On Sat, Jul 26, 2014 at 7:35 PM, Seyyed Mohtadin Hashemi <[email protected]> wrote:
> On Jul 26, 2014 4:52 AM, "Mark Abraham" <[email protected]> wrote: > > > > Hi, > > > > That is indeed very weird - particularly if compiling on the compute > nodes > > with GPU support enabled gives the same result. Both host and compute > nodes > > 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 > stack > > 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? Probably. Mark > Or do > you want "thread info" as well? > > Doing a > > 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. > > > > Mark > > > > > > > > On Fri, Jul 25, 2014 at 10:00 PM, Seyyed Mohtadin Hashemi < > [email protected]> > > 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 > > > -- > > > 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 [email protected]. > > > > > -- > > 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 [email protected]. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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