Posts by dcdc

1) Message boards : Number crunching : The most efficient cruncher rig possible (Message 95691)
Posted 1 May 2020 by Profile dcdc
Post:
Yeah, I set it to 3 threads from the start. Happy to bump it up to 4 to see the impact though.
2) Message boards : Number crunching : The most efficient cruncher rig possible (Message 95674)
Posted 1 May 2020 by Profile dcdc
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I've got a 4Gb Pi4 running 3 threads on Raspian to add to the data pool too. Everything stock, and passive heatsink/case:

https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=4021327
3) Message boards : Rosetta@home Science : CASP14 (Message 95630)
Posted 30 Apr 2020 by Profile dcdc
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The trRosetta and Alphafold work sounds really interesting. Are you likely to push a version of trRosetta out to Ralph in the future?
4) Message boards : Number crunching : The most efficient cruncher rig possible (Message 95451)
Posted 27 Apr 2020 by Profile dcdc
Post:
The threadrippers are awesome, but I think some of these would be a lot more productive for the money:

https://www.ebay.co.uk/itm/143586312188

https://www.ebay.co.uk/itm/143494592135

I think Sandy Bridge servers became a lot cheaper after meltdown and spectre came out because they didn't get patched so loads of data centres had to turn off hyperthreading or get rid of them.

D
5) Message boards : Number crunching : L3 Cache is not a problem, CPU Performance Counter proves it (Message 94434)
Posted 14 Apr 2020 by Profile dcdc
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The Haswell and Broadwell CPUs with L4 cache (intended for the Iris Pro GPU) might be interesting to look at for this too. I believe the Haswell parts with Iris Pro have direct replacements without Iris Pro so makes for relatively easy comparison.
6) Message boards : Number crunching : Running Rosetta on Raspberry Pi 3B+ (how to guide) (Message 94385)
Posted 13 Apr 2020 by Profile dcdc
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Thanks for this- will give it a go.
7) Message boards : Number crunching : COVID 19 FAH and Rosetta the same? (Message 94379)
Posted 13 Apr 2020 by Profile dcdc
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No, different. Both are important. I guess journal entries are a good way to compare the two.

FaH is concerned with the process of how proteins fold. R@h is concerned with where they end up once they have folded.

The folded state is important because that shape determines the proteins function and what it will bind with.

R@H also works on designing new proteins that don't exist in nature, which may well lead to one of the big technological revolutions, like the transistor did.
8) Message boards : Number crunching : The most efficient cruncher rig possible (Message 94366)
Posted 13 Apr 2020 by Profile dcdc
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I guess it depends where you are/ambient temps as to whether stock cooling is sufficient. My basement rarely gets above 15°C, even if it's 25 outside. I'm sure some of you have higher temps to contend with than that 😉
9) Message boards : Number crunching : The most efficient cruncher rig possible (Message 94332)
Posted 13 Apr 2020 by Profile dcdc
Post:
I'm using it quite heavily so that's probably it. It's probably waiting for RAM while in use a lot of the time. Everything is set to 100% though.
10) Message boards : Number crunching : The most efficient cruncher rig possible (Message 94326)
Posted 13 Apr 2020 by Profile dcdc
Post:
I would ignore any benchmark scores and base this entirely on the RAC that a given CPU typically generates.

Also pcpartpicker.com might help.

I would be surprised if an 8 core Ryzen system with stock cooling and a cheap low power 2nd hand GPU didn't come out as the best option, although the 1600AF might be worth looking at too. And a decent PSU - I tend to stick with Seasonic.

I wouldn't consider upgrading anything - high end CPUs retain their value so remain expensive so it's usually better value to buy new.

A3700X should generate around 11k per day at stock speed. My Pi 4 running 3 threads generates 400.

Alternatively there are often deals on old rack mount servers, but they will use more power than a new 7nm Ryzen. I've got a DL380 which was around £200 and does a similar throughout to the 3700X. I need to check the power draw of both though.
11) Message boards : Number crunching : Task start optimisation suggestion (Message 94323)
Posted 13 Apr 2020 by Profile dcdc
Post:
Would this also help reduce RAM requirements? If multiple Rosetta threads each need the same file loading into RAM, does that memory get loaded once or multiple times separately?
12) Message boards : Number crunching : Running on a 4GB Raspberry Pi 4 - How to? (Message 94081)
Posted 10 Apr 2020 by Profile dcdc
Post:
Here is my Pi4 running on 3 cores at stock speed, and using this heatsink:

https://shop.pimoroni.com/products/aluminium-heatsink-case-for-raspberry-pi-4?variant=29430673178707

https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=4021327
13) Message boards : Number crunching : R@H for portable devices (COVID19) not downloading on Android 10 (Message 93747)
Posted 7 Apr 2020 by Profile dcdc
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Is your memory setting % large enough for the tasks? I think it requires 1Gb before it will download any. Ralph@home is testing some smaller ones.

My Android 10 OnePlus 7T will download tasks but won't crunch them, but that's a different issue.
14) Message boards : Number crunching : If You Don't Know Where to Put it, Post it here. (Message 93745)
Posted 7 Apr 2020 by Profile dcdc
Post:
If you can hibernate instead of shutting down then it will restart from where it left off.

If the models are large then it might not be able to checkpoint very often.
15) Message boards : Rosetta@home Science : folding algorithm(s) (Message 93687)
Posted 6 Apr 2020 by Profile dcdc
Post:
Is there a link to an article detailing the algorithms used to perform automated folding? Or is this a lab secret (proprietary and can't be shared)


This might be a good place to start:
https://www.rosettacommons.org/home
HTH
D
16) Message boards : News : Outage notice (Message 93478)
Posted 5 Apr 2020 by Profile dcdc
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Look at Computing->Server Status, not the front page.

15k tasks ready to be sent. Well, I'd like to get one of those ;-)

Further down it says those 15k are all for arm devices.
17) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 93445)
Posted 5 Apr 2020 by Profile dcdc
Post:
Yeah, that's one of the main methods.

The reason this is exciting is because it provides the amino acid sequences for something that binds to a very similar target.
18) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 93376)
Posted 4 Apr 2020 by Profile dcdc
Post:
This looks like an interesting starting point for targeting Coronavirus:

https://science.sciencemag.org/content/early/2020/04/02/science.abb7269.full
19) Message boards : Number crunching : Rosetta running on ARM platforms (Message 93234)
Posted 3 Apr 2020 by Profile dcdc
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Does this include Raspberry Pis? If so, do you know which models/OS?
20) Message boards : News : Rosetta's role in fighting coronavirus (Message 92836)
Posted 1 Apr 2020 by Profile dcdc
Post:

2. Creating these jobs takes human and CPU time on our end and we're stretched thin. I'm working my hardest to get stuff pushed through the pipeline, but for a lot of these, I have to develop new software to get the jobs set up correctly. Additionally, some stuff we can't run on R@H and so it has to be precomputed.

Could you get someone from the community to help with/do some of that work? There seems to be lots of people who are both keen to help and highly capable. If practical, that could free you up to work on the high value work, like getting the new version of Rosetta running, or getting trRosetta ready for BOINC etc.


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