Level1 Techs Folding@Home Team

bedHedd · March 17, 2020, 1:25am

how do I make sure I don’t break compatibility with other python applications, because I use python for jupyter notebook

mihawk90 · March 17, 2020, 1:25am

No need to. See edit in the initial post. Just editing the desktop file is enough.
Most launchers on Linux you can just right click the application > edit properties (or similar) and change it. That’ll also take care of copying the desktop file to your user directory.

Doesn’t require root ad opposed to editing the executable.

mihawk90 · March 17, 2020, 1:26am

The change is only for this application. Your system Python will still be symlinked to Python 3.

draeh · March 17, 2020, 1:39am

I’m suggesting to only edit /usr/bin/FAHControl so that it will explicitly use python 2.

Or you can explicitly start FAHControl with python 2 manually by issuing the following at the command line:

python2 /usr/bin/FAHControl

This will start python 2 and pass it FAHControl to run.

draeh · March 17, 2020, 1:42am

This is probably the best way to go about it.

COGlory · March 17, 2020, 2:21am

For people getting this error, I highly recommend checking out FoldIt as well, if you have the time to devote and want to participate:

Summary

Design a protein to inhibit Coronavirus

As an aside, if anyone has any questions about Coronavirus or proteins in general, I’m a PhD student studying virology and structural biology at a public university in Montana.

F@H has helped understand protein folding, and how it works. It’s helped develop tons of models and algorithms that we use every day. Has it been the single breakthrough in a single advancement? Unfortunately, no, but it’s certainly helped in many.

To date, it’s been cited as a tool in 223 scientific publications. Places where indirect contributions from F@H have been made are things like testing interactions in silico, as well as expanding the dataset for molecular replacement of x-ray models of proteins. Advancements in molecular replacement (essentially just finding similar protein models that you can then take an x-ray of a new, unknown protein, and compare to to figure out its structure) have shortened the amount of time to crystallize a new protein from years to months.

CybeastRaystriker · March 17, 2020, 3:34am

Yeah I read that too. I guess what I was asking was a clear cut answer whether something F@H exclusively processed to find a cure for xyz disease.

SgtAwesomesauce · March 17, 2020, 3:48am

Okay, so I’ve got a question. Is anyone successfully using fahcontrol on Ubuntu 19.10? I couldn’t get it to install due to packages.

I’d like to contribute to the science with my gpus, but I’m not able to get the system up and running.

bedHedd · March 17, 2020, 4:42am

I am getting this wierd error

sudo python2 /usr/bin/FAHControl                                                                                                                                                                  (base) 
Traceback (most recent call last):
  File "/usr/bin/FAHControl", line 25, in <module>
    from fah import FAHControl, load_fahcontrol_db
  File "/usr/lib/python2.7/site-packages/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/__init__.py", line 27, in <module>
    from ClientConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/ClientConfig.py", line 29, in <module>
    from fah import SlotConfig
ImportError: cannot import name SlotConfig

mihawk90 · March 17, 2020, 7:24am

Why are you using sudo exactly?

bedHedd · March 17, 2020, 4:59pm

I thought the folder had a read-only marker.

Running the command without sudo gave the same error

python2 /usr/bin/FAHControl                                                                                                                                                                  (base)       (base) 
fish: base: command not found...
in command substitution
	called on standard input

Traceback (most recent call last):
  File "/usr/bin/FAHControl", line 25, in <module>
    from fah import FAHControl, load_fahcontrol_db
  File "/usr/lib/python2.7/site-packages/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/fah/__init__.py", line 26, in <module>
    from SlotConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/fah/SlotConfig.py", line 23, in <module>
    from fah.util import parse_bool
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/fah/fah/__init__.py", line 27, in <module>
    from ClientConfig import *
  File "/usr/lib/python2.7/site-packages/fah/fah/fah/fah/fah/fah/ClientConfig.py", line 29, in <module>
    from fah import SlotConfig
ImportError: cannot import name SlotConfig

bedHedd · March 17, 2020, 9:18pm

I ended up using windows, I am live streaming it right now

getting an error of

21:19:30:WU01:FS01:0x21:Completed 1750000 out of 25000000 steps (7%)
21:19:36:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:19:52:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:20:08:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:20:24:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:20:39:WU00:FS00:0xa7:Completed 6250 out of 125000 steps (5%)
21:20:40:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:20:56:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:21:12:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:21:28:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.
21:21:44:ERROR:Receive error: 10053: An established connection was aborted by the software in your host machine.

