New blog post about Rosetta@home on RPi4

Author: diegorusso

_posts/2020-04-13-help-with-COVID-19-research-protein-folding-on-raspberry-pi4.md

@@ -0,0 +1,88 @@
+---
+title: Help with COVID-19 research - protein folding on Raspberry Pi4
+categories:
+- howto
+- english
+- personal
+tags:
+- covid19
+- raspberry
+- rosetta
+---
+
+Hello, it has been a while since I wrote here last time.
+
+Today I want to share with you something I've been doing in the last couple of
+days. The lock down measures for COVID-19 and some free time brought me to
+tinker a bit with my Raspberry Pi4.
+
+The project [Rosetta@home](https://boinc.bakerlab.org) allows people to give
+compute power to scientists for designing new proteins. The compute power could
+come from any device: a laptop, a desktop, a server and even a portable device.
+
+Recently I bumped into [the news of running Rosetta@home on aarch64 (arm64)](
+https://twitter.com/mininodes/status/1246091380507553792) hardware and,
+in my case, on my new and shiny Raspebrry Pi4.
+
+In theory what you need is:
+* An account on: [https://boinc.bakerlab.org](https://boinc.bakerlab.org)
+* A Raspberry Pi4
+* A 64-bit OS
+* The BOINC client
+```
+$ sudo apt-get update
+$ sudo apt-get install boinc-client boinctui
+```
+* The client configure with your email/password
+
+A good write-up could be found [here](
+https://www.mininodes.com/how-to-run-rosettahome-on-arm-powered-devices/)
+
+[![Protein Folding on Raspberry Pi4]({{site.url}}/assets/images/protein_folding_on_rpi4.png){: .align-center}]({{site.url}}/assets/images/protein_folding_on_rpi4.png)
+
+While I was setting it up I found few *"issues"*. Hopefully they could save you
+some time.
+
+**Rosetta doesn't work on Raspbian**  
+If you own a Raspberry Pi4, I'm sure you'll have a [Raspbian](
+https://www.raspberrypi.org/downloads/raspbian/) based system. It runs without
+any problem but unfortunately it is not suitable for running Rosetta@home.
+Although the hardware supports 64-bit, Raspbian is a 32-bit OS and this means
+it cannot run 64-bit applications.  
+**Solution: install a 64-bit distribution.**  
+Ubuntu officially supports Raspberry
+Pi4. Download the **64-bit** version from [here](
+https://ubuntu.com/download/raspberry-pi) or follow [this tutorial from
+Ubuntu](https://ubuntu.com/tutorials/how-to-install-ubuntu-on-your-raspberry-pi)
+I had issue with WiFi module hence reverted to wired connection!
+
+**The SD card is a bit slow.**  
+Although SD cards nowadays are fast, they are slower than HDD/SDD and when you
+run high I/O computations on them, they could fail fairly quick.  
+**Solution: move the root file system out from the SD card to an external hard
+disk.**  
+I had a 1TB portable one and it works like a charm.
+It's not that straightforward to move the root file system to an external disk
+but it's a doable. What you need is a [good guide](
+https://www.tomshardware.com/uk/news/boot-raspberry-pi-from-usb,39782.html)
+
+**The Pi4 is slow.**  
+Those are [the specs](
+https://www.raspberrypi.org/products/raspberry-pi-4-model-b/specifications/).
+As you can see it has 4 CPUs running at 1.5GHz. Not bad for a small board.  
+**Solution: overclock the CPU.**  
+Just follow [this tutorial](
+https://magpi.raspberrypi.org/articles/how-to-overclock-raspberry-pi-4).
+I did try to overclock it to 2GHz but it kept power cycling (likely due to
+power consumption) so **I stuck with 1.75GHz**.
+
+**High memory usage**  
+Even I have the 4GB version, I found the Raspberry Pi4 to be very unstable
+while doing computations. Memory is somehow limited and when processes use a
+large amount of it, the OOM killer could be invoked killing processes that
+make the system unstable.  
+**Solution: create a swapfile**  
+Like any other Linux distribution [create swap space](
+https://itsfoss.com/create-swap-file-linux/) to use part of the hard disk as
+_"extention"_ of the memory. I created a 4GB swap file and it seems working OK.
+