[gmx-users] gromacs 4.6 installation error
Fernando Favela
ffavela at fis.cinvestav.mx
Fri Feb 1 15:06:48 CET 2013
Hi justin,
this is the other error message:
[ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o
[ 56%] [ 56%] [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o
Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o
Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o
Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o
[ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o
ld: warning: libimf.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link)
ld: warning: libsvml.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link)
ld: warning: libirng.so, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link)
ld: warning: libintlc.so.5, needed by ../../src/gmxlib/libgmx.so.6, not found (try using -rpath or -rpath-link)
[ 56%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o
ld: template: hidden symbol `__intel_cpu_indicator_init' in /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirc.a(cpu_disp.o) is referenced by DSO
ld: final link failed: Bad value
make[2]: *** [share/template/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs….
then
...
[ 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
That's all.
Thanks,
Fernando.
On Feb 1, 2013, at 7:38 AM, Justin Lemkul wrote:
>
>
> 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
>
> ========================================
> --
> 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
More information about the gromacs.org_gmx-users
mailing list