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The results with Dell EMC Isilon F800 that indicate C6320 with Broadwell/128GB RAM performs roughly 50 genomes per day less
when 3 samples are processed per compute node and 30 genomes per day less when 2 samples are processed in each compute node
compared to C6420. It is not clear if C6320’s performance will drop again when more samples are added to each compute node;
however, it is obvious that C6420 does not show this behavior when the number of samples is increased on each compute node. The
results also allow estimating the maximum performance of Dell EMC Isilon F800. As the total number of genomes increases, the
increment of the number of genomes per day metric is slow down. Unfortunately, we were not able to identify the exact number of
C6420s that would saturate Dell EMC Isilon F800 with four nodes. However, it is safe to say that more than 64x C6420s will require
additional Dell EMC Isilon F800/H600 nodes to maintain high performance with more than 320 10x whole human genome samples. Dell
EMC Lustre Storage did not scale as well as Dell EMC Isilon F800/H600. However, we observed that some optimizations are
necessary to make Dell EMC Lustre Storage perform better. For example, the aligning, sorting, and marking duplicates steps in the
pipeline perform extremely well when the file system’s stripe size was set to 2MB while other steps perform very poorly with 2MB stripe
size. This suggests that Dell EMC Lustre Storage needs to be optimized further for these heterogeneous workloads in the pipeline.
Since there is not any concrete configuration for the pipeline, we will further investigate the idea of using multiple tier file systems to
cover different requirements in each step for both Dell EMC Isilon and Lustre Storage.
Dell EMC PowerEdge C6320 with Dell EMC Isilon H600 performance reached the maximum around 140 concurrent 10x human whole
genomes. Running three 10x samples concurrently on a single node is not ideal. This limit appears to be on the compute node side,
since H600 performance is much better with C6420s running a similar number of samples.
Conclusion
Dell EMC PowerEdge C6420 has at least a 12% performance gain compared to the previous generation. Each C6420 compute node
with 192 GB RAM can process about seven 10x whole human genomes per day. This number could be increased if the C6420
compute node is configured with more memory. In addition to the improvement on the 14G server side, four Isilon F800 nodes in a 4U
chassis can support 64x C6420s and 320 10x whole human genomes concurrently.
Resources
Internal web page
http://en.community.dell.com/techcent
er/blueprints/blueprint_for_hpc/m/medi
agallery/20442903
External web page
https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC3956068/
Contacts
Americas
Kihoon Yoon
Sr. Principal Systems Dev Eng
[e-mail]
[phone]
i
SNPs (pronounced “snips”) represent a difference in a single DNA.
ii
Indel is the addition or removal of a small number of consecutive nucleotides in a DNA sequence.
iii
Structural variation is genomic alterations that involves DNA segments larger than 1Killo base (Kb).
iv
All Dell EMC PowerEdge R730s were configured identically.