Re: [gmx-users] Error while installing GROMACS-2018-rc1
Hi, Please do try again when we make the formal release shortly. If there's still an issue, we'd really appreciate hearing from you, e.g. open a redmine issue and attach a full output of cmake + make check. But so far, we think the issue is caused by something outside of anything we can attempt handle. Mark On Tue, Jan 9, 2018 at 10:44 AM Mark Abrahamwrote: > Hi, > > Thanks again for the testing and feedback. > > On Wed, Jan 3, 2018 at 11:52 AM Yongchul Chung > 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:0.0340.034 100.0 >> >> (ns/day)(hour/ns) >> >> Performance: 53.5840.448 >> > > 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 time0.020 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--- >> >> :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 Passed2.69 sec >> >> Start 34: regressiontests/simple >> >> 34/39 Test #34: regressiontests/simple ... Passed2.33 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 ... Passed5.70 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 . Passed3.10 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]: ***
Re: [gmx-users] Error while installing GROMACS-2018-rc1
Hi, Thanks again for the testing and feedback. On Wed, Jan 3, 2018 at 11:52 AM Yongchul Chungwrote: > 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:0.0340.034 100.0 > > (ns/day)(hour/ns) > > Performance: 53.5840.448 > 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 time0.020 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--- > > :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 Passed2.69 sec > > Start 34: regressiontests/simple > > 34/39 Test #34: regressiontests/simple ... Passed2.33 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 ... Passed5.70 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 . Passed3.10 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 > 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 > > 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 >
Re: [gmx-users] Error while installing GROMACS-2018-rc1
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:0.0340.034 100.0 (ns/day)(hour/ns) Performance: 53.5840.448 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 time0.020 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--- :80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file not found #include "nbnxn_ocl_kernel_pruneonly.clh" ^ ---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 Passed2.69 sec Start 34: regressiontests/simple 34/39 Test #34: regressiontests/simple ... Passed2.33 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 ... Passed5.70 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 . Passed3.10 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 Chungwrote: > 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 > 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 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
Re: [gmx-users] Error while installing GROMACS-2018-rc1
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 Abrahamwrote: > 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 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/ > mdlib/nbnxn_ocl/nbnxn_ocl_data_mgmt.cpp:54: > > > > In file included from > > > > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/ > gpu_utils/oclutils.h:46: > > > > In file included from > > > > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/ > gpu_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-requ...@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-requ...@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-requ...@gromacs.org.
Re: [gmx-users] Error while installing GROMACS-2018-rc1
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 Chungwrote: > 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/mdlib/nbnxn_ocl/nbnxn_ocl_data_mgmt.cpp:54: > > In file included from > > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gpu_utils/oclutils.h:46: > > In file included from > > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/gpu_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-requ...@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-requ...@gromacs.org.