[gmx-users] Error while compiling GROMACS 2018
Hi,
I am trying to install the latest release of GROMACS 2018 on Mac OS X
HighSierrra and ran into the following error message.
cmake worked without errors so this looks strange.
Any help would be appreciated.
Greg
ygchung@Yongchuls-MacBook-Pro:*~/Desktop/codes/gromacs/build*$ make
[ 1%] Built target fftwBuild
[ 2%] Built target tng_io_obj
[ 2%] *Generating git version information*
[ 2%] Built target git-version-info
[ 2%] Built target tng_io_zlib
[ 2%] Building CXX object
src/gromacs/CMakeFiles/libgromacs.dir/listed-forces/bonded_2.cpp.o
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:985:20: **error: **expected '(' for function-style cast or type
construction*
GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)ai[GMX_SIMD_REAL_WIDTH];
*~~~^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:986:20: **error: **expected '(' for function-style cast or type
construction*
GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)aj[GMX_SIMD_REAL_WIDTH];
*~~~^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:987:20: **error: **expected '(' for function-style cast or type
construction*
GMX_ALIGNED(int, GMX_SIMD_REAL_WIDTH)ak[GMX_SIMD_REAL_WIDTH];
*~~~^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:988:17: **error: **unexpected type name 'real': expected expression*
GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) coeff[2*GMX_SIMD_REAL_WIDTH];
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1008:17: **error: **unexpected type name 'real': expected expression*
GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH)
pbc_simd[9*GMX_SIMD_REAL_WIDTH];
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1010:23: **error: **use of undeclared identifier 'pbc_simd'*
set_pbc_simd(pbc, pbc_simd);
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1022:13: **error: **use of undeclared identifier 'ai'*
ai[s] = forceatoms[iu+1];
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1023:13: **error: **use of undeclared identifier 'aj'*
aj[s] = forceatoms[iu+2];
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1024:13: **error: **use of undeclared identifier 'ak'*
ak[s] = forceatoms[iu+3];
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1029:17: **error: **use of undeclared identifier 'coeff'*
coeff[s] =
forceparams[type].harmonic.krA;
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1030:17: **error: **use of undeclared identifier 'coeff'*
coeff[GMX_SIMD_REAL_WIDTH+s] =
forceparams[type].harmonic.rA;
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1039:17: **error: **use of undeclared identifier 'coeff'*
coeff[s] = 0;
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1040:17: **error: **use of undeclared identifier 'coeff'*
coeff[GMX_SIMD_REAL_WIDTH+s] = 0;
*^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1045:68: **error: **use of undeclared identifier 'ai'*
gatherLoadUTranspose<3>(reinterpret_cast(x), ai,
_S, _S, _S);
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1046:68: **error: **use of undeclared identifier 'aj'*
gatherLoadUTranspose<3>(reinterpret_cast(x), aj,
_S, _S, _S);
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1047:68: **error: **use of undeclared identifier 'ak'*
gatherLoadUTranspose<3>(reinterpret_cast(x), ak,
_S, _S, _S);
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1055:36: **error: **use of undeclared identifier 'coeff'*
k_S = load(coeff);
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1056:36: **error: **use of undeclared identifier 'coeff'*
theta0_S = load(coeff+GMX_SIMD_REAL_WIDTH) * deg2rad_S;
* ^*
*/Users/ygchung/Desktop/codes/gromacs/src/gromacs/listed-forces/bonded
2.cpp:1058:56: **error: **use of undeclared identifier 'pbc_simd'*
pbc_correct_dx_simd(_S, _S, _S, pbc_simd);
* ^*
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 Chung <ch...@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.abra...@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 <ch...@northwestern.edu> wrote: >> >> > I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch >> (High >> > Sierr
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 Abraham <mark.j.abra...@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 <ch...@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/ > 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.
[gmx-users] Error while installing GROMACS-2018-rc1
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.
[gmx-users] output dispersion correction and coul. recip. for energy groups
Hi gmx-users, I am using grommacs-5.0.2 with gpu acceleration. I am simulating two energy groups. Is there a way to output reciprocal coulomb and dispersion correction between each energy groups? It is odd to see GROMACS reports LJ and Coulombic interaction energies between two groups without dispersion correction and reciprocal sum. Greg -- Yongchul G. Chung Postdoctoral Fellow Snurr Research Group Department of Chemical and Biological Engineering Northwestern University Evanston, IL 60208 -- 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] output dispersion correction and coul. recip. for energy groups
Hi On Fri, Dec 12, 2014 at 4:17 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Fri, Dec 12, 2014 at 10:42 PM, Yongchul Chung ch...@northwestern.edu wrote: Hi gmx-users, I am using grommacs-5.0.2 with gpu acceleration. I am simulating two energy groups. Is there a way to output reciprocal coulomb and dispersion correction between each energy groups? It is odd to see GROMACS reports LJ and Coulombic interaction energies between two groups without dispersion correction and reciprocal sum. What definitions would you use? Mark Well, I was hoping for GROMACS to output LJ:GROUP1-GROUP2 instead of LJ-SR:GROUP1-GROUP2, and for Coul:GROUP1-GROUP2 instead of Coul-SR:GROUP1-GROUP2 Greg Greg -- Yongchul G. Chung Postdoctoral Fellow Snurr Research Group Department of Chemical and Biological Engineering Northwestern University Evanston, IL 60208 -- 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. -- Yongchul G. Chung Postdoctoral Fellow Snurr Research Group Department of Chemical and Biological Engineering Northwestern University Evanston, IL 60208 -- 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.
