Folding@Home

Roger Cheng

Inviting My FreeNAS Box To The Folding Party

Once my Luggable PC Mark I was up and running, I have one more functional desktop-class CPU in my household that has not yet been drafted into my Folding@Home efforts: it was recently put in charge of running FreeNAS. As a network attached storage device, FreeNAS is focused on its main job of maintaining files and serving them on demand. There are FreeNAS plug-ins to add certain features, such as a home Plex server, but there’s no provision for running arbitrary programs on the FreeBSD-based task-specific appliance.

What FreeNAS does have is the ability to act as a host for separate virtual environments that run independently of core FreeNAS capability. This extension capability is a part of why I upgraded my FreeNAS box to more capable hardware. The lighter-weight mechanism is a “jail”, similar in concept to the Linux container (from which Docker was built) but for applications that can run under the FreeBSD operating system. However, Folding@Home has no native FreeBSD clients, so we can’t run it in a jail and have to fall back to plan B: full virtual machine under bhyve. This incurs more overhead as a virtual machine will need its own operating system instead of sharing the underlying FreeBSD infrastructure, consuming hard disk storage and locking away a portion of RAM unusable by FreeNAS.

But the overhead wasn’t too bad in this particular application. I installed the lightweight Ubuntu 18 server edition in my VM, and Folding@Home protein folding simulation is not a memory-intensive task. The VM consumed less than 10GB of hard drive space, and only 512MB of memory. In the interest of always reserving some processing power for FreeNAS, I only allocated 2 virtual CPUs to the folding VM. The Intel Core i3-4150 processor has four logical CPUs which are actually 2 physical cores with hyperthreading. Giving the folding simulation VM 2 virtual CPUs should allow it to run at full speed on the two physical CPUs and still leave some margin to keep FreeNAS responsive.

Once the VM was up and running, FreeNAS CPU usage report does show occasional workload pushing it above 50% (2 out of 4 logical CPU) load. CPU temperature also jumped up well above ambient temperature, to 60 degrees C. Since this Core i3 is far less powerful than the Core i5 in Luggable PC Mark I and II, it doesn’t generate as much heat to dissipate. I can hear the fan increased speed to keep temperature at 60 degrees, but the difference is minor relative to the other two.

Roger Cheng

Old AMD GPU for Folding@Home: Ubuntu Struggles, Windows Win

The ex-Luggable Mark II is up and running Folding@Home, chewing through work units quickly mostly thanks to its RTX 2070 GPU. An old Windows 8 convertible tablet/laptop is also up and running as fast as it can, though its best speed is far slower than the ex-Luggable. The next recruit for my folding army is Luggable PC Mark I, pulled out of the closet where it had been gathering dust.

My old AMD Radeon HD 7950 GPU was installed in Luggable PC Mark I. It is quite old now and AMD stopped releasing Ubuntu drivers after Ubuntu 14. Given its age I’m not sure if it even works for GPU folding workloads. It was designed and released near the dawn of the age when GPUs started finding work beyond rendering game screens, and its GCN1 architecture probably had problems typical of first versions of any technology.

Fortunately I also have an AMD Radeon R9 380 available. It was formerly in Luggable PC Mark II but during the luggable chassis decommissioning I retired it in favor of a NVIDIA RTX 2070. The R9 380 is a few years younger than the HD 7950, I know it supports OpenCL, and AMD has drivers for Ubuntu 18.

A few minutes of wrenching removed the HD 7950 from Luggable Mark I, putting the R9 380 in its place, and I started working out how to install those AMD Ubuntu drivers. According to this page, the “All-Open stack” is recommended for consumer products, which I mean to include my consumer-level R9 380 card. So the first pass started by running amdgpu-install. To verify OpenCL is up and running, I installed clinfo to verify GPU is visible as OpenCL device.

Number of platforms 0

Hmm. That didn’t work. On advice of this page on Folding@Home forums, I also ran sudo apt install ocl-icd-opencl-dev That had no effect, so I went back to reread the instructions. This time I noticed the feature breakdown chart between “All-Open” and “Pro” and OpenCL is listed as a “Pro” only feature.

