Project News - Poem@Home

[BF]

From the POEM@Home news feed:

POEM@HOME in the news

Tuesday, 9 June 2009 10:00 AM

On 14th of June 09 POEM@HOME will be featured in a short presentation on grid computing in the German TV program 3SAT Neues at 16:30 GMT+1. While the main focus of this program will be grid computing in general, the special efforts of the volunteer computing community will also be featured.

[Dataman]

Message 3973 - Posted 27 Jan 2011 15:19:14 UTC - in response to Message 3972. 
Hi,

1.) Are you happy with the development of POEM++?

Yes, very. In total POEM++ has proven to be very flexible. We can not only simulate Proteins, but also Proteins on surfaces, Membranes (for example for drug transfer, etc.) or even non-proteinogenic systems.

2.) Does the client deliver the expected results?

Yes, Energies of old - and P++ are compatible; POEM++ gives the same energies for the same proteins, but widened to the mentioned domain of 'not-proteins'.

3.) Is the performance alright? Somebody mentioned a 7fold increase.

The SASA (which was a roadblock in jpoem) is faster by far. The nice thing about the new SASA is near linear scaling. Jpoem had lots of problems, when it came to big proteins with runtime and especially memory. This was the reason why we couldn't calculate proteins bigger than 500+ amino acids on POEM@HOME. We can do that now.

4.) At the moment P++ is cpu only. Which cpu arch is the best fit for P++?

Well answering this is quite difficult. The linux client will benefit from everything up from SSE2, because the Matrix Vector operations are optimized for that. One thing is for sure however: Real Cores are better than hyperthreaded cores. In our future bigger clusters we would only put the big AMD CPUs at the moment, because there you simply get more CPUs per surface area.

5.) What are the problems in regards to P++ GPU development? Are the dev tools ok already?

The nice thing about GPU development is: You don't need special dev tools (or at least not so many). One of the reasons why the gpu development takes so much time is that some energy terms simply don't want to be parallelized. Even if of 6 energy terms 5 run 20 times faster, you won't realize a big difference if energy term 6 still takes as long as before. GPU cores cannot really talk with each other.

In regards to the app distribution there are some nice developments recently: From one hand ATI seems to bundle the OpenCL SDK with Catalyst nowadays and on the other hand some BOINC folks spend time in supporting OpenCL.

6.) When will the GPU app be released?

We can't say. At the moment we are preparing a simulation with a special forcefield, which will _only_ run on GPUs without parts on the CPU. It doesn't contain all interactions but the ones we want to investigate. I don't want to give a date, because in science some project comes in between all the time.

7)How big small is your group / the group of devs?

You find our group here:
http://www.research.kit.edu/biostruct/staff.php
At the moment we are quite big, but not everyone is working on the code all the time. Most of us execute simulations with P++. Lately got an additional person, who will now integrate the code for drug-screening.

8.) How good is the interaction with the BOINC people? How open is this interaction? CPU time means power and so I suspect that not everything is as open or as easy, correct? CPU time can be used for bad things afterall.

It is very open, there is also not a single feeling of competition because we all do different stuff. Lately I met some people from Rosetta@Home on a conference and we talked quite nicely about our and their algorithms. Among other things they also told me about their users who wanted to generate a movement against P@H, but thankfully their admins extinguished the flames.^^
We look at each others as scientists: If somebody cures cancer, it doesn't matter who he is; the only thing that matters is that the disease is cured.

Best,
Timo

[kashi]

Expected "hopefully" within the next 2 weeks:

Oct 28 , 2011 - New Client release, Server upgrade

We will release a new client by the end of next week. This client will be incompatible with the current client. Therefore we will starve the server of workunits the next week. Starting Monday no new workunits will be generated. We will then take the server offline on Friday to do a server upgrade to enable GPU client compatibility. This release will still be without GPU support. We expect the GPU support to be ready hopefully one week after. Sorry for the inconvenience.

[Sean]

We expect the GPU support to be ready hopefully one week after.

Any news yet on which GPU's will be compatible?

Hopefully other medical based projects follow their lead.   

