On Tue, Sep 18, 2012 at 10:10 AM, Daniel Kidger <daniel.kid...@gmail.com> wrote: > I touched on the Gromacs port to ClearSpeed when I worked there - I then > went on to write the port of AMBER to CS > plus I have a pair of RPis that I tinker with.
I'm not quite sure what the interest is... GROMACS is quite famous for having non-bonded kernels written in assembler and using features of the modern CPUs, but this is limited to some architectures: IA32 SSE/SSE2, x86_64 SSE/SSE2, IA64 and some versions of the Power processors. There is work in progress to support AVX and FMA4. But the RPi uses an ARM CPU. GROMACS should compile and run on the RPi, but using its generic kernels written in C which are around 2x slower than the optimized ones on the same CPU. So you combine the slow C kernels with a slow CPU... A porting effort would make sense if there would be ARM-specific instructions which are not used by default by the compiler and which are geared towards memory streaming access, simultaneous floating point operations, etc. like SSE and successors. Are there any ? Furthermore, the new(-ish) versions of GROMACS (4.x) use domain decomposition which requires a low latency interconnect to achieve a good scalability. From what I know, the earlier particle decomposition (still available in the new versions, but almost never used) was less demanding in terms of network. But maybe the computation is so slow that the on-board Ethernet is fast enough to keep up... Anyway, the whole cluster is probably going to run the simulation slower than a 4-6 cores Ivy Bridge CPU and will have a larger power consumption; plus with so many components, the risk of one or more breaking and reducing the overall compute power is quite high. So is it worth it ? (as a scientist I look at it from the perspective of getting useful results from calculations; as a learning experience, it's surely useful, but then running any software using MPI would be) Cheers, Bogdan _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
