Posts by Dr. Merkwürdigliebe

1) Message boards : Number crunching : Rosetta@home using AVX / AVX2 ? (Message 90428)
Posted 25 Feb 2019 by Profile Dr. Merkwürdigliebe
Post:
Vote with your feet
2) Message boards : Number crunching : Problems with web site (Message 90377)
Posted 17 Feb 2019 by Profile Dr. Merkwürdigliebe
Post:
Look, nobody except an algorithm chooses these "Users of the day". They, i.e. the admins, have to purge the database and throw out all the ancient accounts with 0 points. I proposed that years ago...nothing happened...nothing like that ever will...

Nobody that matters reads the forums...

You can stop posting here...and wander off to FAH...I did...
3) Message boards : Number crunching : Rosetta@home using AVX / AVX2 ? (Message 87792)
Posted 2 Dec 2017 by Profile Dr. Merkwürdigliebe
Post:
Maybe they should just abandon this nonsensical attempt to support HPC (sort of) on smartphones and tablets...

4, 6 and even 8-core AVX-capable CPUs will be ubiquitous in a few years with a TDP in the 90-140W range.
4) Message boards : Number crunching : Rosetta@home using AVX / AVX2 ? (Message 87783)
Posted 1 Dec 2017 by Profile Dr. Merkwürdigliebe
Post:
My answer to all of this up to this point: FAHCore a7

I don't mean to be rude but most likely I am. Some certain programmers don't know what the hell they're doing.

This is a badly managed project. I draw my conclusions from that.
5) Message boards : Number crunching : Rosetta 4.0+ (Message 87526)
Posted 15 Oct 2017 by Profile Dr. Merkwürdigliebe
Post:
On my Linux x64 - PC BOINC downloads rosetta_4.03_i686-pc-linux-gnu ?





I already got a rosetta_4.03_x86_64-pc-linux-gnu ?



6) Message boards : Number crunching : Rosetta Badges (Message 87496)
Posted 11 Oct 2017 by Profile Dr. Merkwürdigliebe
Post:
Seriously, what for? We are not 10 years old anymore. No need for a junior detective badge. It also slows down loading of the page and distracts from the actual content.
7) Message boards : Number crunching : Stuck on uploading is a new problem? (Message 81490)
Posted 18 Apr 2017 by Profile Dr. Merkwürdigliebe
Post:
Di 18 Apr 2017 17:28:24 CEST | rosetta@home | Started upload of 12dslfv7_gb_0003_0005_11_0001_SAVE_ALL_OUT_480505_41_0_0

Doesn\'t work. 64,00 / 809,82 KB, then stops...
8) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 81170)
Posted 8 Feb 2017 by Profile Dr. Merkwürdigliebe
Post:
IMHO: Science first. Just maintain the original deadlines...

This \"donate your unused CPU cycles\" was probably interesting back in those days when there was no big difference in energy consumption between an idle or fully utilized CPU.

Either have a dedicated machine for the purpose of crunching or stay away and join some stupid project like SETI.

This heterogeneous architecture with all its uncertainties is already bad enough...
9) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80944)
Posted 27 Dec 2016 by Profile Dr. Merkwürdigliebe
Post:

If I shutdown and restart Boinc it will start retrieving work units again but that is a painful process to go through all the systems. These are all running Boinc version 7.6.33 and Rosetta version 3.73.

If there is a better method to keep up production please let me know.


You could use Powershell to restart the service on a number of hosts, e.g. like this.

Theoretically you should also be able to parse the output of
boinccmd --get_messages
and look for the "no work" string.

If you find it, restart the service. Use the Windows task scheduler...

PS: This message board is SLOW. Where's the new hardware?
10) Message boards : Number crunching : Rosetta@home using AVX / AVX2 ? (Message 80919)
Posted 20 Dec 2016 by Profile Dr. Merkwürdigliebe
Post:
Vote with your feet...

Core a7 looks very promising and they have a forum that is actually alive.
11) Message boards : Number crunching : Will there be a 64-bit client in the near future? (Message 80837)
Posted 11 Nov 2016 by Profile Dr. Merkwürdigliebe
Post:
The folks over at folding@home / GROMACS seem to put a little more effort in it...

14:37:02:WU00:FS00:FahCore 0xa7 started
14:37:03:WU00:FS00:0xa7:*********************** Log Started 2016-11-11T14:37:02Z ***********************
14:37:03:WU00:FS00:0xa7:************************** Gromacs Folding@home Core ***************************
14:37:03:WU00:FS00:0xa7:       Type: 0xa7
14:37:03:WU00:FS00:0xa7:       Core: Gromacs
14:37:03:WU00:FS00:0xa7:    Website: http://folding.stanford.edu/
14:37:03:WU00:FS00:0xa7:  Copyright: (c) 2009-2016 Stanford University
14:37:03:WU00:FS00:0xa7:     Author: Joseph Coffland <joseph@cauldrondevelopment.com>
14:37:03:WU00:FS00:0xa7:       Args: -dir 00 -suffix 01 -version 704 -lifeline 3376 -checkpoint 15 -np 8
14:37:03:WU00:FS00:0xa7:     Config: <none>
14:37:03:WU00:FS00:0xa7:************************************ Build *************************************
14:37:03:WU00:FS00:0xa7:    Version: 0.0.11
14:37:03:WU00:FS00:0xa7:       Date: Sep 20 2016
14:37:03:WU00:FS00:0xa7:       Time: 06:40:11
14:37:03:WU00:FS00:0xa7: Repository: Git
14:37:03:WU00:FS00:0xa7:   Revision: 957bd90e68d95ddcf1594dc15ff6c64cc4555146
14:37:03:WU00:FS00:0xa7:     Branch: master
14:37:03:WU00:FS00:0xa7:   Compiler: GNU 4.8.5
14:37:03:WU00:FS00:0xa7:    Options: -std=gnu++98 -O3 -funroll-loops -ffast-math -mfpmath=sse
14:37:03:WU00:FS00:0xa7:             -fno-unsafe-math-optimizations -msse2
14:37:03:WU00:FS00:0xa7:   Platform: linux2 4.6.0-1-amd64
14:37:03:WU00:FS00:0xa7:       Bits: 64
14:37:03:WU00:FS00:0xa7:       Mode: Release
14:37:03:WU00:FS00:0xa7:       [color=red][b]SIMD: avx_256[/b][/color]
12) Message boards : Number crunching : Rosetta won't use 2nd cpu (Message 80735)
Posted 12 Oct 2016 by Profile Dr. Merkwürdigliebe
Post:
You have a dual-core system? Not enough memory? You barely have 2 GB...
13) Message boards : Number crunching : GPU computing (Message 80726)
Posted 9 Oct 2016 by Profile Dr. Merkwürdigliebe
Post:

So you want far fewer processors to be used? None of my computers use a CPU that even has AVXx available, and not enough money is available to replace all the computers available through BOINC with equivalents that have AVXx available.


Your computer does support AVX.

AVX2 however has been introduced with the Haswell CPU generation. AVX-512 will be featured on Skylake-EP CPUs.


It would be possible, though, to produce separate compiles of the application for computers with AVXx and computers without, and add a shell program that tests what the CPU has available, then starts only the version of the program best for the current CPU.


Yes, I know. We've already had that discussion here on this board. We're just waiting for results.
14) Message boards : Number crunching : GPU computing (Message 80712)
Posted 6 Oct 2016 by Profile Dr. Merkwürdigliebe
Post:

There is really no way that scientists have to wait hours or even days for their computation results. Personally, I hope BOINC will die because it's a kludge.


I hope not.
If it is "kludge", why you are here?


Because I want to help. That's why.

One of the problems is the heterogeneous architecture of rosetta@home: There are PCs, Macs and tablets/smartphones (seriously?). Why not an internet-connected dual-core toaster?

There are a lot of issues with these devices and this is IMHO a waste of developer resources.

A homogeneous architecture based on AVXx would alleviate all those problems while yielding a higher performance.

The distributed nature of rosetta also introduces latencies: preparing work, zipping it, sending it and collect the results back over a WAN. Being forced to deal with ultra-lame ancient CPUs and the like are another problem.
15) Message boards : Number crunching : GPU computing (Message 80706)
Posted 5 Oct 2016 by Profile Dr. Merkwürdigliebe
Post:
First things first

1) folding@home for YOUR GPU and probably soon for your CPU, too (AVX support) through GROMACS.

2) but AVXx support first for rosetta.

Is there any progress worth speaking of?

It's interesting: in the past they (poem@home) have started to recruit external personnel in order to optimize their app. Mr. Tankovich obviously did a great job: They no longer depend on the donations of pesky contributors like us.

In the long run (John Maynard Keynes: "In the long run we are all dead...") I predict this solution for rosetta, too. There is really no way that scientists have to wait hours or even days for their computation results. Personally, I hope BOINC will die because it's a kludge.

So unless there is another thing like Charity Engine coming along the way, I think that instead of having to rely on a legion of desktop-grade CPUs, it would be more wise to spend all the resources on a central cluster of AVXx-powered servers under central control.
16) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80697)
Posted 2 Oct 2016 by Profile Dr. Merkwürdigliebe
Post:
Compute error on some rb_10_* job

https://boinc.bakerlab.org/rosetta/result.php?resultid=878604899
17) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 80693)
Posted 29 Sep 2016 by Profile Dr. Merkwürdigliebe
Post:
More validate errors from the rb_*_jobs

https://boinc.bakerlab.org/rosetta/result.php?resultid=878146671

https://boinc.bakerlab.org/rosetta/result.php?resultid=878146673

https://boinc.bakerlab.org/rosetta/result.php?resultid=878146677
18) Message boards : Number crunching : Giving Zero Credit for Work Completed (Message 80691)
Posted 29 Sep 2016 by Profile Dr. Merkwürdigliebe
Post:
Validate error on some rb_job

https://boinc.bakerlab.org/rosetta/result.php?resultid=878146673

19) Message boards : Number crunching : Giving Zero Credit for Work Completed (Message 80676)
Posted 25 Sep 2016 by Profile Dr. Merkwürdigliebe
Post:
Yes, lots of validate errors, all of them are rb_09_* jobs
20) Message boards : Number crunching : Rosetta@home using AVX / AVX2 ? (Message 80474)
Posted 3 Aug 2016 by Profile Dr. Merkwürdigliebe
Post:
I haven\'t had a chance to read that thread yet. But we did look into our donations and it\'s under a couple grand I believe so more would help!

It\'s good to hear from you. :-)

I think experiment.com would be a good place to start. There are already crowdfunding campaigns from other universities.

Random pick:

Bacterial Vesicular Delivery: A One-Step Protein Transport Method

Kickstarter et al. are probably not the right choice, there are some hefty fees and not really science-related.

The r@h users usually participate in other forums, too, so it would be a good idea to come up with a standardized signature for those forum posts and advertise a little ;-)


Next 20



©2019 University of Washington
http://www.bakerlab.org