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        <title>GPUGRID: News</title>
        <link>http://www.gpugrid.net/</link>
        <copyright>Universitat Pompeu Fabra</copyright>
        <lastBuildDate>Wed, 16 May 2012 13:45:22 GMT</lastBuildDate>
        <language>en-us</language>
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            <title>GPUGRID</title>
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    <item>
        <title><![CDATA[3EKObis another conformation]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2985</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2985</guid>
        <description><![CDATA[
Hi all, I am submitting 500 WUs on acemdlong, 56000 credits each. The group and name are 3EKObis...because I have already completed one, but we need more data and I hope that this new conformer should give better results.

The system is a molecular chaperon involved in many cellular functions.

Thanks to all for your computing time,

cheers,

Paola 
]]></description>
        <pubDate>Wed, 16 May 2012 13:45:22 GMT</pubDate>
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    <item>
        <title><![CDATA[Ignasi&#39;s PhD thesis]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2973</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2973</guid>
        <description><![CDATA[
Dear all,

I finally have my thesis printed. 
I thank you all (once again) for your crucial contribution to it. And of course, Gianni, Toni, Kashif, Matt, Nate and Paola for many many reasons.

<a href="http://imageshack.us/photo/my-images/805/thesis.jpg/" rel="nofollow"><img hspace="8" src="http://img805.imageshack.us/img805/7481/thesis.jpg"> </a>

The defense is programmed for the <b>29th of June</b> and <b>you are all invited</b> if you can make it to Barcelona. Drop me a line if you really want to come. There shall be a party :)

cheerios,
i
]]></description>
        <pubDate>Wed, 09 May 2012 10:21:00 GMT</pubDate>
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    <item>
        <title><![CDATA[Problems with fragxa4 and fragxa3 WUs]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2954</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2954</guid>
        <description><![CDATA[
We had to cancel these WUs on-the-fly. fragxa3 were 10 times longer by mistake and would not have finished in most computers. 
On Monday we will look into compensating who was affected by this.

Sorry for the inconvenience.

gdf
]]></description>
        <pubDate>Sun, 22 Apr 2012 17:11:19 GMT</pubDate>
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    <item>
        <title><![CDATA[New *xTRYP* WUs]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2948</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2948</guid>
        <description><![CDATA[
We are submitting a new batch of WUs (~1000) of our beloved trypsin and benzamidine system for a beautiful experiment in collaboration with a crystallographer. 

It seems that these crystallographers and us may have got to similar conclusions on how trypsin and benzamidine like to interact. The nice thing is that we'd have got to the conclusions from VERY different approaches. They make crystals of trypsin/benzamidine and take pictures of their structures using a synchrotron and we make MD simulations of already solved structures and take many snapshots of what happened. And then we compare them.

If experimentalists (protein crystallographers in this case) are able to reproduce what we obtained from computer simulations or viceversa, it would be a beautiful (and necessary) validation of our methods.

Let's hope that all goes well.

Cheers!
]]></description>
        <pubDate>Wed, 18 Apr 2012 09:34:13 GMT</pubDate>
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    <item>
        <title><![CDATA[New WUs of TRYP (*adTRYP*)]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2928</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2928</guid>
        <description><![CDATA[
We have submitted a new batch of TRYP (*adTRYP*), significantly longer than the latest TRYP (met*, eth*, pro*,...). 

The latest TRYP were a real production attempt to straighforwardly obtain binding for small inhibitor molecules. It finally proved harder than first expected, therefore we are improving the underlying analysis method as well as implementing a cleverer scheme to obtain the data. That is what *adTRYP* are for, to prepare a systematic methodological study on how to produce efficiently many events of binding for small protein inhibitors. See <a href="http://www.gpugrid.net/science.php?topic=methods" rel="nofollow">experiments section</a> for more info.

