Hi everyone.
Once again after a few years I have decided to simulate ;)

This is for a new project where I try to automatically build and simulate hundreds of membrane proteins from the OPM database http://opm.phar.umich.edu/ as a proof of concept.
But I will also keep an eye out to see if something fancy happens in those simulations which I am quite sure it will.

Membrane proteins are very interesting in general as they are involved in many diseases and are simulated quite often. So building a protocol to simplify this process would help lots of biologists.

For the moment I sent out just 100 simulations as a quick test, but in the next few days I will send out around 3000 equilibrations.

Beware! The simulations are very very different, so there is no point in comparing them to each other. I have some systems which run on the short queue in an hour and some monstrous ones which run on long for 10 hours. The credits are scaled accordingly to simulation complexity so no one will be cheated of his hard earned credits :)

Also keep in mind that the first batch will be minimization/equilibration simulations, which start the minimization by using the CPU for maybe 1 minute and then should switch to GPU for the equilibration.

I might post here some pictures of the systems as well because some of these proteins are just gorgeous!

Edit: I made some gifs for you here ;)
http://imgur.com/a/YbjOd

For the moment I sent out just 100 simulations as a quick test

ha, I was lucky to get 2 of them for crunching

Nice, impressive structures to simulate.

What specific aspects of the proteins will the simulation address?

For the moment we are just looking if the automatical preparation can produce working simulations. Once the simulations are completed I will check for any big changes that happened (changes in protein structure, detachment from the membrane) and try to determine what caused those changes if possible.

I see tasks ready to send on the server status page :-)

I am sending them now. Please report any serious issues here.
I had to double the runtime of the simulations due to their tricky nature so now we have some which are quite long (up to 24 hours).

What we decided is that runs which are under 6 hours go to short with normal credits. Simulations with from 6-18 hours runtime get 2x normal credits. Simulations with 18-24 hours runtime get 4x normal credits since you will likely miss the day-return bonus.

OPM996 is classed as a Short Run but using 980ti seems it will take around 7 hours

Yet I have it on 2 other machines as a Long Run

Only completed 6% in 30 minutes at 61% GPU utilization

Server Status calls it Short Run but in BOINC under Application it's Long Run. Got 2 already running fine.

On my 980ti it is running as short run and will take over 7 hours or longer to complete at current rate

The runs were tested on 780s. Simulations that run under 6 hours on a 780 are labeled as short.

Are you sure you are not running maybe two simulations on the 980s?

I am sending both short and long runs in this project as I mentioned. They are split accordingly depending on runtime.

OPM996 is the project code. If you want to ask me about a specific job please refer to the job name like 2id4R1 then I can tell you specifics about this protein simulation

No I am only running one at a time and it has only completed 15.57% after 1hr 11min on a 980ti utilization 60%

Projected time is increasing and it is running under short run app

2K1aR7
2K1aR5

You got one of the edge cases apparently. 2k1a has exactly 6.0 hours projected runtime on my 780 so it got put in the short queue since my condition was >6 hours goes to long.
These simulations have a short (1 minute maybe) CPU minimization at the beginning so maybe this is throwing off the estimated completion time?
I am not totally sure.

Not working from what BOINC estimates but from real time and it will take betwen 7 to 8hrs

But never mind HeyHo

Boinc will estimate completion time based on the GFlops you put against the task, but if previous GFlops were not accurate the estimate will not be accurate.
You have 5M GFlops against these tasks.

I have 2 WU's running, one on each of my GTX970's.
My estimated run time is 32h based on 9% completion and almost 3h of runtime.

Most clocks are reasonable but the power is questionable on one card:
GPU0:
10% Power, 1291MHz/1304MHz, 7GHz GDDR5, MCU 40% (slightly high), Power 71% (P2 state), 1.131V, Temp 69C. CPU (i7-3770K) at ~75% usage.
GPU1:
59% GPU Power (MSI Afterburner), 69C, GPU Usage 75%, 1075MHz.

GPU memory usage is 1.287GB and 1.458GB (Quite big).
MY RAM and page file are quite big too (might be other apps though).

Don't see how the 1min of initial CPU usage would drastically effect the estimated runtime.

Will drop the CPU usage to ~60% and give it a spring clean before starting up to see if that improves things.
- update - that allowed the cards to run at slightly higher clocks (and normally) but it's now only looking like 31.5h. That might yet drop a few hours but these are still extra long tasks.
- update - still looking like about 31.5h (55% after 17h and 51% after ~16h).

2b5fR8-SDOERR_opm996-0-1-RND0199_0
2b5fR3-SDOERR_opm996-0-1-RND0810_0

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On my GTX980Ti's, the former long runs were running about 20.000 seconds, yielding 255.000 points.

Today's 2dmgR0-SDOERR_opm996-0-1-RND3256_0 was running 39.000 seconds, yielding 247.050 points.

How come?

On my GTX980Ti's, the former long runs were running about 20.000 seconds, yielding 255.000 points.

Today's 2dmgR0-SDOERR_opm996-0-1-RND3256_0 was running 39.000 seconds, yielding 247.050 points.

How come?

This is what got:

2jp3R4-SDOERR_opm996-0-1-RND2694_0 11593350 9 May 2016 | 9:19:35 UTC 9 May 2016 | 21:02:28 UTC Completed and validated 40,147.05 39,779.98 205,350.00 Long runs (8-12 hours on fastest card) v8.48 (cuda65)

1cbrR7-SDOERR_opm996-0-1-RND5441_0 11593203 9 May 2016 | 9:19:35 UTC 9 May 2016 | 21:32:36 UTC Completed and validated 41,906.29 41,465.53 232,200.00 Long runs (8-12 hours on fastest card) v8.48 (cuda65)

Yeah, they're pretty long, my 980ti is looking like it'll take about 20 hours at 70-75% usage. Don't mind the long run, I'm glad to have work to crunch, though I do hope the credit is equivalently good.

... I'm glad to have work to crunch

me too :-)

I crunched a WU lasting 18.1 hours for 203.850 credits on my GTX970.

This credit ratio is lower then previous "Long run" WUs

Previously I completed "Long run WUs" in 12 hours for 255.000 credits