[gmx-users] Can't run v. 4.6.6 on worker nodes if they are compiled with SIMD
Seyyed Mohtadin Hashemi
haadah at gmail.com
Sat Jul 26 19:35:04 CEST 2014
On Jul 26, 2014 4:52 AM, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
> That is indeed very weird - particularly if compiling on the compute nodes
> with GPU support enabled gives the same result. Both host and compute
> support rdtscp, so that known suspect is OK. I can only guess that there's
> something in the CUDA installation process that targets the CPU on the
> install host. Configuring with -DCMAKE_BUILD_TYPE=Debug and getting a
> trace from the crash might help work out where the problem arises.
Will get back with the stack trace a bit later; is "gdb bt full" ok? Or do
you want "thread info" as well?
> CUDA install on a compute node and compiling against that might help.
You mean install CUDA SDK on the worker nodes? If so, this is already done
and gives same result. I will ask the admin about the configuration of CUDA
on the worker nodes.
> On Fri, Jul 25, 2014 at 10:00 PM, Seyyed Mohtadin Hashemi <
haadah at gmail.com>
> > 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
> > Xeon E5-2630 and are equipped with Tesla K20), but I do not think this
> > the problem - I have compiled GROMACS, using the log-in node, without
> > but with AVX_256 SIMD and everything works. As soon as CUDA is added to
> > 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
> > SIMD=None everything works and I am able to run simulation using GPUs,
> > 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_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
> > without), once I have found the error I will compile with OpenMPI
> > 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
> > 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
> > 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
> > if not then I will file a bug report.
> > Regards,
> > Mohtadin
> > --
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