Tools and Utilities
Monitoring System Health
When DRAGEN runs, a daemon dragend
is started that communicates with the FPGA card.
This daemon will monitor FPGA temperature while DRAGEN is running and abort
DRAGEN when the temperature exceeds a configured threshold.
To display the current temperature of the DRAGEN server FPGA, use the dragen_info -t command.
Logging
All hardware events are logged to /var/log/messages and /var/log/dragen_mond.log. The following shows an example in /var/log/messages of a temperature alarm:
By default, temperature is logged to /var/log/dragen_mond.log every hour:
If DRAGEN is executing when a thermal alarm is detected, the following is displayed in the terminal window of the DRAGEN process:
If you see this message, stop running the DRAGEN software. Do the following to alleviate the overheating condition on the card:
Be sure that there is ample air flow over the card. Consider moving the card to a slot where there is more air flow, adding another fan or increasing the fan speed.
Give the card more space in the box. If there are available PCIe slots, move the card so that it has empty slots on either side.
Contact Illumina Technical Support if you are having trouble resolving the thermal alarm on your system.
Hardware Alarms
The following table lists the hardware events logged by the monitor when an alarm is triggered:
0
Software overheating
Terminate usage until DRAGEN server FPGA cools to software minimum temperature.
1
Hardware overheating
Fatal. Aborts dragen software; system reboot required
2
Board SPD overheating
Logged as nonfatal
3
SODIMM overheating
Logged as nonfatal
4
Power 0
Fatal. Aborts dragen software; system reboot required
5
Power 1
Fatal. Aborts dragen software; system reboot required
6
DRAGEN server FPGA power
Logged as nonfatal
7
Fan 0
Logged as nonfatal
8
Fan 1
Logged as nonfatal
9
SE5338
Fatal. Aborts dragen software; system reboot required
10--30
Undefined (Reserved)
Fatal. Aborts dragen software; system reboot required
Fatal alarms prevent the DRAGEN host software from running and require a system reboot. When a software overheating alarm is triggered, the monitor looks for and aborts any running DRAGEN processes. The monitor continues to abort any new DRAGEN processes until the temperature decreases to the minimum threshold and the hardware clears the chip status alarm. When the software overheating alarm clears, DRAGEN jobs can resume executing.
Contact Illumina Technical Support with details from the log files if any of these alarms are triggered on your system.
Hardware-Accelerated Compression and Decompression
Gzip compression is ubiquitous in bioinformatics. FASTQ files are often gzipped, and the BAM format itself is a specialized version of gzip. For that reason, DRAGEN provides hardware support for accelerating compression and decompression of gzipped data. If your input files are gzipped, DRAGEN detects that and decompresses the files automatically. If your output is BAM files, then the files are automatically compressed.
DRAGEN provides standalone command-line utilities to enable you to compress or decompress arbitrary files. These utilities are analogous to the Linux gzip and gunzip commands, but are named dzip and dunzip (dragen zip and dragen unzip). Both utilities are able to accept as input a single file, and produce a single output file with the .gz file extension removed or added, as appropriate. For example:
Currently, dzip and dunzip have the following limitations and differences from gzip/gunzip:
Each invocation of these tools can handle only a single file. Additional file names (including those produced by a wildcard * character) are ignored.
They cannot be run at the same time as the DRAGEN host software.
They do not support the command line options found in gzip and gunzip (eg, --recursive, --fast, ‑‑best, ‑‑stdout).
Licensing and Usage
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