[gmx-developers] Any news on SIMD intrinsic accelerated kernel for Blue Gene/Q?

Jeff Hammond jhammond at alcf.anl.gov
Wed May 8 23:48:18 CEST 2013

Have you compiled Gromacs with auto-vectorization turned on (e.g.
CFLAGS = -g -O3 -qarch=qp -qtune=qp -qsimd=auto -qhot=level=1
-qprefetch -qunroll=yes -qreport) and run the code through HPM (see
https://wiki.alcf.anl.gov/bgq-earlyaccess/images/4/4a/Hpct-bgq.pdf for
instructions - it requires only modest source changes) to determine
that the compiler is not capable of vectorizing the code?  I am far
from an XL fanboy but it is imprudent to devote human effort when a
machine can do the job already.

The HPM results will be of value no matter what the compiler is doing,
as this level of profiling information is absolutely critical to
making intelligent choices about how to optimize any code for BGQ.
You might discover, for example, that QPX is not the best place to
start tuning anyways.  It could be that there are memory access issues
that are costing Gromacs far more than a factor of 4 (that is the most
one can expect from a 4-way FPU, of course - I assume that the FMA is
already used because it is generic to PowerPC).



On Wed, May 8, 2013 at 3:46 PM, Bin Liu <fdusuperstring at gmail.com> wrote:
> Dear developers,
> In the GROMACS acceleration and parallelization webpage, I found
> We will add Blue Gene P and/or Q and AVX2 in the near future.
> I am quite excited about this news, since I am a researcher in Canada, and
> the University of Toronto has purchased a Blue Gene Q cluster which will be
> operated under Scinet Consortium.
> https://support.scinet.utoronto.ca/wiki/index.php/BGQ#System_Status:_BETA
> Without the SIMD intrinsic accelerated kernel for Blue Gene/Q, perhaps they
> won't install GROMACS on it since a lot of computational resources are going
> to be wasted. If the GROMACS developer can implement  the SIMD intrinsic
> accelerated kernel, I will be more than grateful for that.
> Bin
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Jeff Hammond
Argonne Leadership Computing Facility
University of Chicago Computation Institute
jhammond at alcf.anl.gov / (630) 252-5381
ALCF docs: http://www.alcf.anl.gov/user-guides

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