus: stderr.cactus.txt

In addition, i also used this image to convert hal to maf. It also prompts memory not enough, "InsufficientSystemResources: The job 'hal2maf_batch' kind-hal2maf_batch/instance-tsamre1o v1 is requesting 733836560632 bytes of memory, more than the maximum of 220000000000 bytes of memory that SingleMachineBatchSystem was configured with, or enforced by --maxMemory. Scale is set to 1.0". what's the problem? --maxMomery is not working? #################################commands for cactus-hal2maf step 1: docker run -p 9001:22 --gpus='"device=0,1,2"' --name cactus -v /gpfs/home/mays/MGA_cactus/test.docker.gpu:/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7-gpu /bin/bash step 2: mkdir tmp step3: cactus-hal2maf --maxDisk=10T --workDir=/data/tmp --maxMemory=220G ./js ./241-mammalian-2020v2.hal Fruitbat.maf.gz --refGenome Pteropus_alecto --chunkSize 1000000 --noAncestors 1>&2 2>stderr.fruibat

logs for cactus-hal2maf

stderr.fruitbat.txt

glennhickey commented 10 months ago

--maxMemory doesn't do anything. You can try to set --consMemory for your first error (see last question in FAQ) and --batchMemory for the second.