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Message boards : News : hsp90 with high ligands concentration

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Paola Bisignano
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Message 26646 - Posted: 21 Aug 2012 | 18:17:40 UTC

Hi guys,

I am trying to enhance the sampling in a difficult system....hoping to improve the sampling HSP-90 chaperon.
I sent 500 WU on acemd long 76460 credits each

Thanks for your computing time,

Paola

Profile [PUGLIA] kidkidkid3
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Message 26647 - Posted: 21 Aug 2012 | 19:18:50 UTC - in response to Message 26646.

You are welcome.
What is the name of these WUs ?
Thanks
K.
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(Martin Luther King)

Snow Crash
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Message 26654 - Posted: 22 Aug 2012 | 13:53:25 UTC - in response to Message 26647.

I am trying to enhance the sampling in a difficult system....

I'm not sure you meant it quite in the way that they are *difficult* to crunch but they do have very long runtimes even on my GTX670.

3EKO_8_1-PAOLA_3EKO_8LIGANDS-********

I can't say how far towards completion the first one is as I am not at home
but it has been processing for a little over 13 hours now. This system has processed hundreds of other long tasks without error so it should complete successfully and when it does I will update with final runtime.
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Thanks - Steve

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Message 26656 - Posted: 22 Aug 2012 | 14:23:16 UTC

These workunits will have the name like PAOLA_3EKO_8LIGANDS.

Everyone please note that these workunits will likely require higher CPU utilization than some of our other workunits, and perhaps lower GPU usage as well. Higher CPU usage is the result of some CPU bound calculations, and slows down each step of the simulation. Note that you shouldn't notice the "slowdown" on your end, since the amount of time a WU will run on your machines is benchmarked here, and is not dependent to the time each step of the simulation takes. However, our previous method for computing credits didn't account for the CPU slowdown, and sometimes under-calculated how many credits should have been awarded (by roughly 10% or 20%). With these and future workunits, this issue will be taken into account. In other words, from your perspective the credits/hour should be roughly the same across all types of workunits, regardless of CPU/GPU usage.

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Message 26659 - Posted: 22 Aug 2012 | 15:58:21 UTC
Last modified: 22 Aug 2012 | 15:58:55 UTC

Further discussion on performance issues with this group should be done in the Number crunching forum. It seems many crunchers are taking a long time to finish these and are suffering low GPU usage. Current discussion here.

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Message boards : News : hsp90 with high ligands concentration