On Fri, Jul 25, 2014 at 3:17 PM, Seyyed Mohtadin Hashemi <haa...@gmail.com> wrote:
> On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi <haa...@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. > The logs: 4.6.6: http://pastebin.com/vxagEEZC 5.0: http://pastebin.com/eMemFq1J -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.