[gmx-users] Error while installing GROMACS-2018-rc1

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 9 10:44:16 CET 2018


Hi,

Thanks again for the testing and feedback.

On Wed, Jan 3, 2018 at 11:52 AM Yongchul Chung <chung at northwestern.edu>
wrote:

> Well, celebrated too soon. I received the following error message during
> "make check" step.
>
>
>
> NOTE: The GPU has >25% less load than the CPU. This imbalance causes
>
>       performance loss.
>
>
>                Core t (s)   Wall t (s)        (%)
>
>        Time:        0.034        0.034      100.0
>
>                  (ns/day)    (hour/ns)
>
> Performance:       53.584        0.448
>

Clearly this test ran on a GPU...


> Opened
>
> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr
> as single precision energy file
>
> Reading energy frame     20 time    0.020         Reading file
>
> /Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr,
> VERSION 2018-rc1-dev-20180103-871f2f460-unknown (single precision)
>
> Can not increase nstlist because an NVE ensemble is used
>
> Using 1 MPI thread
>
> 1 GPU auto-selected for this run.
>
> Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
>
>   PP:0
>
> Compilation of source file
> /Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl/
> nbnxn_ocl_kernels.cl failed!
>
> -- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
> -DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw
> -DVDWNAME=_VdwLJ -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
> -DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
> -DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f
> -DIATYPE_SHMEM -cl-fast-relaxed-math
> -I/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl
>
>

> --------------LOG START---------------
>
> <program source>:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
> not found
>
> #include "nbnxn_ocl_kernel_pruneonly.clh"
>
>          ^
>

Yet somehow this file was not found shortly afterwards. It's clearly being
told to look in the right place (from the -I flag in the build options).
That looks to me like an issue in the OpenCL driver / runtime. I see you're
using the latest Mac version, but perhaps trying to update the OpenCL
things will help with a more stable setup.

Mark

---------------LOG END----------------
>
>
> -------------------------------------------------------
>
> Program:     mdrun-test, version 2018-rc1-dev-20180103-871f2f460-unknown
>
> Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)
>
> Function:    cl_program gmx::ocl::compileProgram(FILE *, const std::string
> &, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)
>
>
> Internal error (bug):
>
> Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 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
>
> -------------------------------------------------------
>
>
>       Start 33: MdrunMpiTests
>
> 33/39 Test #33: MdrunMpiTests ....................   Passed    2.69 sec
>
>       Start 34: regressiontests/simple
>
> 34/39 Test #34: regressiontests/simple ...........   Passed    2.33 sec
>
>       Start 35: regressiontests/complex
>
> 35/39 Test #35: regressiontests/complex ..........   Passed   53.42 sec
>
>       Start 36: regressiontests/kernel
>
> 36/39 Test #36: regressiontests/kernel ...........   Passed   32.33 sec
>
>       Start 37: regressiontests/freeenergy
>
> 37/39 Test #37: regressiontests/freeenergy .......   Passed    5.70 sec
>
>       Start 38: regressiontests/pdb2gmx
>
> 38/39 Test #38: regressiontests/pdb2gmx ..........   Passed   15.66 sec
>
>       Start 39: regressiontests/rotation
>
> 39/39 Test #39: regressiontests/rotation .........   Passed    3.10 sec
>
>
> 97% tests passed, 1 tests failed out of 39
>
>
> Label Time Summary:
>
> GTest              =  19.86 sec*proc (33 tests)
>
> IntegrationTest    =  18.38 sec*proc (3 tests)
>
> MpiTest            =   2.73 sec*proc (3 tests)
>
> UnitTest           =   1.48 sec*proc (30 tests)
>
>
> Total Test time (real) = 132.48 sec
>
>
> The following tests FAILED:
>
> 32 - MdrunTests (Failed)
>
> Errors while running CTest
>
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
>
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
>
> make: *** [check] Error 2
>
>
>
>
> On Wed, Jan 3, 2018 at 7:42 PM, Yongchul Chung <chung at northwestern.edu>
> wrote:
>
> > Thanks, I have successfully installed the release-2018 version of GROMACS
> > on Macbook Pro 2017 HighSierra.
> >
> >
> > On Tue, Jan 2, 2018 at 1:43 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> Thanks, we have found and prepared a fix for an issue that looks very
> >> similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac
> OpenCL
> >> compilation cannot tolerate any extra spaces in the command used to
> >> compile
> >> the kernels used on the device.
> >>
> >> You could either compile GROMACS without OpenCL support for now, or if
> you
> >> would like to see if we have fixed the issue for you, that link enables
> >> you
> >> to download a tarball that contains the fix! We'd love to hear that it
> >> works.
> >>
> >> Mark
> >>
> >> On Mon, Jan 1, 2018, 20:05 Yongchul Chung <chung at northwestern.edu>
> wrote:
> >>
> >> > I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch
> >> (High
> >> > Sierra) and got the following error message when issuing "make"
> command
> >> > during the installation steps.
> >> >
> >> > My command for cmake was: cmake .. -DGMX_BUILD_OWN_FFTW=ON
> >> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON
> >> >
> >> > Thanks in advance for the help.
> >> >
> >> > [ 91%] Building CXX object
> >> >
> >> > src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_ocl/nbnxn_
> >> ocl_data_mgmt.cpp.o
> >> >
> >> > In file included from
> >> >
> >> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/md
> >> lib/nbnxn_ocl/nbnxn_ocl_data_mgmt.cpp:54:
> >> >
> >> > In file included from
> >> >
> >> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gp
> >> u_utils/oclutils.h:46:
> >> >
> >> > In file included from
> >> >
> >> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gp
> >> u_utils/gmxopencl.h:61:
> >> >
> >> > In file included from
> >> > /System/Library/Frameworks/OpenCL.framework/Headers/opencl.h:16:
> >> >
> >> > In file included from
> >> > /System/Library/Frameworks/OpenCL.framework/Headers/gcl.h:23:
> >> >
> >> > */usr/include/dispatch/dispatch.h:38:45: **error: **expected value in
> >> > expression*
> >> >
> >> > #if !defined(HAVE_UNISTD_H) || HAVE_UNISTD_H
> >> >
> >> > *                                            ^*
> >> >
> >> > 1 error generated.
> >> >
> >> > make[2]: ***
> >> >
> >> > [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_ocl/
> >> nbnxn_ocl_data_mgmt.cpp.o]
> >> > Error 1
> >> >
> >> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> >> >
> >> > make: *** [all] Error 2
> >> > --
> >> > 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-request at gromacs.org.
> >> >
> >> --
> >> 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-request at gromacs.org.
> >>
> >
> >
> --
> 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-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list