Are There Any Optimized Apps For Docking@Home
Message boards : Number crunching : Are There Any Optimized Apps For Docking@Home
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I have used the optimized apps for seti@home, my question is has anyone written any optimized apps for docking@home? If so I would be very interested in where/how to download and install. |
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5267 | Rating: 0
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I have used the optimized apps for seti@home, my question is has anyone written any optimized apps for docking@home? If so I would be very interested in where/how to download and install. I don't think so as the project uses the CHARMM program package. I doubt they are allowed to provide the source code to someone outside. And I'm not sure they would be willing to allow someone else meddling with that source (or if that is even allowed by the license). But maybe the project itself could compile some versions using the advanced features of newer CPUs? Another point is that these packages are usually huge, often written in Fortran (at least CHARMM is) and it is sometimes quite hard to find the bottlenecks for a given application. Most of the time one simply hopes it was written well and was somehow optimized over the years by its creators. Most people restrict themselves to play around with some compiler switches and that's it (*). These packages often try to be some kind of all-in-one device suitable for every purpose in its field. It's not like a streamlined application that was put together for a very specific purpose. But it does not mean that it can't be fast at what it's doing, it's only hard to change something about it ;) (*) Btw., the current combination of compiler and used switches appear to strongly favour intel CPUs. With the fixed credits now underway, that will get more apparent. Maybe the project should look into that too ;) |
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5269 | Rating: 0
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Yes indeed, the answer of Cluster Physik is accurate.
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5271 | Rating: 0
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Nothing "wrong" with Fortran. Most "old" Fortran programs are highly optimised, but not necessarily in the way that "optimisation" is used today. Memory was expensive - the 1 megabyte of memory we had in our SEL systems comprised 4 PCB's, 19" rack mount PCB's I might add. You had to optimise programs to share that memory between the 20-30 programs that were running on the system.
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5281 | Rating: 0
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Nothing "wrong" with Fortran. Most "old" Fortran programs are highly optimised, but not necessarily in the way that "optimisation" is used today. Memory was expensive - the 1 megabyte of memory we had in our SEL systems comprised 4 PCB's, 19" rack mount PCB's I might add. You had to optimise programs to share that memory between the 20-30 programs that were running on the system. I didn't want to say that there is anything wrong with Fortran. But the code of packages grown over some decades are most of the time hard to understand, it would be the same with C, too. And you are completely right, 20 years ago you were forced to write good code to get something done in reasonable time on the available machines. More often than not some really bright poeple put very efficient algorithms in. But on the other side maintenance may be a problem. Changing some core components and taking out those "4 bit per value optimizations" (as they are hurting modern CPUs) can be a challenging task. And that is nothing a user of the package (as the Docking project) is doing, that have to be done by the group licensing the package. Or to repeat myself, it does not mean that it can't be fast at what it's doing, it's only hard to change something about it ;) |
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ID:
5284 | Rating: 0
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Hi, but you
will
need the
source code
, if you want to 'optimize'
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ID:
5408 | Rating: 0
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Hi, but you will need the source code , if you want to 'optimize' Hi, maybe it could be optimized for SSE3 or SSSE3x or SSE4.1, all 'newer' CPU's, like C2D; C2Q(E), NOT Core Duo, have that capability . Probably, it is already using SSE(3) or higher?! ____________ 
Knight who says N! Ni Ni |
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5458 | Rating: 0
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Message boards : Number crunching : Are There Any Optimized Apps For Docking@Home
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