[gmx-users] Recent successful compile on Mac Pro with OpenCL? Failing Test #20: MdrunTests

Wed Aug 16 22:06:32 CEST 2017

Hi,

That's not an error, but it will make the simulation performance lower than
it could be. But it would be nice to do the build and see if it runs, since
my suggestion was that something might work only with the xcode compiler
because the driver that does that compilation might be hardcoded to expect
that. Otherwise, I can only refer you to eg some blog posts that claim it
works but are short on details.

Mark

On Wed, 16 Aug 2017 17:03 Steffen Graether <graether at uoguelph.ca> wrote:

> Hi Mark,
>
> Are there any other suggestions you would have for me to try? I would
> happily provide someone with remote access to my computer but the
> University now requires all on campus connections to go through a VPN.
>
> Regards,
> Steffen
>
> --
> Steffen Graether, Ph.D.
> Associate Professor
> University of Guelph
> office: SCIE 2255
> phone: 519-824-4120 ext. 56457
> fax: 519-837-1802
>
> On Aug 14, 2017, at 10:21 AM, Mark Abraham <mark.j.abraham at gmail.com
> <mailto:mark.j.abraham at gmail.com>> wrote:
>
> Hi,
>
> OK. That might be hard to work out how to fix, because I'm not sure we have
> a Mac+AMD machine around. My guess is that somehow the compilation in the
> driver assumes the use of xcode compilers, so that might be a thing for you
> to try. The file it can't find is one that is installed as part of GROMACS,
> but which is in a path that ought to be given to the OpenCL compiler with
> -I. Yet somehow that is lost.
>
> Mark
>
> On Mon, Aug 14, 2017 at 2:52 PM Steffen Graether <graether at uoguelph.ca
> <mailto:graether at uoguelph.ca>>
> wrote:
>
> Hi Mark,
>
> Here are the results for a few different runs:
>
> (1) gmx mdrun -v -deffnm md_0_1 -nb cpu
> Runs fine and completes
>
> (2) gmx mdrun -v -deffnm md_0_1
> Gives a similar error message:
> -------------------------------------------------------
> Program:     gmx mdrun, version 2016.2
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
> Function:    cl_program gmx::ocl::compileProgram(FILE *, const std::string
> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
> MPI rank:    0 (out of 2)
>
> Internal error (bug):
> Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
> Compute
> Engine
>  Could not build OpenCL program, error was CL_INVALID_BUILD_OPTIONS
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> (3) gmx mdrun -v -deffnm md_0_1 -gpu_id 0
> Gives the same as (2)
>
> Regards,
> Steffen
>
>
>
>  1. Re: Recent successful compile on Mac Pro with OpenCL? Failing
>     Test #20: MdrunTests (Mark Abraham)
>
>
> From: Mark Abraham <mark.j.abraham at gmail.com<mailto:
> mark.j.abraham at gmail.com><mailto:
> mark.j.abraham at gmail.com<mailto:mark.j.abraham at gmail.com>>>
> Subject: Re: [gmx-users] Recent successful compile on Mac Pro with OpenCL?
> Failing Test #20: MdrunTests
> Date: August 14, 2017 at 8:12:38 AM EDT
> To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org><mailto:
> gmx-users at gromacs.org>, "
> gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se><mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se>>" <
> gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se><mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se<mailto:
> gromacs.org_gmx-users at maillist.sys.kth.se>>>
>
>
> Hi,
>
> That's a bit mysterious, because we check that that works in our automated
> testing. If running a simulation works then everything is fine, but it's
> possible the same error arises. Can you try that, please, and report back?
>
> Mark
>
> On Fri, 11 Aug 2017 23:48 Steffen Graether <graether at uoguelph.ca<mailto:
> graether at uoguelph.ca><mailto:
> graether at uoguelph.ca<mailto:graether at uoguelph.ca>>> wrote:
>
> Hi,
>
> I am trying to compile GROMACS 2016.3 on a Mac Pro (Late 2013) running
> macOS 10.12.6. I can get it to compile fine and it can run my own
> simulation fine on CPU only, but I am having difficulty getting to work
> with the GPU (FirePro D500).
>
> Used cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DGMX_USE_OPENCL=on
> -DREGRESSIONTEST_DOWNLOAD=ON
>
> Tried both clang (version 8) and gcc (version 7), also tried 2016.2 but I
> always get this error from Test #20: MdrunTests:
>
> *******
> Compilation of source file
> /Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl/
> nbnxn_ocl_kernels.cl failed!
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> -DGMX_OCL_FASTGEN -DEL_CUTOFF -DEELNAME=_ElecCut -DLJ_COMB_GEOM
> -DVDWNAME=_VdwLJCombGeom -DCENTRAL=22
> -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8 -DNBNXN_GPU_CLUSTER_SIZE=8
> -DNBNXN_GPU_JGROUP_SIZE=4 -DNBNXN_MIN_RSQ=3.82e-07f -DIATYPE_SHMEM
> -cl-fast-relaxed-math
> -I/Users/graether/Downloads/tmp/gromacs-2016.3/src/gromacs/mdlib/nbnxn_ocl
> --------------LOG START---------------
> <program source>:61:10: fatal error: 'nbnxn_ocl_kernels.clh' file not found
> #include FLAVOR_LEVEL_GENERATOR
>        ^
> <program source>:49:36: note: expanded from macro 'FLAVOR_LEVEL_GENERATOR'
>   #define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels.clh"
>                                  ^
> ---------------LOG END----------------
>
> -------------------------------------------------------
> Program:     mdrun-test, version 2016.3
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 482)
> Function:    _cl_program* gmx::ocl::compileProgram(FILE*, const string&,
> const string&, cl_context, cl_device_id, ocl_vendor_id_t)
>
> Internal error (bug):
> Failed to compile NBNXN kernels for GPU #AMD Radeon HD - FirePro D500
> Compute
> Engine
> Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ******
>
> All the other tests are successful.
>
> Regards,
> Steffen
>
>
> --
>
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