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This happens after 3-4 days of running the server, then I have to restart it manually.
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Seen this before, and almost always has to do with hardware failure or bad hardware config.
Reset the BIOS/CMOS jumper on the board, go back into BIOS setup and set the proper time. Do not touch the CPU or Memory timings. Boot with the defaults and see if it still happens. Check and update the BIOS if there is a newer version as well.
Next longer steps: test memory, then stress test the CPU. I'd be shocked if it was a storage issue as I haven't seen that be the culprit, but might was well run the long SMART tests.
Make sure the microcode package is up to date as well
Yeah, always check all of this stuff. Server hardware gets a lot more updates than like gamer board BIOS, companies invest high millions, even low billions in this stuff and they expect problems to be address promptly for that kind of cash.
Check for any peripherals or cards, too. RAID, backplanes, networking cards; drivers, firmware, anything.
Poorly supported hardware will also do this
An Optiplex 5040 should be well and thoroughly supported for 6+y now
I did reset it. It did not help. I ran memtest86 for over 2 hours and did a CPU stress test for over 15 hours. Nothing crashed during the testing.