Cheers
]]></description>
        <pubDate>Mon, 02 Apr 2012 13:03:47 GMT</pubDate>
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    <item>
        <title><![CDATA[Tests on GTX680 will start early next week [testing has started]]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2916</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2916</guid>
        <description><![CDATA[
We are looking forward to testing the new nvidia architecture. We will report the performance soon and really thank one anonymous cruncher for the donation. 

gdf
]]></description>
        <pubDate>Fri, 23 Mar 2012 09:42:40 GMT</pubDate>
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    <item>
        <title><![CDATA[New GPUGRID team member]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2914</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2914</guid>
        <description><![CDATA[
It is a pleasure for us to introduce you Paola Bisignano, PhD student at IIT (Italy) that is visiting us for 9 months. She has already started to send WUs to the queue, so soon you will be getting them.

Her work is similar to ours (i.e. *TRYP*) where we try to predict small molecule binding affinities and kinetics to protein targets of biomedical interest.


]]></description>
        <pubDate>Wed, 21 Mar 2012 18:42:34 GMT</pubDate>
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    <item>
        <title><![CDATA[New publication, new badges!]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2912</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2912</guid>
        <description><![CDATA[
Dears!

We have recently published a new paper on the Journal of Chemical Theory and Computation: "Visualizing the Induced Binding of SH2-Phosphopeptide", authored by me, ignasi (shared co-authors) and GDF. In the paper we have made (hopefully :) good use of your donated GPU time to <a href="http://www.youtube.com/watch?v=V0Z52u8h2es&list=UU0FjUee927t9QEuygkUTbwg&index=3&feature=plcp" rel="nofollow">find out in detail</a> what happens when a kind of signal is transmitted between proteins in a cell. The signal is the recognition of a short peptide (pYEEI for friends) by a partner "plug", called the SH2 domain. This kind of signaling is in fact very common in cells for responding to all varieties of messages (for example in receptor kinases).

We updated the badges accordingly - and this time we also briefly go down the hall of fame. Of the 3113 contributors, these are the 10 users who contributed the most computation (rank, name, millions of credits):

1	<a href="http://www.gpugrid.net/show_user.php?userid=14310" rel="nofollow">Retvari Zoltan</a>	70.1
2	<a href="http://www.gpugrid.net/show_user.php?userid=63403" rel="nofollow">Venec</a>	66.8
3	<a href="http://www.gpugrid.net/show_user.php?userid=8777" rel="nofollow">davidYuen</a>	49.0
4	<a href="http://www.gpugrid.net/show_user.php?userid=78807" rel="nofollow">WirelessDude</a>	46.8
5	<a href="http://www.gpugrid.net/show_user.php?userid=25378" rel="nofollow">Stoneageman</a>	46.3
6	<a href="http://www.gpugrid.net/show_user.php?userid=34254" rel="nofollow">CTAPbIi</a>	26.0
7	<a href="http://www.gpugrid.net/show_user.php?userid=62481" rel="nofollow">Helmholdt</a>	24.8
8	<a href="http://www.gpugrid.net/show_user.php?userid=64884" rel="nofollow">Nikke</a>	24.3
9	<a href="http://www.gpugrid.net/show_user.php?userid=38072" rel="nofollow">CNT - IQE</a>	24.0
10	<a href="http://www.gpugrid.net/show_user.php?userid=63537" rel="nofollow">Ketzer7</a>	24.0
]]></description>
        <pubDate>Mon, 19 Mar 2012 15:02:58 GMT</pubDate>
        </item>
    <item>
        <title><![CDATA[Update to FAX3 tasks on long queue]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2904</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2904</guid>
        <description><![CDATA[
see details here: <a href="http://www.gpugrid.net/forum_thread.php?id=2903&nowrap=true#23933" rel="nofollow">http://www.gpugrid.net/forum_thread.php?id=2903&nowrap=true#23933</a>
]]></description>
        <pubDate>Tue, 13 Mar 2012 21:06:21 GMT</pubDate>
        </item>
    <item>
        <title><![CDATA[New task on long queue, significantly longer than traditional tasks]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2903</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2903</guid>
        <description><![CDATA[
Hi all,

I have submitted some new work units that will replace some I submitted earlier in the week. The names will be "NATHAN_FAX3". These tasks are in the true spirit of the long queue, and will take about 12+ hours on the fastest cards. Some have already been returned and indeed have been around 13 hours. This is markedly longer than what you have expected traditionally, but we really want the long queue to be for critical tasks, computationally intensive tasks, and the like. I suggest you all take note of how these tasks run on your computers and be mindful of temps and errors as you start to receive them.

