Help with my Fujitsu server fans

[GhostRep]

Hi everyone,
I'm getting closer to joining the homelabber club as I've bought a Fujitsu Primergy TX1330 M2 with a E3 1270 v5 and 16GB of Ram for the low price of 100€.
However, I can barely keep it turned on! The main fan, properly connected to the FAN SYS 1 header as shown on the side panel, just goes max RPM all the time. It's unbearable. The CPU is chilling at 31°C, so it seems unreasonable to me that the main fan just goes as fast as possible. I've tried connecting it to other fan headers and it quiets down, so PWM seems like it's working. I've read here that a similar Fujitsu motherboard set the system fan to 100% when no ambient temperature sensor was recognized. However it seems like my system has got everything installed and opening up the side panel makes no difference whatsoever, apart from the event appearing in the event log.
Does anyone have a similar server and could please share their experience? It seems unlikely that Fujitsu would ship workstations configured like this.
The only thing that scratches my head is that the eBay seller was selling the chassis, CPU and RAM as separate listings, so there may be some missing cable here? Info on this particular system is quite scarce.
I will try installing Windows Server on it with drivers and all, and see how it goes.
Any help would be appreciated, I would love to start playing with Proxmox but I really cant keep it on for more than a few hours straight.
Regards
Gabriele

 

[GhostRep]

Installed Windows Server 2016 with the ServerView agent with no change to fan speed. I feel stuck.

 

[Stankyjawnz]

Do you have to connect it to the sys fan header? Are there other chassis fan headers that could be used? Did you check all bios options for fan control? Did you try logging in to IPMI to see if there is fan control?

Barring any of that you could replace the fan with one that has acceptable noise at 100% speed. There are many options for 120mm that are quiet. I have used nidec gentle typhoon but there are probably better ones now.

Dealing with fans is an essential home lab skill so do not give up

Edit: for some reason I assumed you were talking about a chassis fan. If it's the CPU fan, I would review your motherboard manual to see if there is a connector for a temperature sensor if you think that is the cause.

 

[GhostRep]

Do you have to connect it to the sys fan header? Are there other chassis fan headers that could be used? Did you check all bios options for fan control? Did you try logging in to IPMI to see if there is fan control?

Barring any of that you could replace the fan with one that has acceptable noise at 100% speed. There are many options for 120mm that are quiet. I have used nidec gentle typhoon but there are probably better ones now.

Dealing with fans is an essential home lab skill so do not give up

Edit: for some reason I assumed you were talking about a chassis fan. If it's the CPU fan, I would review your motherboard manual to see if there is a connector for a temperature sensor if you think that is the cause.

Thank for your kind response.
The Bios has only two options for fan control, Auto and Full, and I've already had it set to Auto. The single fan present in this system (not considering the PSU fan) cools both the CPU heatsink and the rest of the system thanks to a plastic shroud.
However digging deeper I found the spec sheet for the fan, a Delta QFR1212EHE, which states that it can reach up to 5k RPM. I tested it with the PWM pin removed from the connector and indeed it spun much faster (and even much louder). So the motherboard is already spinning it down, but it is not enough for me.
I therefore started to think about replacing it as you suggested. However even the best Noctua fans look like toys compared. The Delta can reach up to 21 mmH2O and 5 m3/min where a Noctua IndustrialPPC F12 3000 PWM can barely reach 3 m3/min and under 8 mmH2O, while making around 20dB less noise.
I will probably buy one anyway and see how it goes. HDD cage temperature is what mostly bothers me.

 

[Stankyjawnz]

Glad you figured it out. 20db is very significant. I think trying the 3000 rpm Noctua makes sense given its the only fan.

2000 rpm fans have even lower noise but I think the airflow is too low