Investigating Network Data Copy Performance from Illumina Products on Linux OS
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Background
Networks may have sub-optimal network and storage performance despite operating under the recommended network speed specifications such as 1 Gigabit per second (Gbps) or 10 Gbps connections. This can be due to many factors that are hard to diagnose such as competing traffic, hardware reliability, etc.
Looking at the output of the ethtool command can be used to verify that the instrument has negotiated the correct connection speed. However, it does not provide any practical information about potential network storage hardware bottlenecks.
Troubleshooting actions
The best way to measure actual networkperformance is through empirical testing of write performance to the network storage location. This can be achieved through the following steps:
Minimize the Control Software and then open the Linux Operating System (OS) Terminal app.
For NextSeq 1000/2000, select the Applications menu, then the Terminal app.
For NovaSeq X Series, select the Activities menu and then open Terminal app.
Input the following command, then press Enter to run it:
dd if=/dev/zero of=/path/to/networked/storage/test.txt bs=1M count=1024 oflag=direct
This command will write a dummy file titled "test" using data from a special Linux drive "/dev/zero". The file is written using 1 Mb blocks, for a total of 1024 blocks, amounting to a total write of 1 Gb. The total number of blocks can be increased or decreased to adjust the file size.
The command requires that the network storage is mounted and is accessible through the Terminal.
For the NovaSeq X Series, see .
For the NextSeq 1000/2000, see .
The command returns the time taken to perform the write operation and the calculated data copy speed in Bytes/sec, which can be converted to bits/sec by multiplying this value by 8 bits/Byte.
Figure 1: Example using the dd command to test data copy speed to a network location.
Run the command several times to capture any variability in the network/storage performance.
When testing with the above method, it is important to note that it will not typically return the theoretical maximum speed. For example, a 10 GB switch may hit a maximum transfer speed of 6-7 Gb/s even under optimal conditions.
For recommended minimum network transfer speeds, see instrument-specific Site Preparation Guides.
For any feedback or questions regarding this article (Illumina Knowledge Article #8307), contact Illumina Technical Support .