So I uninstalled “All-Open” and installed “Pro” stack. Once installed and rebooted, clinfo still showed zero platforms. Returning to the manual, on a different page I found the fine print saying OpenCL is an optional component of the Pro stack. So I reinstalled yet again, this time with --opencl=pal,legacy flag.

Running clinfo now returns:

Number of platforms 1
Platform Name AMD Accelerated Parallel Processing
Platform Vendor Advanced Micro Devices, Inc.
Platform Version OpenCL 2.1 AMD-APP (3004.6)
Platform Profile FULL_PROFILE
Platform Extensions cl_khr_icd cl_amd_event_callback cl_amd_offline_devices
Platform Host timer resolution 1ns
Platform Extensions function suffix AMD

Platform Name AMD Accelerated Parallel Processing
Number of devices 0

NULL platform behavior
clGetPlatformInfo(NULL, CL_PLATFORM_NAME, ...) No platform
clGetDeviceIDs(NULL, CL_DEVICE_TYPE_ALL, ...) No platform
clCreateContext(NULL, ...) [default] No platform
clCreateContext(NULL, ...) [other] <error: no devices in non-default plaforms>
clCreateContextFromType(NULL, CL_DEVICE_TYPE_DEFAULT) No devices found in platform
clCreateContextFromType(NULL, CL_DEVICE_TYPE_CPU) No devices found in platform
clCreateContextFromType(NULL, CL_DEVICE_TYPE_GPU) No devices found in platform
clCreateContextFromType(NULL, CL_DEVICE_TYPE_ACCELERATOR) No devices found in platform
clCreateContextFromType(NULL, CL_DEVICE_TYPE_CUSTOM) No devices found in platform
clCreateContextFromType(NULL, CL_DEVICE_TYPE_ALL) No devices found in platform

Finally, some progress. This is better than before, but zero devices is not good. Back to the overview page which says their PAL OpenCL stack supported their Vega 10 and later GPUs. My R9 380 is from their Tonga GCN 3 line, which is quite a bit older than Vega, which is GCN 5. So I’ll reinstall with --opencl=legacy to see if it makes a difference.

It did not. clinfo still reports zero OpenCL devices. AMD’s GPU compute initiative is called ROCm or RadeonOpenCompute but it is restricted to hardware newer than what I have on hand. Getting OpenCL up and running, on Ubuntu, on hardware this old, is out of scope for attention from AMD.

This was the point where I decided I was tired of this Ubuntu driver dance. I wiped the system drive to replace Ubuntu with Windows 10 along with AMD Windows drivers. Folding@Home saw the R9 380 as a GPU compute slot, and I was up and running simulating protein folding. The Windows driver also claimed to support my older 7950, so one potential future project would be to put both of these AMD GPUs in a single system. See if the driver support extends to GPU compute for multi GPU folding.

For today I’m content to have just my R9 380 running on Windows. Ubuntu may have struck out on this particular GPU compute project, but it works well for CPU compute, especially virtual machines.

Roger Cheng

Naked HP Split X2 (13-r010dx) Sitting In A Breeze Runs Faster

Mobile computer processors must operate within tighter constraints than their desktop counterparts. They sip power to prolong battery life, and that power also eventually ends up as heat that must be dissipated. Unfortunately both heat management mechanisms and batteries are heavy and take up space, so finding the proper balance is always a difficult challenge. It is typical for laptop computers to give up its ability to run sustained workloads at full speed. But if we’re not worried about voiding warranties or otherwise rendering a mobile computer immobile, we can lift some of those constraints limiting full performance: run on an AC adapter to provide power, and get creative on ways to enhance heat dissipation.

For this experiment I pulled out the most powerful computer from my NUCC trio of research project machines, the HP Split X2 (13-r010dx). The goal is to see if I can add it to my Folding@Home pool. Looking over the technical specifications published by Intel for Core i3-4012Y CPU, one detail caught my eye: it lists two separate power consumption numbers where most processors only have one. The typically quoted “Thermal Design Power” figure is at 11.5W, but this chip has an additional “Scenario Design Power” of 4.5W. This tells us the processor is designed for computers that only expect to run in short bursts. So even if TDP is 11.5W, it valid to design a system with only 4.5W of heat dissipation.

