[gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD

[Seyyed Mohtadin Hashemi]

On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi <haadah at gmail.com>
wrote:

> Hi everyone,
>
> I'm having a very weird problem with GROMACS 4.6.6:
>
> I am currently testing out GPU capabilities and was trying to compile
> GROMACS with CUDA (v6.0). I can not make this work if I compile GROMACS
> with SIMD, no matter what kernel I choose - I have tried everything from
> SSE2 to AVX_256.
>
> The log-in node, where I compile, has AMD Interlagos CPUs (worker nodes
> use Xeon E5-2630 and are equipped with Tesla K20), but I do not think this
> is the problem - I have compiled GROMACS, using the log-in node, without
> CUDA but with AVX_256 SIMD and everything works. As soon as CUDA is added
> to the mix, I get "Illegal Instruction" every time I try to run on the
> worker nodes.
>
> Compiling on worker nodes gives the same result. However, as soon as I set
> SIMD=None everything works and I am able to run simulation using GPUs, this
> is regardless of if I use log-in node or worker node to compile.
>
>
> The cmake string used to configure is:
> ccmake .. -DCMAKE_INSTALL_PREFIX=/work/gromacs4gpu -DGMX_DOUBLE=OFF
> -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_4gpu -DGMX_LIBS_SUFFIX=_4gpu
> -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
> -GMX_MPI=OFF -DGMX_CPU_ACCELERATION=AVX_256
>
> CUDA v6.0 and FFTW v3.3.4 (single precision) libs are set globally and
> correctly identified by GROMACS. To remove OpenMPI as a problem I am
> compiling without it (compiling with OpenMPI produced the same behavior as
> without), once I have found the error I will compile with OpenMPI v1.6.5.
>
> I get these warnings during the configuration, nothing important:
>
>  A BLAS library was not found by CMake in the paths available to it.
> Falling back on the GROMACS internal version of the BLAS library instead.
> This is fine for normal usage.
>
>  A LAPACK library was not found by CMake in the paths available to it.
> Falling back on the GROMACS internal version of the LAPACK library instead.
> This is fine for normal usage.
>
> I am currently trying to compile and test GROMACS 5.0 to see if it also
> exhibits the same behavior.
>
> I hope that someone can point me in the direction of a possible solution,
> if not then I will file a bug report.
>
> Regards,
> Mohtadin
>

Forgot to attached the md.log. Please find attached md.log for both v4.6.6
and v5.0

Unfortunately, v5.0 seems to exhibit the same behavior as v4.6.6.