[gmx-users] gromacs 4.6 installation error

Fri Feb 1 14:38:31 CET 2013

On 2/1/13 8:35 AM, Fernando Favela wrote:
> 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?
>

Not likely, but you still haven't posted the original error.  Error 2 says that 
somewhere higher up there is an Error 1.  We need that information.

-Justin

> 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
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================