[gmx-users] grimaces 4.6 installation error

[Roland Schulz]

On Thu, Jan 31, 2013 at 8:18 PM, Fernando Favela
<ffavela at fis.cinvestav.mx>wrote:

> Dear Gromacs users,
>
> I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680
> cards, I've already installed the intel compilers, cuda 5 and openmpi.
>
> I do the following procedure:
> CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake ..
>
> then
>
> sudo make -j 12
>
> and I get this error:
>
> Linking CXX shared library libmd.so
> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib &&
> /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt --verbose=1
> /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3 -DNDEBUG
> -shared -Wl,-soname,libmd.so.6 -o libmd.so.6
> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o
> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o
> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o
> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o
> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o
> CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o
> CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o
> CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o
> CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o
> CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o
> CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o
> CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o
> CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o
> CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o
> CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o
> CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o
> CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o
> CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o
> CMakeFiles/md.dir/gmx_wallcycle.c.o CMakeFiles/md.dir/gmx_fft_fftw3.c.o
> CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o
> CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o
> CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o
> CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o
> CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o
> CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o
> CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o
> CMakeFiles/md.dir/shellfc.c.o CMakeFiles/md.dir/iteratedconstraints.c.o
> CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o
> CMakeFiles/md.dir/genborn_sse2_double.c.o CMakeFiles/md.dir/forcerec.c.o
> CMakeFiles/md.dir/nbnxn_atomdata.c.o
> CMakeFiles/md.dir/genborn_sse2_single.c.o CMakeFiles/md.dir/gmx_fft_mkl.c.o
> CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o
> CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o
> CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o
> CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o
> CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o
> CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o
> CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o
> CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o
> CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o
> CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o
> CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o
> CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a
> ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf /usr/lib/liblapack.so.3gf
> /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp /usr/lib/liblapack.so.3gf
> -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a
> ../gmxlib/cuda_tools/libcuda_tools.a /usr/local/cuda/lib64/libcudart.so
> -lcuda -lpthread
> -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64:
> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib &&
> /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so
> make[2]: Leaving directory
> `/home/ffavela/Downloads/gromacs-4.6/build-cmake'
> /usr/bin/cmake -E cmake_progress_report
> /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91 92 93
> 94 95 96 97
> [ 65%] Built target md
> make[1]: Leaving directory
> `/home/ffavela/Downloads/gromacs-4.6/build-cmake'
> make: *** [all] Error 2
>

This isn't the error message. It is further up. Please post it.


> NOTE: after an eventual successful installation, where can I find
> information of how to get the benefits of gromacs-gpu? --
>
see
http://www.gromacs.org/Documentation/Cut-off_schemes
http://www.gromacs.org/Documentation/Performance_checklist

Roland


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