Eden · March 17, 2020, 9:28pm

Could it be because they’re stuffs all broken.

https://foldingforum.org/viewtopic.php?f=24&t=32424

their teams pages dont work either, just get bad gateway errors

bedHedd · March 17, 2020, 9:29pm

I am not sure, it’s wierd because my cpu and gpu fans are cranked up, but the visualization is stuck on demo

Eden · March 17, 2020, 9:30pm

Is the team number still: 232084

bedHedd · March 17, 2020, 9:30pm

That’s what I put

Eden · March 17, 2020, 9:36pm

Im waiting out the could not get assignment errors.

Now its working

Eden · March 17, 2020, 9:44pm

How do I choose to help with the COVID-19 related projects ?
To help in the fight against COVID-19, you need to select

Webcontrol : “Any disease” in the list “I support research fighting”

Advanced Control/FAHControl : Configure > Advanced, select “Any” in the list “Cause Preference”
The COVID-19 related projects are on top priority and will be assigned automatically.

Can I choose to work only on the COVID-19 related projects ?
No, you can’t.
In FoldingHome, you never choose to work on only one project (or family of projects). The setting described above is a preference, but if no work is available to match your preferences, the system is designed to send you what need to be done at the time of your work request.

Is my system able to help ?
There are WU available for both GPUs and CPUs. Folding@Home supports nVidia and AMD GPUs through OpenCL on Windows and Linux.
The CPUs are supported on Windows, Linux and MacOS.

My GPU is supported, but it not detected.
You need to update your drivers with the latest ones downloaded from nVidia or AMD website.
Windows Updates often breaks OpenCL support when it updates the drivers automatically. To fix it, reinstall the drivers you downloaded from nVidia or AMD website.
On Linux, in addition to the proprietary drivers from the GPU maker, you may have to manually install “opencl-icd” matching with the drivers you installed.

Can you add an option to the list of causes to specifically support COVID-19 ?
No the categories are currently hard coded. We are now in the end of the development of a new client.

How do I know that I’m working on COVID-19 related projects ?
If you’re running a project that’s listed here, you’re fighting COVID-19 :
CPU : 14328 - 14329 - 14530 - 14531
GPU : 11741 to 11764

https://foldingforum.org/viewtopic.php?f=24&t=32463

rbtoj · March 18, 2020, 3:28am

The visualization stuck on demo is a known bug. If you open the control interface and see progress, then you are folding ok.

COGlory · March 18, 2020, 3:31am

I wrote a post about how computers help fight Coronavirus, if anyone is interested:

How computers help fight Coronavirus (and other biological problems) Science, Engineering, & Tech

Hi everyone, I’m a PhD virology student working in a structural biology lab at a well-funded public university in Montana, not too far from Rocky Mountain National Labs. I don’t study Coronavirus (although I’m very familiar with it), but rather an obscure virus known as Sulfolobus turreted icosahedral virus (STIV), that infects Archaea (single cellular organisms with similar morphology to bacteria). I also do a decent amount of molecular biology, and macromolecular structure work, including X-ray crystallography, and Cryo-Electron Microscopy. In this work, we use some ridiculously powerful computers, both on-site and remote, and most of our work is done in Linux as well. Because of the huge influx of interest in Folding@Home, I thought I’d highlight how computers help us structural biologists figure out lots of different things. Why is it important that we know the structure of biological macromolecules? Learning mechanisms. The biggest discovery of the 20th century is often argued to be the structure of DNA, because it allowed us to determine how genetic code was made. Virtually all biological and medical achievements since the discovery are reliant on DNA manipulation at some point. Knowing what DNA looks like, and how it’s held together made it possible to manipulate. The same goes for many proteins. Learning how they work can direct us into modifying them, or can shed light on entire metabolic pathways. Drug design. Traditionally, drugs were primarily designed by screening (and to some extent, still are). Screening works by amassing huge libraries of synthetic and natural molecules, putting them in with the target protein, and seeing if it alters its activity in a way that makes sense. However, if we know the structure of our target, we can intelligently design drugs to interact specifically with that. This has the added effects of reducing side effects, preventing resistance, etc. To put this in light of viruses - Tamiflu (Oseltamivir) is a molecule that…