[gmx-users] grimaces 4.6 installation error

[Mark Abraham]

On Fri, Feb 1, 2013 at 2:18 AM, 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
>

Don't use sudo before make. Consider using sudo before "make install", per
the installation instructions.

There's no error message in the output file you posted. I suspect you might
running "sudo make", and then "make" and running into file permissions
problems because of it. Remove your whole build directory (which will
probably need sudo) and start again.

Mark


>
> 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
>
> I think this issue must be related with the compilers because if I use the
> default gnu compilers the problem disappear.
>
> Could anybody help me please?
>
> Thanks in advance.
>
> Fernando.
>
> NOTE: after an eventual successful installation, where can I find
> information of how to get the benefits of gromacs-gpu? --
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