Which is likely the case here, as I found no active cooling on this HP Split X2. The outer case is entirely plastic meaning it doesn’t even have great thermal conduction to the environment. If I put a sustained workload on this computer, I expect it to run for a while and then start slowing itself down to keep the heat manageable. Which is indeed what happened: after a few minutes of Folding@Home, the CPU clock cycle pulled back to roughly half, and utilization was pulled back half again meaning the processor is chugging along at only about a quarter of its maximum capability.

HP Split X2 13-r010dx thermal throttling

For more performance, let’s help that heat escape. Just as I did earlier, I pulled the core out of its white plastic case. This time for better ventilation rather than just curiosity.

HP Split X2 13-r010dx tablet internals removed from case

Removing it from its plastic enclosure helped only a tiny bit. Most of the generated heat are still trapped inside, so I pulled the metal shield off its main processor board. This exposed the slab of copper acting as CPU heat sink.

HP Split X2 13-r010dx CPU heat sink under shield

Exposing that heat sink to ambient air helped a lot more, but passive convection cooling is still not quite enough. The final push was to introduce some active airflow. I was contemplating several different ideas on how to jury-rig an active cooling fan, but this low power processor didn’t actually need very much. All I had to do is to set the computer down in the exhaust fan airflow from a PC tower case. That was enough for it to quickly climb back up to full 1.5 GHz clock speed with 100% utilization, and sustain running at that rate.HP Split X2 13-r010dx receiving cooling

It’s not much, but it is contributing. I can leave it simulating folding proteins and move on to another computer: my Luggable PC Mark I.

Roger Cheng

Desktop PC Component Advantage: Sustained Performance

A few weeks ago I decommissioned Luggable PC Mark II and the components were installed into a standard desktop tower case. Heeding Hackaday’s call for donating computing power to Folding@Home, I enlisted my machines into the effort and set up my own little folding farm. This activity highlighted a big difference between desktop and laptop components: their ability to sustain peak performance.

My direct comparison is between my ex-Luggable PC Mark II and the Dell laptop that replaced it for my mobile computing needs. Working all out folding proteins, both of those computers heated up. Cooling fans of my ex-Luggable sped up to a mild whir, the volume and pitch of the sound roughly analogous to my microwave oven. The laptop fans, however, spun up to a piercing screech whose volume and pitch is roughly analogous to a handheld vacuum cleaner. The resemblance is probably not a coincidence, as both move a lot of air through a small space.

The reasoning is quite obvious when we compare the cooling solution of a desktop Intel processor against one for a mobile Intel processor. (Since my active-duty machines are busy working, I pulled out some old dead parts for the comparison picture above.) Laptop engineers are very clever with their use of heat pipes and other tricks of heat management, but at the end of the day we’re dealing with the laws of physics. We need surface area to transfer heat to air, and a desktop processor HSF (heat sink + fan) has tremendously more of it. When workload is light, laptops keep their fans off for silent operation whereas desktop fans tend to run even when lightly loaded. However, when the going gets rough, the smaller physical volume and surface area of laptop cooling solutions struggle.

This is also the reason why different laptop computers with nearly identical technical specifications can perform wildly differently. When I bought my Inspiron 7577, I noticed that there was a close relative in Dell’s Alienware line that has the same CPU and GPU. I decided against it as it cost a lot more money. Some of that is branding, I’m sure, but I expect part of it goes to more effective heat removal designs.

Since I didn’t buy the Alienware, I will never know if it would have been quieter running Folding@Home. To the credit of this Inspiron, that noisy cooling did keep its i5-7300HQ CPU at a consistent 3.08GHz with all four cores running full tilt. I had expected thermal throttling to force the CPU to drop to a lower speed, as is typical of laptops, so the fact this machine can sustain such performance was a pleasant surprise. I appreciate the capability but that noise got to be too much… when I’m working on my computer I need to be able to hear myself think! So while the ex-Luggable continued to crunch through protein simulations, the 7577 had to drop out. I switched my laptop to the “Finish” option where it completed the given work unit overnight (when I’m not sitting next to it) and fetched no more work.

This experience taught me one point in favor of a potential future Luggable PC Mark III: the ability to run high performance workloads on a sustained basis without punishing hearing of everyone nearby. But this doesn’t mean mobile oriented processors are hopeless. They are actually a lot of fun to hack, especially if an old retired laptop doesn’t need to be mobile anymore.