There Is Hope; Update On New FAH Cores And Clients

[LCB001]

From the blog of Prof. Vijay Pande;

September 25, 2009

Update on new FAH cores and clients
We have been pretty busy with new cores for FAH and I wanted to give donors an update.

1) SMP2: Gromacs and Desmond. Much effort has gone into our "SMP2" project, the codename for the second generation SMP client. The main goal here was to make it MUCH easier to use. In order to do that, it meant getting rid of our use of MPI. We have had two approaches to this. Both ditch MPI by using threads instead. One was to switch to a new piece of software for the core. This has led to the "Desmond" core, based on software from DE Shaw Research. The second approach was to communicate the MPI issues with the Gromacs developer team and work with them to push for a threads-based Gromacs implementation. Both of these are coming along well and we are testing cores in house. You should hopefully see these cores "in the wild" (i.e. running on FAH) in a month or two, assuming that tests go well.

2) Normal Mode Langevin (NML) Dynamics in the Protomol core. We have been working on another approach to speeding dynamics greatly, based on a new technique called Normal Mode Langevin (NML) dynamics. This method uses the same style models as normal MD (same force fields, etc) and thus should have the same accuracy, but with a pretty significant speedup due to algorithmic advances. NML is complementary to our other methods, so we're hoping to add it to everything else (in particular to the GPU core). To start, we will be testing it in a new core, based on the Protomol software. Protomol is designed to allow for rapid prototyping of molecular simulations, which is perfect for NML.

3) GPU3: Next generation GPU core, based on OpenMM. We have been making major advances in GPU simulation, with the key advances going into OpenMM, our open library for molecular simulation. OpenMM started with our GPU2 code as a base, but has really flourished since then. Thus, we have rewritten our GPU core to use OpenMM and we have been testing that recently as well. It is designed to be completely backward compatible, but should make simulations much more stable on the GPU as well as add new science features. A key next step for OpenMM is OpenCL support, which should allow much more efficient use of new ATI GPUs and beyond.

I'm very excited about these new advances. It really should fundamentally improve the key science software behind FAH as well as making the donor experience much more smooth on our more experimental clients (i.e. on GPU and SMP).

[Arinoth]

That's good to hear they are trying to increase the PPD out of new/next generation ATI cards so we don't all have stuck with Nvidia if we want to fold

[LCB001]

I'm hoping they get the new SMP2 client out soon so we can get some decent PPD without having to do the VM thingy...

[Arinoth]

What's wrong with doing the VM thingy? Its rather easy and straight forward to use, but i guess you can only use it only multi-core processors, though don't most people have those these days?

[crazyhorsejohnny]

Originally Posted by Arinoth

What's wrong with doing the VM thingy? Its rather easy and straight forward to use, but i guess you can only use it only multi-core processors, though don't most people have those these days?

Seems like lately many people have had problems.

[JMCD]

Well if you could get just as many ppd without VM that'd be ideal.

[Dr_BenD_over]

A key next step for OpenMM is OpenCL support, which should allow much more efficient use of new ATI GPUs and beyond.

Yay!!

[enaberif]

Originally Posted by JMCD

Well if you could get just as many ppd without VM that'd be ideal.

You can.

Setup a dedicated linux box.

[Exmortis]

I just bought a new 5870, cant wait to hammer up some folding numbers when they release new core. for now im down to CPU only folding.

[geokilla]

Can't wait for the new changes. But thanks to the changes, Folding just got a lot more competitive xD

As for asking what's wrong with using VMWare. Some of us can't run it because our CPUs lack VT.