[Furlozza]

Hopefully it will be NVidia.... and from 250GTS, or 9800s...... cause poor ol' Gnatty can't handle the Beast that was in one of the other I7s.... 5780??... anyways, be nice to have something else to switch to, when I cross the 2.5 million mark with Einstein.

[kashi]

12 Feb 2012 | 10:35:02 UTC

Switching to fixed credits

As we discovered an overgranting for our resent workunits, we decided to change our credit system to fixed credits on Monday. All overestimated credit points will be normalized.
We apologise for the trouble caused.

The credits will be set as follows:

firstdrug: 80.8275865915366
gpucrystal: 2925.23047140266
rigiddock: 113.608330044946
barrelcompare: 20.6341535290809




I'm very glad POEM has stopped using the inconsistent, unfair and unreliable CreditNew system. The new POEM admins handled the change to fixed credits very quickly and professionally after the inevitable CreditNew disaster. Hopefully now WCG will reconsider their decision to use CreditNew with a GPU application before trouble strikes instead of after.

For anyone who tried the ATI/AMD application previously and gave up due to poor availability of work there has been no shortage of GPU work since the change to fixed credits.

[JugNut]

POEM WU's have run dry. 

There server status says they have "1" Tasks ready to send.    ???

I mean I know i've been chopping into em',  but I didn't think i'd crunched enough to run them dry? 

[LawryB]

@Jugnut

You broke their servers though.  :furious:

[JugNut]

 biggrin   I stopped crunching for a bit so there servers could catch up.   So now there's enough work for all..  biggrin

[LawryB]

 

[JugNut]

POEM GPU Work shortages?..  Maybe for a long spell?

QUOTE: From: Thomas Koch. POEM ADMIN
------------------------------------------------------------------------------------------------------
Message 7389 - Posted: 26 Nov 2012 | 10:01:02 UTC

Hi everybody,

I have to apologize for the long period of silence regarding this topic, but I didn't want to give any misleading information before we discussed the problem here.
We are still waiting for our new server hardware, but unfortunately this won't fix the problem here entirely.

Fact is, these GPU calculations are running so rapid, that we have to evaluate real floods of information. We were talking about possibilities to send out more GPU work units, but at the moment there is no way to process it in time.

I want to thank all of you for spending so much computing time. It's absolutely okay to give your GPU power to another project now, there may be more use for it at the moment. The crystallization studies will still continue, but the follow-up projects with GPU support are not yet in a state to be sent out over the BOINC network, so the situation is not likely to get better in the near future.

I hope you can understand this, and are still willing to support us.

Best regards
Thomas
-------------------------------------------------------------------------------------------------------------
end quote:   :cry2:

EDIT: CPU work still available ATM
There's still some GPU work but it's sporadic.  But I can't snag any?
Anyone else with more info?

[LawryB]

 

[Sean]

 The current 'gpucrystal' tasks are drawing to an end with a new POEM GPU project planned for early next year. Hopefully they last out the AA but it sounds unlikely...  :-\

boinc.fzk.de/poem/forum_thread.php?id=1028#9236

[JugNut]

New test POEM GPU work may start as early as next week. *fingers crossed*

QUOTE from Thomas Koch admin.. 23 Jan 2014

* Status Update *

Bad news first: The announced MOF simulation takes more time than expected.
We are currently working on a backup GPU project, which now seems to be more readily available.

The Test Server is up and running. Our IT Department is now configuring the Firewall for external access. I'll get the input files for our simulation next week, and will create POEM jobs as soon as possible. The URL will be announced when work units are prepared, because it only serves the dummy BOINC example_app at the moment.

If the jobs run fine on the test server, we will set them up on the live system the first week in February.

Thanks for your patience.
http://boinc.fzk.de/poem/forum_thread.php?id=1028&postid=9298#9298

[JugNut]

Well the new POEM site is up & running with all new GPU & CPU tasks.    Albeit just test jobs to make sure all is working well before full release.

But.. linux only ATM.   

This is the address for the test site. http://int-boinctest.int.kit.edu/poem/index.php  Windows work to come later this week.