[gmx-developers] Re: GROMACS 4.6 pre-release: new algorithms, parallelization schemes, & GPU acceleration

Berk Hess hess at kth.se
Mon Mar 5 22:15:49 CET 2012

Thanks for the information.
I replaced 3 erf/erfc entries with gmx_erf. I assume there were three?

I hope Szilard can provide answers for the other issues.

We will put a new version in the repository when we have fixed all the 



On 03/05/2012 08:06 PM, Mirco Wahab wrote:
> Am 01.03.2012 18:55, schrieb Szilárd Páll:
>> Not that many have complained, but the one-liner is broken. A correct
>> alternative:
>> git clone git://git.gromacs.org/gromacs.git -b nbnxn_hybrid_acc&&  cd
>> gromacs&&  mkdir buid&&  cd build&&  cmake ../&&  make install -j4
> I did a "working" Win64 build (VERSION 4.6-GPU-dev-20120301-d16fc-dirty)
> and couldn't find out how do I "select" the gpu?
> "mdrun -v -nb gpu" doesn't do anything. Is there something
> that allows mdrun to detect a device?
> Some small problems encountered during the adventure: You used
> at some places a 'erf[c]()' function which is nowhere defined,
> and at some other places a 'gmx_erf[c]()'. Can I replace all
> erf[c]() calls by gmx_erf[c]()? (This is what I did.)
> There are several places where C99 constructs (variable declaration
> not on the start of a block) had to be compensated for. One
> macro in mdlib/nbnxn_kernels/nbnxn_kernel_sse_inner.h:715
> did cause error on expansion, I had to rewrite:
>  #ifndef ENERGY_GROUPS
>        VvdwtotSSE = gmx_add_pr(VvdwtotSSE,
>    #ifndef HALF_LJ
> gmx_sum4_pr(VLJ_SSE0,VLJ_SSE1,VLJ_SSE2,VLJ_SSE3)
>    #else
>                                gmx_add_pr(VLJ_SSE0,VLJ_SSE1)
>    #endif
>                               );
>  #else
> and hope it's still correct ...
> On the cuda side - this seem to compile and link fine so far
> (I had to patch one cmake-1.8.7 FindCUDA macro), but there are
> some warnings I don't understand. The generated cl options
> include -fPIC which doesn't seem to belong to Windows. Maybe
> this comes from cmake itself, dunno.
> The "default build" for Win64 seems to be "static libs"
> and huge binaries. OK, they work fine.
> But I can't find out how to get mdrun to select a gpu.
> Thanks & regards
> M.

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