A way to speed up Repeatmodeler

Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool

Other

182 stars 23 forks source link

A way to speed up Repeatmodeler #184

Closed yangfangyuan0102 closed 1 year ago

yangfangyuan0102 commented 1 year ago

For users with enough memory, maybe we can improve the running speed by mounting RAM as a virtual disk, or directly run repeatmodeler in the tmpfs filesystem (the RAM) directory (e.g. "/dev/shm" in most Linux). Use commond df to show the existing tmpfs directory, or mount a new "tmpfs" directory using: sudo mount - t tmpfs - o size=20g tmpfs ./work_dir Shutdown or umount will cause file loss. Remember to copy the file out when finished.

Best Fangyuan Yang

rmhubley commented 1 year ago

RepeatModeler runtimes are improved by faster I/O rates (local HDs, SSDs, RAM disks etc). This is a good suggestion for those with enough RAM on their machine.