This question is for anyone on this who has experience running STAR on the EC2 instances.
We are using STAR (2.5.2a_modified) to align reads from a targeted library against a small pseudo-genome of 20,000 50 mers, on an Amazon EC2 instance (i3.8xlarge, optimized for IO, 32 Virtual Cores -AWS uses hyperthreading- and 244 GB RAM. The analyzer results are validated, and our next step is to optimize the application by reducing run-time (increasing Nthreads) or using incorporating the shared memory feature.
Does anyone understand how the EC2 hyperthreading impacts the STAR shared memory model? Would we gain any advantage using the genomeLoad options, which requires that we modify the system shared memory settings? On the EC2, does changing the shared memory blocks (in /etc/sysctl.conf) impact the system or have any effect on STAR?
Thanks in advance.