[gmx-users] gromacs 4.6 installation error

[Fernando Favela]

Dear Mark Abraham,

without the sudo, the problem is still there:
...
…
...
[ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o
[ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o
Linking CXX shared library libmd.so
[ 65%] Built target md
make: *** [all] Error 2

It could be possible that after a previous gromacs installation (removed) there's still a linked library or something?

Thanks in advance.

Fernando.
 
On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote:

> 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? --
>> gmx-users mailing list    gmx-users at gromacs.org
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>> * Please search the archive at
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>> 
> -- 
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