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viruses and protein complexes at molecular resolution. A rapid vitrification at cryogenic temperature is the key step to avoid water
molecule crystallization and forming amorphous solid that does almost no damage to the sample structure. Regular electron
microscopy requires samples to be prepared in complex ways, and the sample preparations make hard to retaining the original
molecular structures. Cryo-EM is not perfect like X-ray crystallography; however, it has quickly gained the popularity in the research
community due to the simple sample preparation steps and flexibility of the sample size, complexity, and non-rigid structure. As the
resolution revolution in Cryo-EM progresses due to the 40+ years of dedicated work from the structural biology community, we now can
yield accurate, detailed 3D models of intricate biological structures at the sub-cellular and molecular scales.
The tests were performed on 8 nodes of Dell PowerEdge C6420s which is a part of Dell EMC Ready Bundle for HPC Life Sciences.
Dell EMC PowerEdge C6420 shows that it is an ideal compute platform for the Optimized Relion. It scales well over various number of
compute nodes with Plasmodium ribosome data. In the future study, we plan to use a larger protein data and more compute nodes to
accomplish more comprehensive scaling tests.
CONCLUSION
Overall, 14th generation servers with Skylake and larger/faster memory size (due to higher number of memory channels compare with
Broadwell) show a better throughput on BWA-GATK pipeline. The throughput for this type of work improved from four 30x genomes per
day per C6320 to seven 30x genomes per day per C6420. Also, we verified that Dell EMC Isilon storage, F800 and H600, can be used
for high-performance scratch storage while they provide all the conveniences of easy maintenance, scaling, and various supported file
systems. In addition to that, we observed a better performance on Cryo-EM data process with Intel
®
’s optimized Relion codes.
Unfortunately, we could not test Dell EMC PowerEdge C4140 with NVIDIA
®
Tesla™ V100; however, the V100 with PowerEdge C4130
still shows impressive performance compared to P100. We believe the current version of Dell EMC Ready Bundle for HPC Life
Sciences is ready for data centric high-performance computing.
Figure 22 Optimized Relion Benchmark