I have noticed some crunchers expressing concern/dismay that perhaps they will not be able to get the 24h bonus with such long tasks. We are mindful of that concern, and will keep an eye on this group as an experiment. If we think it is too unfair to people with fast but not <i>the fastest</i> cards, we'll be sure to correct that in future groups. But the less send/recieve we have to do, the better. We are also mindful of the fact that longer tasks might be more susceptible to errors/crashes, and we want to see how this goes. I'll be looking out for the severe error percentage over the next few days for any problems.

Also, a note about tasks beginning with NATHAN_FA... These tasks are unique in that they are quite large simulations, compared to many others we have done in the past which are smaller (bigger biomolecules mean bigger simulations). They not only take longer per step, but require more memory. Cards with lower memory (below 1GB) may suffer additional performance loss. There is nothing we can do about this, unfortunately.

Happy crunching.

Nate
]]></description>
        <pubDate>Sat, 10 Mar 2012 20:05:30 GMT</pubDate>
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    <item>
        <title><![CDATA[Server back online after power cut]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2895</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2895</guid>
        <description><![CDATA[
We are attached to a temporary powerline, so we need to restart sooner or later to attach it to the proper one.

gdf
]]></description>
        <pubDate>Tue, 06 Mar 2012 11:42:26 GMT</pubDate>
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    <item>
        <title><![CDATA[Do not use 295.x driver on windows]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2893</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2893</guid>
        <description><![CDATA[
The driver causes CUDA WUs to fail - here and on other projects. Please don't use it until NVIDIA fixes the bug.
]]></description>
        <pubDate>Mon, 05 Mar 2012 14:25:25 GMT</pubDate>
        </item>
    <item>
        <title><![CDATA[New wus on long, old project that needs validation.]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2892</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2892</guid>
        <description><![CDATA[
Hey crunchers, I have put a batch of work units in the long queue that should make up for the drought. The work units themselves are not from a new system, but rather are an important validation of work I have already been doing. These work units require the long queue, and will likely take 12 hours on the fastest cards. Let us know if you have any problems or concerns and we'll do what we can to address them.
]]></description>
        <pubDate>Mon, 05 Mar 2012 11:09:12 GMT</pubDate>
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    <item>
        <title><![CDATA[acemdlong also updated now]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2889</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2889</guid>
        <description><![CDATA[
The update process is finished also for acemdlong.

gdf
]]></description>
        <pubDate>Sun, 04 Mar 2012 17:52:03 GMT</pubDate>
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    <item>
        <title><![CDATA[New application acemd2 6.16 (WIN/LINUX)]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2886</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2886</guid>
        <description><![CDATA[
We have upgraded the acemd2 application to get some features which we need in order to execute new WUs.

Soon, we will upgrade also acemdlong. 

All the rest in the application stays the same and you should not notice any change.

gdf
]]></description>
        <pubDate>Sun, 04 Mar 2012 13:10:38 GMT</pubDate>
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    <item>
        <title><![CDATA[monitor suspend/resume bug in 295/296 drivers]]></title>
        <link>http://www.gpugrid.net/forum_thread.php?id=2870</link>
        <guid isPermaLink="true">http://www.gpugrid.net/forum_thread.php?id=2870</guid>
        <description><![CDATA[
There are some reports of bugs concerning the latest NVIDIA drivers (failures when monitor goes to sleep).  GPUGRID may not be immune to the bug. If it occurs to you, either 

 * rollback to previous drivers
 * or configure the monitor so that it does not turn off
]]></description>
        <pubDate>Fri, 24 Feb 2012 21:49:03 GMT</pubDate>
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