TY - GEN
T1 - A performance evaluation of sequence alignment software in virtualized environments
AU - Estrada, Zachary J.
AU - Stephens, Zachary
AU - Pham, Cuong
AU - Kalbarczyk, Zbigniew T
AU - Iyer, Ravishankar K
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2014
Y1 - 2014
N2 - The prospect of simpler infrastructure management and affordability has garnered interest in cloud computing from bioinformaticians. However, the performance cost of adopting such an infrastructure model for bioinformatics is not fully known. In an effort to help quantify this performance cost, we ran synthetic benchmarks and measured the runtimes of two short-read alignment applications on cloud-like virtualization environments. The environments were implemented utilizing the KVM hypervisor, the Xen hypervisor, and Linux Containers. We compare the runtime in each environment against a physical server and offer discussion and insights. Though the applications perform similar operations, we observe that their performance characteristics differ, as do their performance in the different virtualized environments. We attribute the differences to the way that these programs utilize system resources. We find that the more CPU-bound Novo align is much less sensitive to virtualization environments than BWA is, and has near-physical server performance even when virtualized. Additionally, we find that static CPU pinning can improve performance, and we demonstrate that Linux Containers offer performance comparable to that of a physical server.
AB - The prospect of simpler infrastructure management and affordability has garnered interest in cloud computing from bioinformaticians. However, the performance cost of adopting such an infrastructure model for bioinformatics is not fully known. In an effort to help quantify this performance cost, we ran synthetic benchmarks and measured the runtimes of two short-read alignment applications on cloud-like virtualization environments. The environments were implemented utilizing the KVM hypervisor, the Xen hypervisor, and Linux Containers. We compare the runtime in each environment against a physical server and offer discussion and insights. Though the applications perform similar operations, we observe that their performance characteristics differ, as do their performance in the different virtualized environments. We attribute the differences to the way that these programs utilize system resources. We find that the more CPU-bound Novo align is much less sensitive to virtualization environments than BWA is, and has near-physical server performance even when virtualized. Additionally, we find that static CPU pinning can improve performance, and we demonstrate that Linux Containers offer performance comparable to that of a physical server.
KW - KVM
KW - Linux containers
KW - Xen
KW - bioinformatics
KW - cloud computing
KW - container based virtualization
KW - genomics
KW - high performance computing
KW - sequence alignment
KW - virtualization
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U2 - 10.1109/CCGrid.2014.125
DO - 10.1109/CCGrid.2014.125
M3 - Conference contribution
AN - SCOPUS:84904559077
SN - 9781479927838
T3 - Proceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014
SP - 730
EP - 737
BT - Proceedings - 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2014
PB - IEEE Computer Society
T2 - 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGrid 2014
Y2 - 26 May 2014 through 29 May 2014
ER -