search

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
Other
520 stars 111 forks source link

segalign didn't run with --gpu option #607

Open lizihe21 opened 2 years ago

lizihe21 commented 2 years ago

Hi, i was testing cactus on 4 gpus 64 cores single machine. After cactus finished on the example dataset, I checked the log and found that only segalign_repeatmasker was called. There was no segalign in the log. Is there anything wrong with my config? Here is my command and log file is attached: cactus ./jobstore ./evolverMammals.txt ./evolverMammals.hal --realTimeLogging --workDir=./log --binariesMode local --gp cactuslog.txt best with you

glennhickey commented 2 years ago

Good catch. This will be fixed in the next release. In the meantime, you can work around it by:

sed src/cactus/cactus_progressive_config.xml -e  's/gpuLastz="false"/gpuLastz="true"/g' > ./config-gpu.xml

then running with --configFile ./config-gpu.xml

Note: this bug only affects cactus and not cactus-blast, nor should it be an issue when using the GPU docker image.