A customer involved in research on developmental biology asked us for a Linux machine that can perform a series of data analyzes (preprocessing, mapping, DEGs calculation, etc.) on rice transcriptome and genome data without complaint.
Your requirements are as follows.
・CPU: CPU with 24 cores and 48 threads or more |
The transcriptome analysis of rice is approximately 1 Gbp in size, and the whole genome resequencing analysis is approximately 10 Gbp in size.
During the examination, we asked questions and consulted on the following two points.
・The CPU is assumed to be Xeon, but how should performance and cost be considered compared to AMD Threadripper? ・The OS is scheduled to be Ubuntu or Rocky Linux, but which distribution is suitable for Linux beginners? |
Based on the above information, we would like to propose a budget of 90 yen or less.
Based on the information you provided, we proposed the following configuration.
【Main Specifications】
CPU | Xeon Silver 4310 (2.10GHz 12 cores) x2 |
memory | 256GB REG ECC |
storage | 1TB SSD S-ATA |
video | Nvidia T400 |
network | On Board (1000Base-T X2) |
Housing + power supply | Tower type housing + 850W |
OS | Ubuntu 22.04 |
With a 3 CPU configuration equipped with 2rd generation Xeon Scalable, the system has a total of 24 cores/48 threads.
■ Storage Although the genome size of rice is not that large compared to that of humans, the volume of analysis data is considered to be quite large.In this case, we have heard that the customer will prepare an external storage for data storage, but if you are using only the PC itself, we recommend that you install a storage for data. |
■ CPU When comparing 24-core Xeon and Threadripper PRO, Threadripper PRO is superior in terms of performance. Since the number of CPU cores and memory capacity is important for next-generation sequencer analysis, it is not very effective to increase the calculation speed by reducing the number of cores and focusing on the clock.Therefore, even if the single-core performance is somewhat low, please think that it is desirable to give priority to the configuration that can secure the number of cores. |
■OS When it comes to OS, Rocky Linux is less flexible than Ubuntu. Rocky Linux is based on RHEL, which puts long-term operational stability first. If you don't have a strong reason to choose Rocky Linux, we recommend Ubuntu. |
The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.
■FAQ・What is transcriptome analysis?
・What is Ubuntu? reference:Ubuntu (Ubuntu Japanese Team) *Jumps to an external site
・What is Rocky Linux? reference:Rocky Linux (Rocky Enterprise Software Foundation) *Jumps to an external site
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